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Genomic Designing for Climate-Smart Tomato

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Genomic Designing of Climate-Smart Vegetable Crops

Abstract

Tomato is the first vegetable consumed in the world. It is grown in very different conditions and areas, mainly in field for processing tomatoes while fresh-market tomatoes are often produced in greenhouses. Tomato faces many environmental stresses, both biotic and abiotic. Today many new genomic resources are available allowing an acceleration of the genetic progress. In this chapter, we will first present the main challenges to breed climate-smart tomatoes. The breeding objectives relative to productivity, fruit quality, and adaptation to environmental stresses will be presented with a special focus on how climate change is impacting these objectives. In the second part, the genetic and genomic resources available will be presented. Then, traditional and molecular breeding techniques will be discussed. A special focus will then be presented on ecophysiological modeling, which could constitute an important strategy to define new ideotypes adapted to breeding objectives. Finally, we will illustrate how new biotechnological tools are implemented and could be used to breed climate-smart tomatoes.

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References

  • Aarts J, Hontelez JGJ, Fischer P, Verkerk R, Vankammen A, Zabel P (1991) Acid phosphatase-11, a tightly linked molecular marker for root-knot nematode resistance in tomato—from protein to gene, using pcr and degenerate primers containing deoxyinosine. Plant Mol Biol 16:647–661

    Article  CAS  PubMed  Google Scholar 

  • Abraitiene A, Girgzdiene R (2013) Impact of the short-term mild and severe ozone treatments on the potato spindle tuber viroid-infected tomato (Lycopersicon esculentum Mill.). Zemdirbyste-Agriculture 100:277–282

    Article  Google Scholar 

  • Achuo EA, Prinsen E, Hofte M (2006) Influence of drought, salt stress and abscisic acid on the resistance of tomato to Botrytis cinerea and Oidium neolycopersici. Plant Pathol 55:178–186

    Article  CAS  Google Scholar 

  • Adams SR, Cockshull KE, Cave CRJ (2001) Effect of temperature on the growth and development of tomato fruits. Ann Bot 88:869–877

    Article  Google Scholar 

  • Adams P, Ho LC (1993) Effects of environment on the uptake and distribution of calcium in tomato and on the incidence of blossom-end rot. Plant Soil 154:127–132

    Article  CAS  Google Scholar 

  • Adato A, Mandel T, Mintz-Oron S, Venger I, Levy D, Yativ M, Domínguez E, Wang Z, De Vos RC, Jetter R, Schreiber L, Heredia A, Rogachev I, Aharoni A (2009) Fruit-surface flavonoid accumulation in tomato is controlled by a SlMYB12-regulated transcriptional network. PLoS Genetics. e1000777. https://doi.org/10.1371/journal.pgen.1000777

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Adli M (2018) The CRISPR tool kit for genome editing and beyond. Nat Commun 9(1):1911

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Agrama HA, Scott JW (2006) Quantitative trait loci for tomato yellow leaf curl virus and tomato mottle virus resistance in tomato. J Am Soc Hort Sci 131:267–272

    Article  CAS  Google Scholar 

  • Ahmad A, Zhang Y, Cao X-F (2010) Decoding the epigenetic language of plant development. Mol Plant 3:719–728

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Al-Abdallat A, Al-Debei H, Ayad J, Hasan S, Al-Abdallat AM, Al-Debei HS et al (2014) Over-expression of SlSHN1 gene improves drought tolerance by increasing cuticular wax accumulation in tomato. Int J Mol Sci 15:19499–19515

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Albacete A, Cantero-Navarro E, Großkinsky DK, Arias CL, Balibrea ME, Bru R, Fragner L, Ghanem ME, González MDLC, Hernández JA et al (2015) Ectopic overexpression of the cell wall invertase gene CIN1 leads to dehydration avoidance in tomato. J Exp Bot 66:863–878

    Article  CAS  PubMed  Google Scholar 

  • Albacete A, Martínez-Andújar C, Ghanem ME, Acosta M, Sánchez-Bravo J, Asins MJ, et al (2009) Rootstock-mediated changes in xylem ionic and hormonal status are correlated with delayed leaf senescence, and increased leaf area and crop productivity in salinized tomato. Plant Cell Environ 32:928–938

    Article  CAS  Google Scholar 

  • Albert E, Duboscq R, Latreille M, Santoni S, Beukers M, Bouchet JP, Bitton F, Gricourt J, Poncet C, Gautier V et al (2018) Allele-specific expression and genetic determinants of transcriptomic variations in response to mild water deficit in tomato. Plant J 96(3):635–650

    Article  CAS  PubMed  Google Scholar 

  • Albert E, Gricourt J, Bertin N, Bonnefoi J, Pateyron S, Tamby J-P, Bitton F, Causse M (2016a) Genotype by watering regime interaction in cultivated tomato: lessons from linkage mapping and gene expression. Theor Appl Genet 129:395–418

    Article  PubMed  Google Scholar 

  • Albert E, Segura V, Gricourt J, Bonnefoi J, Derivot L, Causse M (2016b) Association mapping reveals the genetic architecture of tomato response to water deficit: focus on major fruit quality traits. J Exp Bot 67:6413–6430

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Albrecht E, Escobar M, Chetelat RT (2010) Genetic diversity and population structure in the tomato-like nightshades Solanum lycopersicoides and S. sitiens. Ann Bot 105:535–554

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Alian A, Altman A, Heuer B (2000) Genotypic difference in salinity and water stress tolerance of fresh market tomato cultivars. Plant Sci 152:59–65

    Article  CAS  Google Scholar 

  • Allwood JW, De Vos RCH, Moing A, Deborde C, Erban A, Kopka J, Goodacre R, Hall RD (2011) Plant metabolomics and its potential for systems biology research: background concepts, technology, and methodology. In: Methods Enzymol, 1st edn. https://doi.org/10.1016/b978-0-12-385118-5.00016-5

    Google Scholar 

  • Almeida J, Quadrana L, Asís R et al (2011) Genetic dissection of vitamin E biosynthesis in tomato. J Exp Bot 62(11):3781–3798

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Alpert KB, Tanksley SD (1996) High-resolution mapping and isolation of a yeast artificial chromosome contig containing fw2.2: a major fruit weight quantitative trait locus in tomato. Proc Natl Acad Sci USA 93:15503–15507

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Alseekh S, Fernie AR (2018) Metabolomics 20 years on: what have we learned and what hurdles remain? Plant J 94:933–942

    Article  CAS  PubMed  Google Scholar 

  • Alseekh S, Ofner I, Pleban T, Tripodi P, Di Dato F, Cammareri M, Mohammad A, Grandillo S, Fernie AR, Zamir D (2013) Resolution by recombination: breaking up Solanum pennellii introgressions. Trends Plant Sci 18:536–538

    Article  CAS  PubMed  Google Scholar 

  • Alseekh S, Tong H, Scossa F, Brotman Y, Vigroux F, Tohge T et al (2017) Canalization of tomato fruit metabolism. Plant Cell 29(11):2753–2765

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Alseekh S, Tong H, Scossa F, Brotman Y, Vigroux F, Tohge T et al (2017) Canalization of tomato fruit metabolism. Plant Cell 29(11):2753–2765

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ambros V (2004) The functions of animal microRNAs. Nature 431:350–355

    Article  CAS  PubMed  Google Scholar 

  • Andolfo G, Jupe F, Witek K, Etherington GJ, Ercolano MR, Jones JDG (2014) Defining the full tomato NB-LRR resistance gene repertoire using genomic and cDNA RenSeq. BMC Plant Biol 14

    Google Scholar 

  • Anfoka G, Moshe A, Fridman L, Amrani L, Rotem O, Kolot M, Zeidan M, Czosnek H, Gorovits R (2016) Tomato yellow leaf curl virus infection mitigates the heat stress response of plants grown at high temperatures. Sci Rep 6:19715

    Article  PubMed  CAS  Google Scholar 

  • Apse MP, Aharon GS, Snedden WA, Blumwald E (1999) Salt tolerance conferred by overexpression of a vacuolar Na+/H+ antiport in Arabidopsis. Science 285:1256–1258

    Article  CAS  PubMed  Google Scholar 

  • Arafa RA, Rakha MT, Soliman NEK, Moussa OM, Kamel SM, Shirasawa K (2017) Rapid identification of candidate genes for resistance to tomato late blight disease using next-generation sequencing technologies. PLoS ONE 12:e0189951

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Archak S, Karihaloo JL, Jain A (2002) RAPD markers reveal narrowing genetic base of Indian tomato cultivars. Curr Sci 82:1139–1143

    Google Scholar 

  • Arms EM, Lounsbery JK, Bloom AJ, St. Clair DA (2016) Complex relationships among water use efficiency-related traits, yield, and maturity in tomato lines subjected to deficit irrigation in the field. Crop Sci 56:1698

    Article  CAS  Google Scholar 

  • Ashrafi H, Kinkade MP, Merk HL, Foolad MR (2012) Identification of novel quantitative trait loci for increased lycopene content and other fruit quality traits in a tomato recombinant inbred line population. Mol Breed 30:549–567

    Article  CAS  Google Scholar 

  • Ashrafi-Dehkordi E, Alemzadeh A, Tanaka N, Razi H (2018) Meta-analysis of transcriptomic responses to biotic and abiotic stress in tomato. PeerJ 6:e4631

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Asins MJ, Albacete A, Martinez-Andujar C, Pérez-Alfocea F, Dodd IC, Carbonell EA, Dieleman JA (2017) Genetic analysis of rootstock-mediated nitrogen (N) uptake and root-to-shoot signalling at contrasting N availabilities in tomato. Plant Sci 263:94–106

    Article  CAS  PubMed  Google Scholar 

  • Asins MJ, Bolarín MC, Pérez-Alfocea F, Estañ MT, Martínez-Andújar C, Albacete A et al (2010) Genetic analysis of physiological components of salt tolerance conferred by Solanum rootstocks. What is the rootstock doing for the scion? Theor Appl Genet 121:105–115

    Article  CAS  PubMed  Google Scholar 

  • Asins MJ, Raga V, Roca D, Belver A, Carbonell EA (2015) Genetic dissection of tomato rootstock effects on scion traits under moderate salinity. Theor Appl Genet 128:667–679

    Article  CAS  PubMed  Google Scholar 

  • Asins MJ, Villalta I, Aly MM, Olías R, Álvarez De Morales P, Huertas R et al (2013) Two closely linked tomato HKT coding genes are positional candidates for the major tomato QTL involved in Na+/K+ homeostasis. Plant Cell Environ 36:1171–1191

    Article  CAS  Google Scholar 

  • Atanassova B (1999) Functional male sterility (ps2) in tomato (Lycopersicon esculentum Mill.) and its application in breeding and seed production. Euphytica 107: 1, 13–21

    Google Scholar 

  • Auerswald H, Schwarz D, Kornelson C, Krumbein A, Brückner B (1999) Sensory analysis, sugar and acid content of tomato at different EC values of the nutrient solution. Sci Hort (Amsterdam) 82:227–242

    Article  CAS  Google Scholar 

  • Bai Y, Lindhout P (2007) Domestication and breeding of tomatoes: what have we gained and what can we gain in the future? Ann Bot 100(5):1085–1094

    Article  PubMed  PubMed Central  Google Scholar 

  • Bai YL, Huang CC, van der Hulst R, Meijer-Dekens F, Bonnema G, Lindhout P (2003) QTLs for tomato powdery mildew resistance (Oidium lycopersici) in Lycopersicon parviflorum G1.1601 co-localize with two qualitative powdery mildew resistance genes. Mol Plant-Microbe Interact 16:169–176

    Article  CAS  PubMed  Google Scholar 

  • Bai YL, Kissoudis C, Yan Z, Visser RGF, van der Linden G (2018) Plant behaviour under combined stress: tomato responses to combined salinity and pathogen stress. Plant J 93:781–793

    Article  CAS  PubMed  Google Scholar 

  • Bai YL, Pavan S, Zheng Z, Zappel NF, Reinstadler A, Lotti C, De Giovanni C, Ricciardi L, Lindhout P, Visser R, Theres K, Panstruga R (2008) Naturally occurring broad-spectrum powdery mildew resistance in a central American tomato accession is caused by loss of Mlo function. Mol Plant-Microbe Interact 21:30–39

    Article  CAS  PubMed  Google Scholar 

  • Baldazzi V, Bertin N, Jong H, Genard M (2012) Towards multiscale plant models: integrating cellular networks. Trends Plant Sci 17:728–736

    Article  CAS  PubMed  Google Scholar 

  • Baldazzi V, Génard M, Bertin N (2017) Cell division, endoreduplication and expansion processes: setting the cell and organ control into an integrated model of tomato fruit development. Acta Hort 1182

    Google Scholar 

  • Baldazzi V, Pinet A, Vercambre G, Benard C, Biais B, Génard M (2013) In-silico analysis of water and carbon relations under stress conditions. A multi-scale perspective centered on fruit. Front Plant Sci 4. https://doi.org/10.3389/fpls.2013.00495

  • Baldazzi V, Valsesia P, Génard M, Bertin N (2019) Organ-wide and ploidy-dependent regulations both contribute to cell size determination: evidence from a computational model of tomato fruit. J Exp Bot. https://doi.org/10.1093/jxb/erz398

    Article  PubMed  PubMed Central  Google Scholar 

  • Baldet P, Stevens R, Causse M, Duffe P, Buret M, Rothan C, Garchery C, Duffé P, Carchery C, Baldet P et al (2007) Candidate genes and quantitative trait loci affecting fruit ascorbicacid content in three tomato populations. Plant Physiol 143:1943–1953

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Baldwin E, Scott J, Shewmaker C, Schuch W (2000) Flavor trivia and tomato aroma: biochemistry and possible mechanisms for control of important aroma components. HortScience 35:1013–1022

    Article  CAS  Google Scholar 

  • Baldwin EA, Nisperos-Carriedo MO, Baker R, Scott JW (1991) Quantitative analysis of flavor parameters in six Florida tomato cultivars (Lycopersicon esculentum Mill). J Agri Food Chem 39:1135–1140

    Article  CAS  Google Scholar 

  • Baldwin EA, Scott JW, Einstein MA, Malundo TMM, Carr BT, Shewfelt RL, Tandon KS (1998) Relationship between sensory and instrumental analysis for tomato flavor. J Am Soc Hort Sci 123:906–915

    Article  CAS  Google Scholar 

  • Ballester A-R, Bovy AG, Viquez-Zamora M, Tikunov Y, Grandillo S, de Vos R, de Maagd RA, van Heusden S, Molthoff J (2016) Identification of loci affecting accumulation of secondary metabolites in tomato fruit of a Solanum lycopersicum × Solanum chmielewskii introgression line population. Front Plant Sci 7:1428

    Article  PubMed  PubMed Central  Google Scholar 

  • Bandillo N, Raghavan C, Muyco P, Sevilla MAL, Lobina IT, Dilla-Ermita C, Tung C-W, McCouch S, Thomson M, Mauleon R et al (2013) Multi-parent advanced generation inter-cross (MAGIC) populations in rice: progress and potential for genetics research and breeding. Rice 6:11

    Article  PubMed  PubMed Central  Google Scholar 

  • Bastet A, Zafirov D, Giovinazzo N, Guyon-Debast A, Nogué F, Robaglia C, Gallois J-L (2019) Mimicking natural polymorphism in eIF4E by CRISPR-Cas9 base editing is associated with resistance to potyviruses. Plant Biotechnol J. https://doi.org/10.1111/pbi.13096

    Article  PubMed  PubMed Central  Google Scholar 

  • Bauchet G, Causse M (2012) Genetic diversity in tomato (Solanum lycopersicum) and its wild relatives. In: Caliskan M (ed) Genetic Divers Plants. ISBN: 978-953-51-0185-7, InTech, http://www.intechopen.com/books/genetic-diversity-in-plants/genetic-diversity-in-tomatosolanum-lycopersicum-and-its-wild-relatives. https://doi.org/10.5772/33073

    Google Scholar 

  • Bauchet G, Grenier S, Samson N, Bonnet J, Grivet L, Causse M (2017a) Use of modern tomato breeding germplasm for deciphering the genetic control of agronomical traits by Genome Wide Association study. Theor Appl Genet 130:875–889

    Article  CAS  PubMed  Google Scholar 

  • Bauchet G, Grenier S, Samson N, Segura V, Kende A, Beekwilder J, Cankar K, Gallois J-L, Gricourt J, Bonnet J et al (2017b) Identification of major loci and genomic regions controlling acid and volatile content in tomato fruit: implications for flavor improvement. New Phytol 215:624–641

    Article  CAS  PubMed  Google Scholar 

  • Baxter CJ, Liu JL, Fernie AR, Sweetlove LJ (2007) Determination of metabolic fluxes in a non-steady-state system. Phytochemistry 68:2313–2319

    Article  CAS  PubMed  Google Scholar 

  • Beauvoit B, Belouah I, Bertin N, Belmys Cakpo C, Colombié S, Dai Z, Gautier H, Génard M, Moing A, Roch L, Vercambre G, Gibon Y (2018) Putting primary metabolism into perspective to obtain better fruits. Ann Bot 122(1):1–21

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Beauvoit BP, Colombié S, Monier A, Andrieu MH, Biais B, Bérnard C, Chéniclet C, Dieuaide-Noubhani M, Nazaret C, Mazat JP et al (2014) Model-assisted analysis of sugar metabolism throughout tomato fruit development reveals enzyme and carrier properties in relation to vacuole expansion. Plant cell 26(8):3224–3242

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Belfanti E, Malatrasi M, Orsi I, Boni AG (2015) Isolated nucleotide sequence from solanum lycopersicum for improved resistance to tomato spotted wilt virus, TSWV. Patent WO/2015/090468; International Application No: PCT/EP2013/077799

    Google Scholar 

  • Bernacchi D, Beck-Bunn T, Emmatty D, Eshed Y, Inai S, Lopez J, Petiard V, Sayama H, Uhlig J, Zamir D, Tanksley S (1998) Advanced backcross QTL analysis in tomato. II. Evaluation of near-isogenic lines carrying single-donor introgressions for desirable wild QTL-alleles derived from Lycopersicon hirsutum and L. pimpinellifolium. Theor Appl Genet 97(1/2): 170–180; erratum 97(7): 1191–1196

    Article  CAS  Google Scholar 

  • Bernacchi D, Beck-Bunn T, Eshed Y, Lopez J, Petiard V, Uhlig J, Zamir D, Tanksley S (1998b) Advanced backcross QTL analysis in tomato. I. Identification of QTLs for traits of agronomic importance from Lycopersicon hirsutum. Theor Appl Genet 97:381–397

    Article  CAS  Google Scholar 

  • Berr A, Shafiq S, Shen WH (2011) Histone modifications in transcriptional activation during plant development. Biochim Biophys Acta Gene Regul Mech 1809:567–576

    Article  CAS  Google Scholar 

  • Bertin N, Borel C, Brunel B, Cheniclet C, Causse M (2003) Do genetic make-up and growth manipulation affect tomato fruit size by cell number, or cell size and DNA endoreduplication? Ann Bot 92(3):415–424

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bertin N, Guichard S, Leonardi C, Longuenesse JJ, Langlois D, Navez B (2000) Seasonal evolution of the quality of fresh glasshouse tomatoes under mediterranean conditions, as affected by air vapour pressure deficit and plant fruit load. Ann Bot 85:741–750

    Article  Google Scholar 

  • Bertin N, Gautier H, Roche C (2002) Number of cells in tomato fruit depending on fruit position and source-sink balance during plant development. Plant Growth Regul 36(2):105–112

    Article  CAS  Google Scholar 

  • Bertin N, Martre P, Génard M, Quilot B, Salon C (2010) Why and how can process-based simulation models link genotype to phenotype for complex traits? Case-study of fruit and grain quality traits. J Exp Bot 61:955–967

    Article  CAS  PubMed  Google Scholar 

  • Bhatia P, Ashwath N, Senaratna T, Midmore D (2004) Tissue culture studies of tomato (Lycopersicon esculentum). Plant Cell Tiss Org Cult 78(1):1–21

    Article  Google Scholar 

  • Bhatt RM, Srinivasa Rao NK (1987) Seed germination and seedling growth responses of tomato cultivars to imposed water stress. J Hort Sci 62:221–225

    Article  Google Scholar 

  • Birchler JA, Yao H, Chudalayandi S, Vaiman D, Veitia RA (2010) Heterosis. Plant Cell 22:2105–2112

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Blanca J, Cañizares J, Cordero L, Pascual L, Diez MJ, Nuez F (2012) Variation revealed by SNP genotyping and morphology provides insight into the origin of the tomato. PLoS ONE 7:e48198

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Blanca J, Montero-Pau J, Sauvage C, Bauchet G, Illa E, Díez MJ, Francis D, Causse M, van der Knaap E, Cañizares J (2015) Genomic variation in tomato, from wild ancestors to contemporary breeding accessions. BMC Genom 16:257

    Article  CAS  Google Scholar 

  • Bloom AJ, Zwieniecki MA, Passioura JB, Randall LB, Holbrook NM, St. Clair DA (2004) Water relations under root chilling in a sensitive and tolerant tomato species. Plant, Cell Environ 27:971–979

    Article  Google Scholar 

  • Boison SA, Utsunomiya ATH, Santos DJA, Neves HHR, Carvalheiro R, Mészáros G, Utsunomiya YT, do Carmo AS, MA RS, Machado SA et al (2017) Accuracy of genomic predictions in Gyr (Bos indicus) dairy cattle. J Dairy Sci 100:5479–5490

    Article  CAS  PubMed  Google Scholar 

  • Bolger A, Scossa F, Bolger ME, Lanz C, Maumus F, Tohge T, Quesneville H, Alseekh S, Sørensen I, Lichtenstein G et al (2014) The genome of the stress-tolerant wild tomato species Solanum pennellii. Nat Genet 46:1034–1038

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Boote K (2016) Modelling crop growth and yield in tomato cultivation. ID: 9781786760401-010

    Google Scholar 

  • Boureau L, How-Kit A, Teyssier E, Drevensek S, Rainieri M, Joubès J, Stammitti L, Pribat A, Bowler C, Hong Y et al (2016) A CURLY LEAF homologue controls both vegetative and reproductive development of tomato plants. Plant Mol Biol 90:485–501

    Article  CAS  PubMed  Google Scholar 

  • Bovy A, de Vos R, Kemper M, Schijlen E, Pertejo MA, Muir S, Collins G, Robinson S, Verhoeyen M, Hughes S, Santos-Buelga C (2002) High-flavonol tomatoes resulting from the heterologous expression of the maize transcription factor genes LC and C1. Plant Cell 14:2509–2526

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bovy A, Schijlen E, Hall RD (2007) Metabolic engineering of flavonoids in tomato (Solanum lycopersicum): the potential for metabolomics. Metabolomics 3:399–412

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Boote KJ, Rybak MR, Scholberg JM, Jones JW (2012) Improving the CROPGRO-Tomato model for predicting growth and yield response to temperature. HortScience 47:1038–1049

    Article  Google Scholar 

  • Brachi B, Morris GP, Borevitz JO (2011) Genome-wide association studies in plants: the missing heritability is in the field. Genome Biol 12:232

    Article  PubMed  PubMed Central  Google Scholar 

  • Bramley PM (2000) Is lycopene beneficial to human health? Phytochemistry 54:233–236

    Article  CAS  PubMed  Google Scholar 

  • Brandwagt BF, Mesbah LA, Takken FLW, Laurent PL, Kneppers TJA, Hille J, Nijkamp HJJ (2000) A longevity assurance gene homolog of tomato mediates resistance to Alternaria alternata f. sp lycopersici toxins and fumonisin B(1). In: Proceedings of the national academy of sciences of the United States of America 97:4961-4966

    Article  CAS  Google Scholar 

  • Breiman L (2001) Random forests. Mach Learn 45:5–32

    Article  Google Scholar 

  • Brommonschenkel SH, Frary A, Tanksley SD (2000) The broad-spectrum tospovirus resistance gene Sw-5 of tomato is a homolog of the root-knot nematode resistance gene Mi. Mol Plant-Microbe Interact 13:1130-1138

    Article  CAS  PubMed  Google Scholar 

  • Brooks C, Nekrasov V, Lippman ZB, Van Eck J (2014) Efficient gene editing in tomato in the first generation using the clustered regularly interspaced short palindromic repeats/CRISPR-associated9 system. Plant Physiol 166(3):1292–1297

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Brouwer DJ, Jones ES, St Clair DA (2004) QTL analysis of quantitative resistance to Phytophthora infestans (late blight) in tomato and comparisons with potato. Genome 47:475–492

    Article  CAS  PubMed  Google Scholar 

  • Brouwer DJ, St Clair DA (2004) Fine mapping of three quantitative trait loci for late blight resistance in tomato using near isogenic lines (NILs) and sub-NILs. Theor Appl Genet 108:628–638

    Article  CAS  PubMed  Google Scholar 

  • Browning BL, Browning SR (2016) Genotype imputation with millions of reference samples. Amer J Hum Genet 98:116–126

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bruhn CM, Feldman N, Garlitz C, Harwood J, Ivans E, Marshall M, Riley A, Thurber D, Williamson E (1991) Consumer perceptions of quality: apricots, cantaloupes, peaches, pears, strawberries, and tomatoes. J Food Qual 14:187–195

    Article  Google Scholar 

  • Brummell DA, Harpster MH, Civello PM, Palys JM, Bennett AB, Dunsmuir P (1999) Modification of expansin protein abundance in tomato fruit alters softening and cell wall polymer metabolism during ripening. Plant Cell 11(11):2203–2216

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Bucheli P, Voirol E, De La Torre R, López J, Rytz A, Tanksley SD, Pétiard V (1999) Definition of nonvolatile markers for flavor of tomato (Lycopersicon esculentum Mill.) as tools in selection and breeding. J Agri Food Chem 47:659–664

    Article  CAS  Google Scholar 

  • Budiman MA, Chang S-B, Lee S, Yang TJ, Zhang H-B, de Jong H, Wing RA (2004) Localization of jointless-2 gene in the centromeric region of tomato chromosome 12 based on high resolution genetic and physical mapping. Theor Appl Genet 108:190–196

    Article  CAS  PubMed  Google Scholar 

  • Bush DS (1995) Calcium regulation in plant cells and its role in signaling. Annu Rev Plant Physiol 46:95–122

    Article  CAS  Google Scholar 

  • Bussières P (1994) Water import rate in tomato fruit: a resistance model. Ann Bot 73:75–82

    Article  Google Scholar 

  • Butler L (1952) The linkage map of the tomato. J Hered 43:25–36

    Article  Google Scholar 

  • Cagas CC, Lee ON, Nemoto K, Sugiyama N (2008) Quantitative trait loci controlling flowering time and related traits in a Solanum lycopersicum × S. pimpinellifolium cross. Sci Hort (Amsterdam) 116:144–151

    Article  CAS  Google Scholar 

  • Calin GA, Croce CM (2006) MicroRNA signatures in human cancers. Nat Rev Cancer 6:857–866

    Article  CAS  PubMed  Google Scholar 

  • Callaway E (2018) CRISPR plants now subject to t ough GM l aws in European Union. Nature 560:16. https://doi.org/10.1038/d41586-018-05814-6

    Article  CAS  PubMed  Google Scholar 

  • Calus MPL, Meuwissen THE, de Roos APW, Veerkamp RF (2008) Accuracy of genomic selection using different methods to define haplotypes. Genetics 178:553–561

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Canady MA, Meglic V, Chetelat RT (2005) A library of Solanum lycopersicoides introgression lines in cultivated tomato. Genome 48:685–697

    Article  CAS  PubMed  Google Scholar 

  • Cantero-Navarro E, Romero-Aranda R, Fernández-Muñoz R, Martínez-Andújar C, Pérez-Alfocea F, Albacete A (2016) Improving agronomic water use efficiency in tomato by rootstock-mediated hormonal regulation of leaf biomass. Plant Sci 251:90–100

    Article  CAS  PubMed  Google Scholar 

  • Cao K, Xu H, Zhang R, Xu D, Yan L, Sun Y, Xia L, Zhao J, Zou Z, Bao E (2019) Renewable and sustainable strategies for improving the thermal environment of Chinese solar greenhouses. Energy Build. In Press

    Google Scholar 

  • Cárdenas PD, Sonawane PD, Pollier J, Vanden Bossche R, Dewangan V, Weithorn E, Tal L, Meir S, Rogachev I, Malitsky S, Giri AP, Goossens A, Burdman S, Aharoni A (2016) GAME9 regulates the biosynthesis of steroidal alkaloids and upstream isoprenoids in the plant mevalonate pathway. Nat Commun 7:10654

    Google Scholar 

  • Carelli BP, Gerald LTS, Grazziotin FG, Echeverrigaray S (2006) Genetic diversity among Brazilian cultivars and landraces of tomato Lycopersicon esculentum Mill. revealed by RAPD markers. Genet Resour Crop Evol 53:395–400

    Article  CAS  Google Scholar 

  • Carmeille A, Caranta C, Dintinger J, Prior P, Luisetti J, Besse P (2006) Identification of QTLs for Ralstonia solanacearum race 3-phylotype II resistance in tomato. Theor Appl Genet 113:110–121

    Article  CAS  PubMed  Google Scholar 

  • Carmel-Goren L, Liu YS, Lifschitz E, Zamir D (2003) The SELF-PRUNING gene family in tomato. Plant Mol Biol 52:1215–1222

    Article  CAS  PubMed  Google Scholar 

  • Caro M, Cruz V, Cuartero J, Estañ MT, Bolarin MC (1991) Salinity tolerance of normal-fruited and cherry tomato cultivars. Plant Soil 136:249–255

    Article  CAS  Google Scholar 

  • Caromel B, Hamers C, Touhami N, Renaudineau A, Bachellez A, Massire A, Damidaux R, Lefebvre V (2015) Screening tomato germplasm for resistance to late blight. In: INNOHORT, innovation in integrated & organic horticulture. ISHS International Symposium, Avignon, France, 8–12 June 2015, pp 15–16

    Google Scholar 

  • Carrari F, Baxter C, Usadel B, Urbanczyk-Wochniak E, Zanor M-I, Nunes-Nesi A, Nikiforova V, Centero D, Ratzka A, Pauly M et al (2006) Integrated analysis of metabolite and transcript levels reveals the metabolic shifts that underlie tomato fruit development and highlight regulatory aspects of metabolic network behavior. Plant Physiol 142:1380–1396

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Casteel CL, Walling LL, Paine TD (2007) Effect of Mi-1.2 gene in natal host plants on behavior and biology of the tomato psyllid Bactericerca cockerelli (Sulc) (Hemiptera: Psyllidae). J Entomol Sci 42:155–162

    Article  CAS  Google Scholar 

  • Catanzariti AM, Do HTT, Bru P, de Sain M, Thatcher LF, Rep M, Jones DA (2017) The tomato I gene for Fusarium wilt resistance encodes an atypical leucine-rich repeat receptor-like protein whose function is nevertheless dependent on SOBIR1 and SERK3/BAK1. Plant J 89:1195–1209

    Article  CAS  PubMed  Google Scholar 

  • Catanzariti AM, Lim GTT, Jones DA (2015) The tomato I-3 gene: a novel gene for resistance to Fusarium wilt disease. New Phytol 207:106–118

    Article  CAS  PubMed  Google Scholar 

  • Catchen JM, Boone JQ, Davey JW, Hohenlohe PA, Etter PD, Blaxter ML (2011) Genome-wide genetic marker discovery and genotyping using next-generation sequencing. Nat Rev Genet 12:499–510

    Article  PubMed  CAS  Google Scholar 

  • Causse M, Buret M, Robini K, Verschave P (2003) Inheritance of nutritional and sensory quality traits in fresh market tomato and relation to consumer preferences. J Food Sci 68:2342–2350

    Article  CAS  Google Scholar 

  • Causse M, Friguet C, Coiret C, Lépicier M, Navez B, Lee M, Holthuysen N, Sinesio F, Moneta E, Grandillo S (2010) Consumer preferences for fresh tomato at the European scale: a common segmentation on taste and firmness. J Food Sci 75(9):531–541

    Article  CAS  Google Scholar 

  • Causse M, Chaïb J, Lecomte L, Buret M, Hospital F (2007a) Both additivity and epistasis control the genetic variation for fruit quality traits in tomato. Theor Appl Genet 115:429–442

    Article  CAS  PubMed  Google Scholar 

  • Causse M, Duffe P, Gomez MC, Buret M, Damidaux R, Zamir D, Gur A, Chevalier C, Lemaire-Chamley M, Rothan C (2004) A genetic map of candidate genes and QTLs involved in tomato fruit size and composition. J Exp Bot 55:1671–1685

    Article  CAS  PubMed  Google Scholar 

  • Causse M, Damidaux R, Rousselle P (2007) Traditional and enhanced breeding for fruit quality traits in tomato. In: Razdan MK, Mattoo AK (eds) Genetic improvement of solanaceous crops, Vol. 2: Tomato. Science Publishers, Enfield, USA, pp 153–192

    Google Scholar 

  • Causse M, Saliba-Colombani V, Lesschaeve I, Buret M (2001) Genetic analysis of organoleptic quality in fresh market tomato. 2. Mapping QTLs for sensory attributes. Theor Appl Genet 102:273–283

    Article  CAS  Google Scholar 

  • Causse M, Saliba-Colombani V, Lecomte L, Duffé P, Rousselle P, Buret M (2002) QTL analysis of fruit quality in fresh market tomato: a few chromosome regions control the variation of sensory and instrumental traits. J Exp Bot 53:2089–2098

    Article  CAS  PubMed  Google Scholar 

  • Causse M, Desplat N, Pascual L et al (2013) Whole genome resequencing in tomato reveals variation associated with introgression and breeding events. BMC Genomics 14, 791

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Chakrabarti M, Zhang N, Sauvage C, Muños S, Blanca J, Cañizares J, Diez MJ, Schneider R, Mazourek M, McClead J et al (2013) A cytochrome P450 regulates a domestication trait in cultivated tomato. Proc Natl Acad Sci USA 110:17125–17130

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Chen FQ, Foolad MR, Hyman J, St. Clair DA, Beelaman RB (1999) Mapping of QTLs for lycopene and other fruit traits in a Lycopersicon esculentum × L. pimpinellifolium cross and comparison of QTLs across tomato species. Mol Breed 5:283–299

    Article  CAS  Google Scholar 

  • Chen J, Kang S, Du T, Qiu R, Guo P, Chen R (2013) Quantitative response of greenhouse tomato yield and quality to water deficit at different growth stages. Agri Water Manag 129:152–162

    Article  Google Scholar 

  • Chen X (2005) microRNA biogenesis and function in plants. FEBS Lett 579:5923

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Chen X (2009) Small RNAs and their roles in plant development. Annu Rev Cell Dev Biol 25:21–44

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Chetelat RT, DeVerna JW, Bennett AB (1995) Introgression into tomato (Lycopersicon esculentum) of the L. chmielewskii sucrose accumulator gene (sucr) controlling fruit sugar composition. Theor Appl Genet 91:327–333

    Article  CAS  PubMed  Google Scholar 

  • Cho SK, Ben Chaabane S, Shah P, Poulsen CP, Yang SW (2014) COP1 E3 ligase protects HYL1 to retain microRNA biogenesis. Nat Commun 5:5867

    Article  CAS  PubMed  Google Scholar 

  • Chunwongse J, Chunwongse C, Black L, Hanson P (2002) Molecular mapping of the Ph-3 gene for late blight resistance in tomato. J Hort Sci Biotechnol 77:281–286

    Article  CAS  Google Scholar 

  • Clark AG (2004) The role of haplotypes in candidate gene studies. Genet Epidemiol 27:321–333

    Article  PubMed  Google Scholar 

  • Clough SJ, Bent AF (1998) Floral dip: a simplified method for Agrobacterium-mediated transformation of Arabidopsis thaliana. Plant J16(6):735–743

    Google Scholar 

  • Coaker GL, Francis DM (2004) Mapping, genetic effects, and epistatic interaction of two bacterial canker resistance QTLs from Lycopersicon hirsutum. Theor Appl Genet 108:1047–1055

    Article  CAS  PubMed  Google Scholar 

  • Colliver S, Bovy A, Collins G, Muir S, Robinson S, de Vos CHR, Verhoeyen ME (2002) Improving the nutritional content of tomatoes through reprogramming their flavonoid biosynthetic pathway. Phytochem Rev 1:113–123

    Article  CAS  Google Scholar 

  • Colombié S, Beauvoit B, Nazaret C, Bénard C, Vercambre G, Le Gall S, Biais B, Cabasson C, Maucourt M, Bernillon S, Moing A, Dieuaide-Noubhani M, Mazat J-P, Gibon Y (2017) Respiration climacteric in tomato fruits elucidated by constraint-based modelling. New Phytol 213:1726–1739

    Article  PubMed  CAS  Google Scholar 

  • Colombié S, Nazaret C, Bénard C, Biais B, Mengin V, Solé M, Fouillen L, Dieuaide-Noubhani M, Mazat J-P, Beauvoit B, Gibon Y (2015) Modelling central metabolic fluxes by constraint-based optimization reveals metabolic reprogramming of developing Solanum lycopersicum (tomato) fruit. Plant J 81:24–39

    Article  PubMed  CAS  Google Scholar 

  • Comai L, Henikoff S (2006) TILLING: practical single-nucleotide mutation discovery. Plant J 45:684–694

    Article  CAS  PubMed  Google Scholar 

  • Coneva V, Frank MH, Balaguer MAL, Li M, Sozzani R, Chitwood DH (2017) Genetic architecture and molecular networks underlying leaf thickness in desert-adapted Tomato Solanum pennellii. Plant Physiol 175(1):376–391

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Constantinescu D, Memmah M-M, Vercambre G, Génard M, Baldazzi V, Causse M et al (2016) Model-assisted estimation of the genetic variability in physiological parameters related to tomato fruit growth under contrasted water conditions. Front Plant Sci 7:1841. https://doi.org/10.3389/fpls.2016.01841

    Article  PubMed  PubMed Central  Google Scholar 

  • Costa JM, Ortuño MF, Chaves MM (2007) Deficit irrigation as a strategy to save water: physiology and potential application to horticulture. J Integr Plant Biol 49:1421–1434

    Article  Google Scholar 

  • Cournède P-H et al (2013) Development and evaluation of plant growth models: methodology and implementation in the pygmalion platform. Math Mod Nat Phen 8(4):112–130

    Article  Google Scholar 

  • Cowger C, Brown JKM (2019) Durability of quantitative resistance in crops: greater than we know? Annu Rev Phytopathol 57:253–277

    Article  CAS  PubMed  Google Scholar 

  • Crain J, Mondal S, Rutkoski J, Singh RP, Poland J (2018) Combining high-Throughput phenotyping and genomic information to increase prediction and selection accuracy in wheat breeding. Plant Genome 11: 0

    Article  Google Scholar 

  • Crossa J, Pérez-Rodríguez P, Cuevas J, Montesinos-López O, Jarquín D, de los Campos G, Burgueño J, Camacho-González JM, Pérez-Elizalde S, Beyene Y, et al (2017) Genomic selection in plant breeding: methods, models, and perspectives. Trends Plant Sci. https://doi.org/10.1016/j.tplants.2017.08.011

    Article  CAS  PubMed  Google Scholar 

  • Cui J, Jiang N, Zhou X, Hou X, Yang G, Meng J, Luan Y (2018) Tomato MYB49 enhances resistance to Phytophthora infestans and tolerance to water deficit and salt stress. Planta 248:1487–1503

    Article  CAS  PubMed  Google Scholar 

  • Cui J, You C, Chen X (2017a) The evolution of microRNAs in plants. Curr Opin Plant Biol 35:61–67

    Article  CAS  PubMed  Google Scholar 

  • Cui J, Zhou B, Ross SA, Zempleni J (2017b) Nutrition, microRNAs, and human health. Adv Nutr 8:105–112

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Cuyabano BC, Su G, Lund MS (2014) Genomic prediction of genetic merit using LD-based haplotypes in the Nordic Holstein population. BMC Genom. https://doi.org/10.1186/1471-2164-15-1171

    Article  Google Scholar 

  • Cuyabano BCD, Su G, Lund MS (2015a) Selection of haplotype variables from a high-density marker map for genomic prediction. Genet Sel Evol 47:61

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Cuyabano BCD, Su G, Rosa GJM, Lund MS, Gianola D (2015b) Bootstrap study of genome-enabled prediction reliabilities using haplotype blocks across Nordic Red cattle breeds. J Dairy Sci 98:7351–7363

    Article  CAS  PubMed  Google Scholar 

  • Dal Cin V, Kevany B, Fei Z, Klee HJ (2009) Identification of Solanum habrochaites loci that quantitatively influence tomato fruit ripening-associated ethylene emissions. Theor Appl Genet 119:1183–1192

    Article  CAS  Google Scholar 

  • Danecek P, Huang J, Min JL, Timpson NJ, Trabetti E, Richards JB, Durbin R, Howie B, Gambaro G, Zheng H-F et al (2015) Improved imputation of low-frequency and rare variants using the UK10K haplotype reference panel. Nat Commun 6:8111

    Article  PubMed  CAS  Google Scholar 

  • Danilo B, Perrot L, Botton E, Nogué F, Mazier M (2018) The DFR locus: a smart landing pad for targeted transgene insertion in tomato. PLoS ONE 13(12):e0208395

    Article  PubMed  PubMed Central  Google Scholar 

  • Danilo B, Perrot L, Mara K, Botton E, Nogué F, Mazier M (2019) Efficient and transgene-free gene targeting using Agrobacterium-mediated delivery of the CRISPR/Cas9 system in tomato. Plant Cell Rep 38(4):459–462

    Article  CAS  PubMed  Google Scholar 

  • Das S, Forer L, Schönherr S, Sidore C, Locke AE, Kwong A, Vrieze SI, Chew EY, Levy S, McGue M et al (2016) Next-generation genotype imputation service and methods. Nat Genet 48:1284–1287

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Davies JN, Hobson GE (1981) The constituents of tomato fruit—the influence of environment, nutrition, and genotype. Crit Rev Food Sci Nutr 15:205–280

    Article  CAS  PubMed  Google Scholar 

  • Davila Olivas NH, Kruijer W, Gort G, Wijnen CL, van Loon JJA, Dicke M (2017) Genome-wide association analysis reveals distinct genetic architectures for single and combined stress responses in Arabidopsis thaliana. New Phytol 213:838–851

    Article  CAS  PubMed  Google Scholar 

  • Davis J, Yu DZ, Evans W, Gokirmak T, Chetelat RT, Stotz HU (2009) Mapping of loci from Solanum lycopersicoides conferring resistance or susceptibility to Botrytis cinerea in tomato. Theor Appl Genet 119:305–314

    Article  PubMed  PubMed Central  Google Scholar 

  • de Freitas ST, Martinelli F, Feng B, Reitz NF, Mitcham EJ (2018) Transcriptome approach to understand the potential mechanisms inhibiting or triggering blossom-end rot development in tomato fruit in response to plant growth regulators. J Plant Growth Regul 37:183–198

    Google Scholar 

  • de Groot CC, Marcelis LFM, van den Boogaard R, Lambers H (2004) Response of growth of tomato to phosphorus and nitrogen nutrition. Acta Hort 357–364

    Google Scholar 

  • de Jong CF, Takken FLW, Cai XH, de Wit P, Joosten M (2002) Attenuation of Cf-mediated defense responses at elevated temperatures correlates with a decrease in elicitor-binding sites. Mol Plant-Microbe Interact 15:1040–1049

    Article  PubMed  Google Scholar 

  • de Los Campos G, Hickey JM, Pong-Wong R, Daetwyler HD, Calus MPL, Kirst M, Huber D, Peter GF (2013) Whole-genome regression and prediction methods applied to plant and animal breeding. Genetics 193:327–345

    Article  Google Scholar 

  • De Swaef T, Mellisho CD, Baert A, De Schepper V, Torrecillas A, Conejero W, Steppe K (2014) Model-assisted evaluation of crop load effects on stem diameter variations and fruit growth in peach. Trees 28:1607–1622

    Article  Google Scholar 

  • Delhaize E, Gruber BD, Ryan PR (2007) The roles of organic anion permeases in aluminium resistance and mineral nutrition. FEBS Lett 581:2255–2262

    Article  CAS  PubMed  Google Scholar 

  • DeVicente MC, Tanksley SD (1993) QTL analysis of transgressive segregation in an interspecific tomato cross. Genetics 134:585–596

    CAS  PubMed  PubMed Central  Google Scholar 

  • Dileo MV, Pye MF, Roubtsova TV, Duniway JM, MacDonald JD, Rizzo DM, Bostock RM (2010) Abscisic acid in salt stress predisposition to Phytophthora root and crown rot in tomato and chrysanthemum. Phytopathology 100:871–879

    Article  CAS  PubMed  Google Scholar 

  • Diouf IA, Derivot L, Bitton F, Pascual L, Causse M (2018) Water deficit and salinity stress reveal many specific QTL for plant growth and fruit quality traits in tomato. Front Plant Sci 9:279

    Article  PubMed  PubMed Central  Google Scholar 

  • Dixon MS, Hatzixanthis K, Jones DA, Harrison K, Jones JDG (1998) The tomato Cf-5 disease resistance gene and six homologs show pronounced allelic variation in leucine-rich repeat copy number. Plant Cell 10:1915–1925

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Dixon MS, Jones DA, Keddie JS, Thomas CM, Harrison K, Jones JD (1996) The tomato Cf-2 disease resistance locus comprises two functional genes encoding leucine-rich repeat proteins. Cell 84:451–459

    Article  CAS  PubMed  Google Scholar 

  • Do PT, Prudent M, Sulpice R, Causse M, Fernie AR (2010) The influence of fruit load on the tomato pericarp metabolome in a Solanum chmielewskii introgression line population. Plant Physiol 154:1128–1142

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Doganlar S, Dodson J, Gabor B, Beck-Bunn T, Crossman C, Tanksley SD (1998) Molecular mapping of the py-1 gene for resistance to corky root rot (Pyrenochaeta lycopersici) in tomato. Theor Appl Genet 97:784–788

    Article  CAS  Google Scholar 

  • Doganlar S, Frary A, Ku H-M, Tanksley SD (2003) Mapping quantitative trait loci in inbred backcross lines of Lycopersicon pimpinellifolium (LA1589). Genome 45:1189–1202

    Article  Google Scholar 

  • Domínguez T, Hernández ML, Pennycooke JC, Jiménez P, Martínez-Rivas JM, Sanz C, Stockinger EJ, Sánchez-Serrano JJ, Sanmartín M (2010) Increasing ω-3 desaturase expression in tomato results in altered aroma profile and enhanced resistance to cold stress. Plant Physiol 153(2):655–665

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Donald 1968 C.M. The breeding of crop idéotypes. Euphytica, 17 (1968), pp. 385–403

    Google Scholar 

  • Dong QL, Liu DD, An XH, Hu DG, Yao YX, Hao YJ (2011) MdVHP1 encodes an apple vacuolar H+-PPase and enhances stress tolerance in transgenic apple callus and tomato. JPlant Physiol 168(17):2124–2133

    Article  CAS  Google Scholar 

  • Dong Z, Men Y, Li Z, Zou Q, Ji J (2019) Chlorophyll fluorescence imaging as a tool for analyzing the effects of chilling injury on tomato seedlings. Sci Hort (Amsterdam) 246:490–497

    Article  CAS  Google Scholar 

  • Dorais M, Papadopoulos AP, Gosselin A (2001) Greenhouse tomato fruit quality. Hortic Rev 26:239–319

    CAS  Google Scholar 

  • Dreissig S, Schiml S, Schindele P, Weiss O, Rutten T, Schubert V, Gladilin E, Mette MF, Puchta H, Houben A (2017) Live-cell CRISPR imaging in plants reveals dynamic telomere movements. Plant J 91(4):565–573

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Driedonks N, Wolters-Arts M, Huber H, de Boer G-J, Vriezen W, Mariani C, Rieu I (2018) Exploring the natural variation for reproductive thermotolerance in wild tomato species. Euphytica 214:67

    Article  Google Scholar 

  • Du Y-D, Niu W-Q, Gu X-B, Zhang Q, Cui B-J (2018) Water- and nitrogen-saving potentials in tomato production: a meta-analysis. Agri Water Manag 210:296–303

    Article  Google Scholar 

  • Duangjit J, Causse M, Sauvage C (2016) Efficiency of genomic selection for tomato fruit quality. Mol Breed 36(36):29

    Article  CAS  Google Scholar 

  • Edwards SM, Buntjer JB, Jackson R, Bentley AR, Lage J, Byrne E, Burt C, Jack P, Berry S, Flatman E et al (2019) The effects of training population design on genomic prediction accuracy in wheat. Theor Appl Genet 443267

    Google Scholar 

  • El-hady E, Haiba A, El-hamid NRA, Rizkalla A, Phylogenetic AR (2010) Phylogenetic diversity and relationships of some tomato varieties by electrophoretic protein and RAPD analysis. J Amer Sci 6:434–441

    Google Scholar 

  • Elvanidi A, Katsoulas N, Augoustaki D, Loulou I, Kittas C (2018) Crop reflectance measurements for nitrogen deficiency detection in a soilless tomato crop. Biosyst Eng 176:1–11

    Article  Google Scholar 

  • Endelman JB (2011) Ridge regression and other kernels for genomic selection with R package rrBLUP. Plant Genome J 4:250

    Article  Google Scholar 

  • Ercolano MR, Sanseverino W, Carli P, Ferriello F, Frusciante L (2012) Genetic and genomic approaches for R-gene mediated disease resistance in tomato: retrospects and prospects. Plant Cell Rep 31:973–985

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Eriksson EM, Bovy A, Manning K, Harrison L, Andrews J, De Silva J, Tucker GA, Seymour GB, Thompson J, Tor M et al (2004) Effect of the colorless non-ripening mutation on cell wall biochemistry and gene expression during tomato fruit development and ripening 1[w]. Plant Physiol 136:4184–4197

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ernst K, Kumar A, Kriseleit D, Kloos DU, Phillips MS, Ganal MW (2002) The broad-spectrum potato cyst nematode resistance gene (Hero) from tomato is the only member of a large gene family of NBS-LRR genes with an unusual amino acid repeat in the LRR region. Plant J 31:127–136

    Article  CAS  PubMed  Google Scholar 

  • Eshed Y, Gera G, Zamir D (1996) A genome-wide search for wild-species alleles that increase horticultural yield of processing tomato. Theor Appl Genet 93:877–886

    Article  CAS  PubMed  Google Scholar 

  • Eshed Y, Zamir D (1995) An introgression line population of Lycopersicon pennellii in the cultivatedtomato enables the identification and fine mapping of yield-associated QTL. Genetics 141:1147–1162

    CAS  PubMed  PubMed Central  Google Scholar 

  • Estañ MT, Villalta I, Bolarín MC, Carbonell EA, Asins MJ (2009) Identification of fruit yield loci controlling the salt tolerance conferred by solanum rootstocks. Theor Appl Genet 118:305–312

    Article  PubMed  Google Scholar 

  • Evangelou E, Ioannidis JPA (2013) Meta-analysis methods for genome-wide association studies and beyond. Nat Rev Genet 14:379–389

    Article  CAS  PubMed  Google Scholar 

  • Fan ZQ, Ba LJ, Shan W, Xiao YY, Lu WJ, Kuang JF, Chen JY (2018) A banana R2R3-MYB transcription factor MaMYB3 is involved in fruit ripening through modulation of starch degradation by repressing starch degradation-related genes and MabHLH6. Plant J 96(6):1191–1205

    Article  CAS  PubMed  Google Scholar 

  • Fang X, Cui Y, Li Y, Qi Y (2015) Transcription and processing of primary microRNAs are coupled by Elongator complex in Arabidopsis. Nat Plants 1:15075

    Article  CAS  PubMed  Google Scholar 

  • Fanwoua J, de Visser PHB, Heuvelink E, Yin X, Struik PC, Marcelis LFM (2013) A dynamic model of tomato fruit growth integrating cell division, cell growth and endoreduplication. Funct Plant Biol 40(11):1098–1114

    Article  PubMed  Google Scholar 

  • FAO (2015) Coping with climate change—the roles of genetic resources for food and agriculture

    Google Scholar 

  • Farashi S, Kryza T, Clements J, Batra J (2019) Post-GWAS in prostate cancer: from genetic association to biological contribution. Nat Rev Cancer 19:46–59

    Article  CAS  PubMed  Google Scholar 

  • Fereres E, Soriano MA (2006) Deficit irrigation for reducing agricultural water use. J Exp Bot 58:147–159

    Article  PubMed  CAS  Google Scholar 

  • Fernandes SB, Dias KOG, Ferreira DF, Brown PJ (2018) Efficiency of multi-trait, indirect, and trait-assisted genomic selection for improvement of biomass sorghum. Theor Appl Genet 131:747–755

    Article  CAS  PubMed  Google Scholar 

  • Fernandez AI, Viron N, Alhagdow M, Karimi M, Jones M, Amsellem Z, Sicard A, Czerednik A, Angenent G, Grierson D, May S (2009) Flexible tools for gene expression and silencing in tomato. Plant Physiol 151(4):1729–1740

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Fernie AR, Aharoni A, Willmitzer L, Stitt M, Tohge T, Kopka J, Carroll AJ, Saito K, Fraser PD, DeLuca V (2011) Recommendations for reporting metabolite data. Plant Cell 23:2477–2482

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Fernie AR, Schauer N (2009) Metabolomics-assisted breeding: a viable option for crop improvement? Trends Genet 25:39–48

    Article  CAS  PubMed  Google Scholar 

  • Finkers R, Bai YL, van den Berg P, van Berloo R, Meijer-Dekens F, ten Have A, van Kan J, Lindhout P, van Heusden AW (2008) Quantitative resistance to Botrytis cinerea from Solanum neorickii. Euphytica 159:83–92

    Article  Google Scholar 

  • Finkers R, van den Berg P, van Berloo R, ten Have A, van Heusden AW, van Kan JAL, Lindhout P (2007a) Three QTLs for Botrytis cinerea resistance in tomato. Theor Appl Genet 114:585–593

    Article  PubMed  Google Scholar 

  • Finkers R, Van Heusden AW, Meijer-Dekens F, Van Kan JAL, Maris P, Lindhout P (2007b) The construction of a Solanum habrochaites LYC4 introgression line population and the identification of QTLs for resistance to Botrytis cinerea. Theor Appl Genet 114:1071–1080

    Article  PubMed  PubMed Central  Google Scholar 

  • Fishman S, Génard M (1998) A biophysical model of fruit growth: simulation of seasonal and diurnal dynamics of mass. Plant Cell Environ 21:739–752

    Article  Google Scholar 

  • Foolad MR (2007) Genome mapping and molecular breeding of tomato. Int J Plant Genomics 2007:64358

    PubMed  PubMed Central  Google Scholar 

  • Foolad MR, Merk HL, Ashrafi H (2008) Genetics, genomics and breeding of late blight and early blight resistance in tomato. Crit Rev Plant Sci 27:75–107

    Article  CAS  Google Scholar 

  • Foolad MR, Panthee DR (2012) Marker-assisted selection in tomato breeding. Crit Rev Plant Sci 31:93–123

    Article  Google Scholar 

  • Foolad MR, Sullenberger MT, Ohlson EW, Gugino BK (2014) Response of accessions within tomato wild species, Solanum pimpinellifolium to late blight. Plant Breed 133:401–411

    Article  CAS  Google Scholar 

  • Foolad MR, Zhang LP, Khan AA, Nino-Liu D, Lin GY (2002) Identification of QTLs for early blight (Alternaria solani) resistance in tomato using backcross populations of a Lycopersicon esculentum x L. hirsutum cross. Theor Appl Genet 104:945–958

    Article  CAS  PubMed  Google Scholar 

  • Fragkostefanakis S, Mesihovic A, Simm S, Paupière MJ, Hu Y, Paul P, Mishra SK, Tschiersch B, Theres K, Bovy A et al (2016) HsfA2 controls the activity of developmentally and stress-regulated heat stress protection mechanisms in tomato male reproductive tissues. Plant Physiol 170:2461–2477

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Fragkostefanakis S, Röth S, Schleiff E, Scharf KD (2015) Prospects of engineering thermotolerance in crops through modulation of heat stress transcription factor and heat shock protein networks. Plant, Cell Environ 38:1881–1895

    Article  CAS  Google Scholar 

  • Frary A, Doganlar S, Daunay MC, Tanksley SD (2003) QTL analysis of morphological traits in eggplant and implications for conservation of gene function during evolution of solanaceous species. Theor Appl Genet 107:359–370

    Article  CAS  PubMed  Google Scholar 

  • Frary A, Fulton TM, Zamir D, Tanksley SD (2004) Advanced backcross QTL analysis of a Lycopersicon esculentum × L. pennellii cross and identification of possible orthologs in the Solanaceae. Theor Appl Genet 108:485–496

    Article  CAS  PubMed  Google Scholar 

  • Frary A, Keleş D, Pinar H, Göl D, Doğanlar S (2011) NaCl tolerance in Lycopersicon pennellii introgression lines: QTL related to physiological responses. Biol Plant 55:461–468

    Article  CAS  Google Scholar 

  • Frary A, Nesbitt TC, Frary A, Grandillo S, Van Der Knaap E, Cong B, Liu J, Meller J, Elber R, Alpert KB et al (2000) fw2.2: a quantitative trait locus key to the evolution of tomato fruit size. Science (80-) 289: 85–88

    Article  CAS  PubMed  Google Scholar 

  • Frary A, Göl D, Keleş D, Ökmen B, Pınar H, Şığva HÖ et al (2010) Salt tolerance in Solanum pennellii: antioxidant response and related QTL. BMC Plant Biol 10:58

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Fridman E, Carrari F, Liu YS, Fernie AR, Zamir D (2004) Zooming in on a quantitative trait for tomato yield using interspecific introgressions. Science (80-) 305: 1786–1789

    Article  CAS  PubMed  Google Scholar 

  • Fridman E, Liu YS, Carmel-Goren L, Gur A, Shoresh M, Pleban T, Eshed Y, Zamir D (2002) Two tightly linked QTLs modify tomato sugar content via different physiological pathways. Mol Genet Genom 266: 821–826

    Article  CAS  PubMed  Google Scholar 

  • Fridman E, Pleban T, Zamir D (2000) A recombination hotspot delimits a wild-species quantitative trait locus for tomato sugar content to 484 bp within an invertase gene. Proc Natl Acad Sci USA 97:4718–4723

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Fridman E, Zamir D (2003) Functional divergence of a syntenic invertase gene family in tomato, potato, and Arabidopsis. Plant Physiol 131:603–609

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Fry WE, Goodwin SB (1997) Re-emergence of potato and tomato late blight in the United States. Plant Dis 81:1349–1357

    Article  PubMed  Google Scholar 

  • Fujita M, Fujita Y, Noutoshi Y, Takahashi F, Narusaka Y, Yamaguchi-Shinozaki K, Shinozaki K (2006) Crosstalk between abiotic and biotic stress responses: a current view from the points of convergence in the stress signaling networks. Curr Opin Plant Biol 9:436–442

    Article  PubMed  Google Scholar 

  • Fulop D, Ranjan A, Ofner I, Covington MF, Chitwood DH, West D, Ichihashi Y, Headland L, Zamir D, Maloof JN, et al. (2016) A new advanced backcross tomato population enables high resolution leaf QTL mapping and gene identification. G3: GenesGenomesGenet 6:3169–3184

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Fulton TM (2002) Identification, analysis, and utilization of conserved ortholog set markers for comparative genomics in higher plants. Plant Cell 14:1457–1467

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Fulton TM, Beck-Bunn T, Emmatty D, Eshed Y, Lopez J, Petiard V, Uhlig J, Zamir D, Tanksley SD (1997) QTL analysis of an advanced backcross of Lycopersicon peruvianum to the cultivated tomato and comparisons with QTLs found in other wild species. Theor Appl Genet 95:881–894

    Article  CAS  Google Scholar 

  • Fulton TM, Grandillo S, Beck-Bunn T, Fridman E, Frampton A, Lopez J, Petiard V, Uhlig J, Zamir D, Tanksley SD (2000) Advanced backcross QTL analysis of a Lycopersicon esculentum × Lycopersicon parviflorum cross. Theor Appl Genet 100:1025–1042

    Article  CAS  Google Scholar 

  • Gaion LA, Muniz JC, Barreto RF, D’Amico-Damião V, de Mello Prado R, Carvalho RF (2019) Amplification of gibberellins response in tomato modulates calcium metabolism and blossom end rot occurrence. Sci Hortic (Amsterdam) 246:498–505

    Article  CAS  Google Scholar 

  • Gaj T, Gersbach CA, Barbas CF (2013) ZFN, TALEN, and CRISPR/Cas-based methods for genome engineering. Trends Biotechnol 31(7):397–405

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Gallusci P, Hodgman C, Teyssier E, Seymour GB (2016) DNA methylation and chromatin regulation during fleshy fruit development and ripening. Front Plant Sci 7:807

    Article  PubMed  PubMed Central  Google Scholar 

  • Gao C, Ju Z, Cao D, Zhai B, Qin G, Zhu H, Fu D, Luo Y, Zhu B (2015) MicroRNA profiling analysis throughout tomato fruit development and ripening reveals potential regulatory role of RIN on microRNAs accumulation. Plant Biotechnol J 13:370–382

    Article  CAS  PubMed  Google Scholar 

  • Gao L, Gonda I, Sun H et al (2019) The tomato pan-genome uncovers new genes and a rare allele regulating fruit flavor. Nat Genet 51:1044–1051

    Article  CAS  PubMed  Google Scholar 

  • Garcia V, Bres C, Just D, Fernandez L, Tai FWJ, Mauxion JP, Le Paslier MC, Bérard A, Brunel D, Aoki K et al (2016) Rapid identification of causal mutations in tomato EMS populations via mapping-by-sequencing. Nat Protoc 11:2401–2418

    Article  CAS  PubMed  Google Scholar 

  • Gauffier C, Lebaron C, Moretti A, Constant C, Moquet F, Bonnet G, Caranta C, Gallois J-L (2016) A TILLING approach to generate broad-spectrum resistance to potyviruses in tomato is hampered by eIF4E gene redundancy. Plant J 85:717–729

    Article  CAS  PubMed  Google Scholar 

  • Gautier H, Diakou-Verdin V, Bénard C, Reich M, Buret M, Bourgaud F, Poëssel JL, Caris-Veyrat C, Génard M (2008) How does tomato quality (sugar, acid, and nutritional quality) vary with ripening stage, temperature, and irradiance? J Agri Food Chem 56:1241–1250

    Article  CAS  Google Scholar 

  • Génard M, Bertin N, Gautier H, Lescourret F, Quilot B (2010) Virtual profiling: a new way to analyse phenotypes. Plant J 62:344–355

    Article  PubMed  CAS  Google Scholar 

  • Génard M, Lescourret F (2004) Modelling fruit quality: ecophysiological, agronomical and ecological perspectives. In: Dris R, Jain SM (eds) Production practices and quality assessment of food crops, vol 1. Preharvest practice. Kluwer Academic Publisher, Netherlands, pp 47–82

    Chapter  Google Scholar 

  • Génard M, Memmah M-M, Quilot-Turion B, Vercambre G, Baldazzi V, Le Bot J, Bertin N, Gautier H, Lescourret F, Pagès L (2016) Process-based simulation models are essential tools for virtual profiling and design of ideotypes: example of fruit and root. In: Yin X, Struik PC (eds) Crop systems biology: narrowing the gaps between crop modelling and genetics, pp 83–104

    Chapter  Google Scholar 

  • Gerszberg A, Hnatuszko-Konka K, Kowalczyk T, Kononowicz AK (2015) Tomato (Solanum lycopersicum L.) in the service of biotechnology. Plant Cell Tiss Org Cult 120(3):881–902

    Article  CAS  Google Scholar 

  • Geshnizjani N, Ghaderi-Far F, Willems LAJ, Hilhorst HWM, Ligterink W (2018) Characterization of and genetic variation for tomato seed thermo-inhibition and thermo-dormancy. BMC Plant Biol 18:229

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Gest N, Gautier H, Stevens R (2013) Ascorbate as seen through plant evolution: the rise of a successful molecule? J Exp Bot 64:33–53

    Article  CAS  PubMed  Google Scholar 

  • Gianola D, van Kaam JBCHM (2008) Reproducing Kernel Hilbert spaces regression methods for genomic assisted prediction of quantitative traits. Genetics 178:2289

    Article  PubMed  PubMed Central  Google Scholar 

  • Giovannoni J, Nguyen C, Ampofo B, Zhong S, Fei Z (2017) The epigenome and transcriptional dynamics of fruit ripening. Annu Rev Plant Biol 68:61–84

    Article  CAS  PubMed  Google Scholar 

  • Giovannucci E (1999) Tomatoes, tomato-based products, lycopene, and cancer: review of the epidemiologic literature. J Natl Cancer Inst 91:317–331

    Article  CAS  PubMed  Google Scholar 

  • Giroux RW, Filion WG (1992) A comparison of the chilling-stress response in two differentially tolerant cultivars of tomato (Lycopersicon esculentum). Biochem Cell Biol 70:191–198

    Article  CAS  PubMed  Google Scholar 

  • Goff SA, Klee HJ (2006) Plant volatile compounds: sensory cues for health and nutritional value? Science 311:815–819

    Article  CAS  PubMed  Google Scholar 

  • Gonatopoulos-Pournatzis T, Cowling VH (2015) Cap-binding complex (CBC). Biochem J 458:185

    Article  Google Scholar 

  • Gonzalez-Cendales Y, Catanzariti AM, Baker B, McGrath DJ, Jones DA (2016) Identification of I-7 expands the repertoire of genes for resistance to Fusarium wilt in tomato to three resistance gene classes. Mol Plant Pathol 17:448–463

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Goodwin S, McPherson JD, McCombie WR (2016) Coming of age: ten years of next-generation sequencing technologies. Nat Rev Genet 17:333–351

    Article  CAS  PubMed  Google Scholar 

  • Grandillo S, Cammareri M (2016) Molecular mapping of quantitative trait loci in tomato. In: Causse M, Giovannoni J, Bouzayen M, Zouine M (eds) The tomato genome. Springer, Berlin, pp 39–73

    Chapter  Google Scholar 

  • Grandillo S, Chetelat R, Knapp S, Spooner D, Peralta I, Cammareri M, Perez O, Termolino P, Tripodi P, Chiusano ML et al (2011) Solanum sect. Lycopersicon. In: Kole C (ed) Wild crop relatives: genomic and breeding resources. Springer, Berlin, pp 129–215

    Chapter  Google Scholar 

  • Grandillo S, Ku HM, Tanksley SD (1996) Characterization of fs8.1, a major QTL influencing fruit shape in tomato. Mol Breed 2:251–260

    Article  CAS  Google Scholar 

  • Grandillo S, Ku HM, Tanksley SD (1999) Identifying the loci responsible for natural variation in fruit size and shape in tomato. Theor Appl Genet 99:978–987

    Article  CAS  Google Scholar 

  • Grandillo S, Tanksley SD (1996a) Genetic analysis of RFLPs, GATA microsatellites and RAPDs in a cross between L. esculentum and L. pimpinellifolium. Theor Appl Genet 92:957–965

    Article  CAS  PubMed  Google Scholar 

  • Grandillo S, Tanksley SD (1996b) QTL analysis of horticultural traits differentiating the cultivated tomato from the closely related species Lycopersicon pimpinellifolium. Theor Appl Genet 92:935–951

    Article  CAS  PubMed  Google Scholar 

  • Grandillo S, Termolino P, van der Knaap E (2013) Molecular mapping of complex traits in tomato. In: Liedl BE, Labate JA, Stommel JR, Slade A, Kole C (eds) Genetics, genomics and breeding of tomato. CRC Press, Boca Raton, FL, pp 150–227

    Chapter  Google Scholar 

  • Grierson D (2016) Identifying and silencing tomato ripening genes with antisense genes. Plant Biotechnol J14(3):835–838

    Article  Google Scholar 

  • Grilli G, Trevizan Braz L, Gertrudes E, Lemos M (2007) QTL identification for tolerance to fruit set in tomatoby fAFLP markers. Crop Breed Appl Biotechnol 7:234–241

    Article  CAS  Google Scholar 

  • Grimson A, Srivastava M, Fahey B, Woodcroft BJ, Chiang HR, King N, Degnan BM, Rokhsar DS, Bartel DP (2008) Early origins and evolution of microRNAs and Piwi-interacting RNAs in animals. Nature 455:1193–1197

    Article  CAS  PubMed  Google Scholar 

  • Guan Y, Stephens M (2008) Practical issues in imputation-based association mapping. PLoS Genet. https://doi.org/10.1371/journal.pgen.1000279

    Article  PubMed  PubMed Central  Google Scholar 

  • Guichard S, Bertin N, Leonardi C, Gary C (2001) Tomato fruit quality in relation to water and carbon fluxes. Agronomie 21:385–392

    Article  Google Scholar 

  • Guichard S, Gary C, Leonardi C, Bertin N (2005) Analysis of growth and water relations of tomato fruits in relation to air vapor pressure deficit and plant fruit load. J Plant Growth Regul 24:201–213

    Article  CAS  Google Scholar 

  • Gupta A, Pal RK, Rajam MV (2013) Delayed ripening and improved fruit processing quality in tomato by RNAi-mediated silencing of three homologs of 1-aminopropane-1-carboxylate synthase gene. JPlant Physiol 170(11):987–995

    Article  CAS  Google Scholar 

  • Gur A, Osorio S, Fridman E, Fernie AR, Zamir D (2010) hi2-1, A QTL which improves harvest index, earliness and alters metabolite accumulation of processing tomatoes. Theor Appl Genet 121:1587–1599

    Article  PubMed  PubMed Central  Google Scholar 

  • Gur A, Semel Y, Osorio S, Friedmann M, Seekh S, Ghareeb B et al (2011) Yield quantitative trait loci from wild tomato are predominately expressed by the shoot. Theor Appl Genet 122:405–420

    Article  PubMed  Google Scholar 

  • Gur A, Zamir D (2015) Mendelizing all components of a pyramid of three yield QTL in tomato. Front Plant Sci 6:1096. https://doi.org/10.3389/fpls.2015.01096

    Article  PubMed  PubMed Central  Google Scholar 

  • Haanstra JPW, Wye C, Verbakel H, Meijer-Dekens F, Van Den Berg P, Odinot P, Van Heusden AW, Tanksley S, Lindhout P, Peleman J (1999) An integrated high-density RFLP-AFLP map of tomato based on two Lycopersicon esculentum x L. pennellii F2 populations. Theor Appl Genet 99:254–271

    Article  CAS  Google Scholar 

  • Habier D, Fernando RL, Kizilkaya K, Garrick DJ (2011) Extension of the bayesian alphabet for genomic selection. BMC Bioinformatics 12:186

    Article  PubMed  PubMed Central  Google Scholar 

  • Hagassou D, Francia E, Ronga D, Buti M (2019) Blossom end-rot in tomato (Solanum lycopersicum L.): A multi-disciplinary overview of inducing factors and control strategies. Sci Hortic (Amsterdam) 249:49–58

    Article  CAS  Google Scholar 

  • Haggard JE, Johnson EB, St. Clair DA (2013) Linkage relationships among multiple QTL for horticultural traits and late blight (P. infestans) resistance on chromosome 5 introgressed from wild tomato solanum habrochaites. G3: GenesGenomes|Genet 3: 2131–2146

    Google Scholar 

  • Halperin E, Stephan DA (2009) SNP imputation in association studies. Nat Biotechnol 27:349–351

    Article  CAS  PubMed  Google Scholar 

  • Hamilton JP, Sim S-C, Stoffel K, Van Deynze A, Buell CR, Francis DM (2012) Single nucleotide polymorphism discovery in cultivated tomato via sequencing by synthesis. Plant Genome J 5:17

    Article  CAS  Google Scholar 

  • Han P, Lavoir A-V, Le Bot J, Amiens-Desneux E, Desneux N (2015) Nitrogen and water availability to tomato plants triggers bottom-up effects on the leafminer Tuta absoluta. Sci Rep 4:4455

    Article  CAS  Google Scholar 

  • Hanson PM, Yang R, Wu J, Chen J, Ledesma D, Tsou SCS, Lee T-C (2004) Variation for antioxidant activity and antioxidants in tomato. J Amer Soc Hort Sci 129:704–711

    Article  CAS  Google Scholar 

  • Hanssen IM, Thomma B (2010) Pepino mosaic virus: a successful pathogen that rapidly evolved from emerging to endemic in tomato crops. Mol Plant Pathol 11:179–189

    Article  CAS  PubMed  Google Scholar 

  • Hanssens J, De Swaef T, Steppe K (2015) High light decreases xylem contribution to fruit growth in tomato. Plant Cell Environ 38:487–498

    Article  CAS  PubMed  Google Scholar 

  • Harborne JB (1994) The flavonoids. Advances in research since 1986, 1st edn. Chapman Hall, London

    Google Scholar 

  • Harvell CD, Mitchell CE, Ward JR, Altizer S, Dobson AP, Ostfeld RS, Samuel MD (2002) Climate warming and disease risks for terrestrial and marine biota. Science 296:2158–2162

    Article  CAS  PubMed  Google Scholar 

  • Haseneyer G, Schmutzer T, Seidel M, Zhou R, Mascher M, Schön CC, Taudien S, Scholz U, Stein N, Mayer KFX, et al. (2011) From RNA-seq to large-scale genotyping—genomics resources for rye (Secale cereale L.). BMC Plant Biol 11: 131

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Hayashi T, Iwata H (2010) EM algorithm for Bayesian estimation of genomic breeding values. BMC Genet 11:3

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • He S, Schulthess AW, Mirdita V, Zhao Y, Korzun V, Bothe R, Ebmeyer E, Reif JC, Jiang Y (2016) Genomic selection in a commercial winter wheat population. Theor Appl Genet 129:641–651

    Article  CAS  PubMed  Google Scholar 

  • He Y (2012) Chromatin regulation of flowering. Trends Plant Sci 17:556–562

    Article  CAS  PubMed  Google Scholar 

  • Hepler PK (2005) Calcium: a central regulator of plant growth and development. Plant Cell 17:2142–2155

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Heslot N, Yang HP, Sorrells ME, Jannink JL (2012) Genomic selection in plant breeding: a comparison of models. Crop Sci 52:146–160

    Article  Google Scholar 

  • Hess M, Druet T, Hess A, Garrick D (2017) Fixed-length haplotypes can improve genomic prediction accuracy in an admixed dairy cattle population. Genet Sel Evol 49:54

    Article  PubMed  PubMed Central  Google Scholar 

  • Heuvelink E (2005) Tomatoes. CABI Publishers, Wallingford, UK

    Book  Google Scholar 

  • Heuvelink E, Bertin N (1994) Dry matter partitioning in a tomato crop: comparison of two simulation models. J Hort Sci 69:885–903

    Article  Google Scholar 

  • Hill M, Tran N (2018) MicroRNAs regulating MicroRNAs in cancer. Trends Cancer 4:465–468

    Article  CAS  PubMed  Google Scholar 

  • Hirschi KD (2004) The calcium conundrum. Both versatile nutrient and specific signal. Plant Physiol 136:2438–2442

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ho LC (1996) The mechanism of assimilate partitioning and carbohydrate compartmentation in fruit in relation to the quality and yield of tomato. J Exp Bot 47:1239–1243

    Article  CAS  PubMed  Google Scholar 

  • Hobson G, Grierson D (1993) Tomato. In: Biochemistry of fruit ripening. Springer, Dordrecht, pp 405–442

    Chapter  Google Scholar 

  • Hobson GE, Bedford L (1989) The composition of cherry tomatoes and its relation to consumer acceptability. J Hort Sci 64:321–329

    Article  Google Scholar 

  • Hospital F, Charcosset A (1997) Marker-assisted introgression of quantitative trait loci. Genetics 147:1469–1485

    CAS  PubMed  PubMed Central  Google Scholar 

  • Hospital F, Chevalet C, Mulsant P (1992) Using markers in gene introgression breeding programs. Genetics 132:1199–1210

    CAS  PubMed  PubMed Central  Google Scholar 

  • How Kit A, Boureau L, Stammitti-Bert L, Rolin D, Teyssier E, Gallusci P (2010) Functional analysis of SlEZ1 a tomato Enhancer of zeste (E(z)) gene demonstrates a role in flower development. Plant Mol Biol 74:201–213

    Article  CAS  PubMed  Google Scholar 

  • Huang BE, George AW, Forrest KL, Kilian A, Hayden MJ, Morell MK, Cavanagh CR (2012) A multiparent advanced generation inter-cross population for genetic analysis in wheat. Plant Biotechnol J 10:826–839

    Article  CAS  PubMed  Google Scholar 

  • Huang WJ, Liu HK, McCormick S, Tang WH (2014) Tomato pistil factor STIG1 promotes in vivo pollen tube growth by binding to phosphatidylinositol 3-phosphate and the extracellular domain of the pollen receptor kinase LePRK2. Plant Cell 26(6):2505–2523

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Huang Z, van der Knaap E (2011) Tomato fruit weight 11.3 maps close to fasciated on the bottom of chromosome 11. Theor Appl Genet 123:465–474

    Article  PubMed  Google Scholar 

  • Hutton SF, Scott JW, Yang WC, Sim SC, Francis DM, Jones JB (2010) Identification of QTL associated with resistance to bacterial spot race T4 in tomato. Theor Appl Genet 121:1275–1287

    Article  CAS  PubMed  Google Scholar 

  • Ishibashi K, Masuda K, Naito S, Meshi T, Ishikawa M (2007) An inhibitor of viral RNA replication is encoded by a plant resistance gene. In: Proceedings of the national academy of sciences of the United States of America 104:13833–13838

    Article  CAS  Google Scholar 

  • Isidro J, Jannink J-L, Akdemir D, Poland J, Heslot N, Sorrells ME (2015) Training set optimization under population structure in genomic selection. Theor Appl Genet 128:145–158

    Article  PubMed  Google Scholar 

  • Islam MN, Hasanuzzaman ATM, Zhang Z-F, Zhang Y, Liu T-X (2017) High level of nitrogen makes tomato plants releasing less volatiles and attracting more Bemisia tabaci (Hemiptera: Aleyrodidae). Front Plant Sci 8:466

    PubMed  PubMed Central  Google Scholar 

  • Ito Y, Nishizawa-Yokoi A, Endo M, Mikami M, Shima Y, Nakamura N, Kotake-Nara E, Kawasaki S, Toki S (2017) Re-evaluation of the rin mutation and the role of RIN in the induction of tomato ripening. Nat Plants 3(11):866–874

    Article  CAS  PubMed  Google Scholar 

  • Iwata H, Jannink JL (2010) Marker genotype imputation in a low-marker-density panel with a high-marker-density reference panel: accuracy evaluation in barley breeding lines. Crop Sci 50:1269–1278

    Article  Google Scholar 

  • Janse J, Schols M (1995) Une préférence pour un goût sucré et non farineux. Groenten Fruit 26:16–17

    Google Scholar 

  • Jatoi SA, Fujimura T, Yamanaka S, Watanabe J, Watanabe KN, Watanabe KN (2008) Potential loss of unique genetic diversity in tomato landraces by genetic colonization of modern cultivars at a non-center of origin. Plant Breed 127:189–196

    Article  CAS  Google Scholar 

  • Jha UC, Bohra A, Jha R (2017) Breeding approaches and genomics technologies to increase crop yield under low-temperature stress. Plant Cell Rep 36:1–35

    Article  CAS  PubMed  Google Scholar 

  • Jiang Y, Schmidt RH, Reif JC (2018) Haplotype-based genome-wide prediction models exploit local epistatic interactions among markers. G3: GenesGenomesGenet 8: g3.300548.2017

    Google Scholar 

  • Jiménez-Gómez JM, Alonso-Blanco C, Borja A, Anastasio G, Angosto T, Lozano R, Martínez-Zapater JM (2007) Quantitative genetic analysis of flowering time in tomato. Genome 50:303–315

    Article  PubMed  CAS  Google Scholar 

  • Johansson L, Haglund Å, Berglund L, Lea P, Risvik E (1999) Preference for tomatoes, affected by sensory attributes and information about growth conditions. Food Qual Prefer 10:289–298

    Article  Google Scholar 

  • Johnstone PR, Hartz TK, LeStrange M, Nunez JJ, Miyao EM (2005) Managing fruit soluble solids with late-season deficit irrigation in drip-irrigated processing tomato production. HortScience 40:1857–1861

    Article  Google Scholar 

  • Jonas E, de Koning D-J (2013) Does genomic selection have a future in plant breeding? Trends Biotechnol 31:497–504

    Article  CAS  PubMed  Google Scholar 

  • Jones JB (1986) Survival of Xanthomonas campestris pv. vesicatoria in Florida on tomato crop residue, weeds, seeds, and volunteer tomato plants. Phytopathology 76: 430

    Article  Google Scholar 

  • Jones JW, Dayan E, Allen LH, Van Keulen H, Challa H (1991) A dynamic tomato growth and yield model (Tomgro). Am Soc Agri Eng 34: 663–672

    Google Scholar 

  • Jones DA, Thomas CM, Hammondkosack KE, Balintkurti PJ, Jones JDG (1994) Isolation of the tomato cf-9 gene for resistance to Cladosporium fulvum by transposon tagging. Science 266:789–793

    Article  CAS  PubMed  Google Scholar 

  • Kabelka E, Franchino B, Francis DM (2002) Two loci from Lycopersicon hirsutum LA407 confer resistance to strains of Clavibacter michiganensis subsp michiganensis. Phytopathology 92:504–510

    Article  CAS  PubMed  Google Scholar 

  • Kamal HM, Takashina T, Egashira H, Satoh H, Imanishi S (2001) Introduction of aromatic fragrance into cultivated tomato from the “peruvianum complex”. Plant Breed 120:179–181

    Article  Google Scholar 

  • Kang BC, Yeam I, Li HX, Perez KW, Jahn MM (2007) Ectopic expression of a recessive resistance gene generates dominant potyvirus resistance in plants. Plant Biotechnol J 5:526–536

    Article  CAS  PubMed  Google Scholar 

  • Karimi Z, Sargolzaei M, Robinson JAB, Schenkel FS (2018) Assessing haplotype-based models for genomic evaluation in Holstein cattle. Can J Sci 1–10

    Google Scholar 

  • Karlova R, Van Haarst JC, Maliepaard C, Van De Geest H, Bovy AG, Lammers M, Angenent GC, De Maagd RA (2013) Identification of microRNA targets in tomato fruit development using high-throughput sequencing and degradome analysis. J Exp Bot 64:1863–1878

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kawchuk LM, Hachey J, Lynch DR, Kulcsar F, Van Rooijen G, Waterer DR, Robertson A, Kokko E, Byers R, Howard RJ et al (2001) Tomato Ve disease resistance genes encode cell surface-like receptors. Proc Natl Acad Sci USA 98:6511–6515

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kazmi RH, Khan N, Willems LAJ, Van Heusden AW, Ligterink W, Hilhorst HWM (2012) Complex genetics controls natural variation among seed quality phenotypes in a recombinant inbred population of an interspecific cross between Solanum lycopersicum × Solanum pimpinellifolium. Plant Cell Environ 35:929–951

    Article  CAS  PubMed  Google Scholar 

  • Keller M, Simm S (2018) The coupling of transcriptome and proteome adaptation during development and heat stress response of tomato pollen. BMC Genom 19:447

    Article  CAS  Google Scholar 

  • Kenchanmane Raju SK, Barnes AC, Schnable JC, Roston RL (2018) Low-temperature tolerance in land plants: are transcript and membrane responses conserved? Plant Sci 276:73–86

    Article  CAS  PubMed  Google Scholar 

  • Kimbara J, Ohyama A, Chikano H, Ito H, Hosoi K, Negoro S, Miyatake K, Yamaguchi H, Nunome T, Fukuoka H et al (2018) QTL mapping of fruit nutritional and flavor components in tomato (Solanum lycopersicum) using genome-wide SSR markers and recombinant inbred lines (RILs) from an intra-specific cross. Euphytica 214:210

    Article  CAS  Google Scholar 

  • King SR, Davis AR, Zhang X, Crosby K (2010) Genetics, breeding and selection of rootstocks for Solanaceae and Cucurbitaceae. Sci Hortic (Amsterdam) 127:106–111

    Article  Google Scholar 

  • Kinkade MP, Foolad MR (2013) Validation and fine mapping of lyc12.1, a QTL for increased tomato fruit lycopene content. Theor Appl Genet 126:2163–2175

    Article  CAS  PubMed  Google Scholar 

  • Kissoudis C, Chowdhury R, van Heusden S, van de Wiel C, Finkers R, Visser RGF, Bai Y, van der Linden G (2015) Combined biotic and abiotic stress resistance in tomato. Euphytica 202:317–332

    Article  CAS  Google Scholar 

  • Klay I, Gouia S, Liu M, Mila I, Khoudi H, Bernadac A et al (2018) Ethylene Response Factors (ERF) are differentially regulated by different abiotic stress types in tomato plants. Plant Sci 274:137–145

    Article  CAS  PubMed  Google Scholar 

  • Klee HJ (2010) Improving the flavor of fresh fruits: genomics, biochemistry, and biotechnology. New Phytol 187:44–56

    Article  CAS  PubMed  Google Scholar 

  • Klee HJ (2013) Purple tomatoes: Longer lasting, less disease, and better for you. Curr Biol 23:R520–R521

    Article  CAS  PubMed  Google Scholar 

  • Klee HJ, Tieman DM (2013) Genetic challenges of flavor improvement in tomato. Trends Genet 29:257–262

    Article  CAS  PubMed  Google Scholar 

  • Klee HJ, Tieman DM (2018) The genetics of fruit flavour preferences. Nat Rev Genet 19:347–356

    Article  CAS  PubMed  Google Scholar 

  • Klein RJ, Zeiss C, Chew EY, Tsai J-Y, Sackler RS, Haynes C, Henning AK, Paul SanGiovanni J, Mane SM, Mayne ST et al (2005) Complement factor H polymorphism in age-related macular degeneration. Science 308:385–389

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kooke R, Kruijer W, Bours R, Becker F, Kuhn A, van de Geest H, Buntjer J, Doeswijk T, Guerra J, Bouwmeester H et al (2016) Genome-wide association mapping and genomic prediction elucidate the genetic architecture of morphological traits in arabidopsis. Plant Physiol 170:2187–2203

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Korte A, Vilhjálmsson BJ, Segura V, Platt A, Long Q, Nordborg M (2012) A mixed-model approach for genome-wide association studies of correlated traits in structured populations. Nat Genet 44:1066–1071

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kover PX, Valdar W, Trakalo J, Scarcelli N, Ehrenreich IM, Purugganan MD, Durrant C, Mott R (2009) A multiparent advanced generation inter-cross to fine-map quantitative traits in Arabidopsis thaliana. PLoS Genet 5:e1000551

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Kramer M, Sanders R, Bolkan H, Waters C, Sheeny RE, Hiatt WR (1992) Postharvest evaluation of transgenic tomatoes with reduced levels of polygalacturonase: processing, firmness and disease resistance. Postharv Biol Technol 1(3):241–255

    Article  CAS  Google Scholar 

  • Kramer MG, Redenbaugh K (1994) Commercialization of a tomato with an antisense polygalacturonase gene: the FLAVR SAVR? tomato story. Euphytica 79:293–297

    Article  Google Scholar 

  • Krieger U, Lippman ZB, Zamir D (2010) The flowering gene SINGLE FLOWER TRUSS drives heterosis for yield in tomato. Nat Genet 42:459–463

    Article  CAS  PubMed  Google Scholar 

  • Kromdijk J, Bertin N, Heuvelink E, Molenaar J, de Visser PHB, Marcelis LFM, Struik PC (2013) Crop management impacts the efficiency of QTL detection and use—case study of fruit load x QTL interactions. J Exp Bot. https://doi.org/10.1093/jxb/ert365

    Article  PubMed  Google Scholar 

  • Kropff MJ, Haverkort AJ, Aggarwal PK, Kooman PL (1995) Using systems approaches to design and evaluate ideotypes for specific environments. In: Bouma J, Bouman BAM, Luyten JC, Zandstra HG (eds) Eco-regional approaches for sustainable land use and food production. Kluwer Academic Publ, Dordrecht, Netherlands, pp 417–435

    Chapter  Google Scholar 

  • Kumar M, Ashok I, Chandrawat S (2016) Gene pyramiding: an overview. Intl J Curr Res Biosci Plant Biol. https://doi.org/10.20546/ijcrbp.2016.307.004

    Article  Google Scholar 

  • Kusmec A, Srinivasan S, Nettleton D, Schnable PS (2017) Distinct genetic architectures for phenotype means and plasticities in Zea mays. Nat Plants 3:715–723

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kyriacou MC, Rouphael Y, Colla G, Zrenner R, Schwarz D (2017) Vegetable grafting: the implications of a growing agronomic imperative for vegetable fruit quality and nutritive value. Front Plant Sci 8:741

    Google Scholar 

  • Labate JA, Grandillo S, Fulton T, Muños S, Caicedo AL, Peralta I, Ji Y, Chetelat RT, Scott JW, Gonzalo MJ et al (2007) Tomato. In: Kole C (ed) Genome mapping and molecular breeding in plants, vol 5. Vegetables. Springer, Berlin, pp 1–125

    Google Scholar 

  • Lanfermeijer FC, Warmink J, Hille J (2005) The products of the broken Tm-2 and the durable Tm-2(2) resistance genes from tomato differ in four amino acids. J Exp Bot 56:2925–2933

    Article  CAS  PubMed  Google Scholar 

  • Lang Z, Wang Y, Tang K, Tang D, Datsenka T, Cheng J, Zhang Y, Handa AK, Zhu JK (2017) Critical roles of DNA demethylation in the activation of ripening-induced genes and inhibition of ripening-repressed genes in tomato fruit. Proc Natl Acad Sci USA 114(22):E4511–E4519

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lapidot M, Karniel U, Gelbart D, Fogel D, Evenor D, Kutsher Y, Makhbash Z, Nahon S, Shlomo H, Chen L, Reuveni M, Levin I (2015) A novel route controlling begomovirus resistance by the messenger RNA surveillance factor Pelota. PLoS Genetics 11

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Larbat R, Olsen KM, Slimestad R, Løvdal T, Bénard C, Verheul M, Bourgaud F, Robin C, Lillo C (2012) Influence of repeated short-term nitrogen limitations on leaf phenolics metabolism in tomato. Phytochemistry 77:119–128

    Article  CAS  PubMed  Google Scholar 

  • Laterrot H (1996) Twenty-one near isogenic lines in Moneymaker type with different genes for disease resistances. Rep Tomato Genet Coop 46:34

    Google Scholar 

  • Laterrot H (2000) Disease resistance in tomato: practical situation. Acta Physiol Plant 22:328–331

    Article  Google Scholar 

  • Laterrot H, Moretti A (1989) Linkage between Pto and susceptibility to fenthion. Tomato Genet Coop Rep 39:21–22

    Google Scholar 

  • Le Nguyen K, Grondin A, Courtois B, Gantet P (2018) Next-generation sequencing accelerates crop gene discovery. Trends Plant Sci 24:263–274

    Google Scholar 

  • Le LQ, Lorenz Y, Scheurer S, Fötisch K, Enrique E, Bartra J, Biemelt S, Vieths S, Sonnewald U (2006) Design of tomato fruits with reduced allergenicity by dsRNAi-mediated inhibition of ns-LTP (Lyc e 3) expression. Plant Biotechnol J 4(2):231–242

    Article  CAS  PubMed  Google Scholar 

  • Lecompte F, Abro MA, Nicot PC (2010) Contrasted responses of Botrytis cinerea isolates developing on tomato plants grown under different nitrogen nutrition regimes. Plant Pathol 59:891–899

    Article  CAS  Google Scholar 

  • Lecompte F, Nicot PC, Ripoll J, Abro MA, Raimbault AK, Lopez-Lauri F, Bertin N (2017) Reduced susceptibility of tomato stem to the necrotrophic fungus Botrytis cinerea is associated with a specific adjustment of fructose content in the host sugar pool. Ann Bot 119:931–943

    CAS  PubMed  PubMed Central  Google Scholar 

  • Lecomte L, Saliba-Colombani V, Gautier A, Gomez-Jimenez MC, Duffé P, Buret M, Causse M (2004a) Fine mapping of QTLs for the fruit architecture and composition in fresh market tomato, on the distal region of the long arm of chromosome 2. Mol Breed 13:1–14

    Article  CAS  Google Scholar 

  • Lecomte L, Duffé P, Buret M, Servin B, Hospital F, Causse M (2004b) Marker-assisted introgression of 5 QTLs controlling fruit quality traits into three tomato lines revealed interactions between QTLs and genetic backgrounds. Theor Appl Genet 109:658–668

    Article  CAS  PubMed  Google Scholar 

  • Lee DR (1990) A unidirectional water flux model of fruit growth. Can J Bot 68:1286–1290

    Article  Google Scholar 

  • Lee JM, Oh CS, Yeam I (2015) Molecular markers for selecting diverse disease resistances in tomato breeding programs. Plant Breed Biotechnol 3:308–322

    Article  Google Scholar 

  • Lee JT, Prasad V, Yang PT, Wu JF, David Ho TH, Charng YY, Chan MT (2003) Expression of Arabidopsis CBF1 regulated by an ABA/stress inducible promoter in transgenic tomato confers stress tolerance without affecting yield. Plant Cell Environ 26(7):1181–1190

    Article  CAS  Google Scholar 

  • Lee SY, Luna-Guzman I, Chang S, Barrett DM, Guinard JX (1999) Relating descriptive analysis and instrumental texture data of processed diced tomatoes. Food Qual Pref 10:447–455

    Article  Google Scholar 

  • Lefebvre V, Boissot N, Gallois J-L (2018) Host plant resistance to pests and pathogens, the genetic leverage in integrated pest and disease management. In: Gullino ML, Albajes R, Nicot P, van Lenteren JC (eds) Pest and disease management in greenhouse crops. Developments in Plant Pathology. Springer International Publishing, Cham

    Google Scholar 

  • Length F (2011) Genetic diversity in 14 tomato (Lycopersicon esculentum Mill.) varieties in Nigerian markets by RAPD-PCR technique. Afr J Biotechnol 10(11):4961–4967

    Google Scholar 

  • Letort V, Mahe P, Cournede PH, De Reffye P, Courtois B (2008) Quantitative genetics and functional-structural plant growth models: Simulation of quantitative trait loci detection for model parameters and application to potential yield optimization. Ann Bot-London 101:1243–1254

    Article  Google Scholar 

  • Levin I, Gilboa N, Yeselson E, Shen S, Schaffer AA (2000) Fgr, a major locus that modulates the fructose to glucose ratio in mature tomato fruits. Theor Appl Genet 100:256–262

    Article  CAS  Google Scholar 

  • Li YM, Gabelman WH (1990) Inheritance of calcium use efficiency in tomatoes grown under low-calcium stress. J Am Soc Hortic Sci 115:835–838

    Article  CAS  Google Scholar 

  • Li J, Liu L, Bai Y, Zhang P, Finkers R, Du Y et al (2011) Seedling salt tolerance in tomato. Euphytica 178:403–414

    Article  Google Scholar 

  • Li T, Yang X, Yu Y, Si X, Zhai X, Zhang H, Dong W, Gao C, Xu C (2018) Domestication of wild tomato is accelerated by genome editing. Nat Biotechnol 36:1160–1163

    Article  CAS  Google Scholar 

  • Lin KH, Yeh WL, Chen HM, Lo HF (2010) Quantitative trait loci influencing fruit-related characteristics of tomato grown in high-temperature conditions. Euphytica 174:119–135

    Article  CAS  Google Scholar 

  • Lin T, Zhu G, Zhang J, Xu X, Yu Q, Zheng Z, Zhang Z, Lun Y, Li S, Wang X et al (2014) Genomic analyses provide insights into the history of tomato breeding. Nat Genet 46:1220–1226

    Article  CAS  PubMed  Google Scholar 

  • Lindemose S, O’Shea C, Jensen M, Skriver K, Lindemose S, O’Shea C et al (2013) Structure, function and networks of transcription factors involved in abiotic stress responses. Int J Mol Sci 14:5842–5878

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lippman ZB, Zamir D (2007) Heterosis: revisiting the magic. Trends Genet 23:60–66

    Article  CAS  PubMed  Google Scholar 

  • Liu Z, Alseekh S, Brotman Y, Zheng Y, Fei Z, Tieman DM, Giovannoni JJ, Fernie AR, Klee HJ (2016b) Identification of a Solanum pennellii chromosome 4 fruit flavor and nutritional quality-associated metabolite QTL. Front Plant Sci 7:1–15

    CAS  Google Scholar 

  • Liu H, Genard M, Guichard S, Bertin N (2007) Model-assisted analysis of tomato fruit growth in relation to carbon and water fluxes. J Exp Bot 58:3567–3580

    Article  CAS  PubMed  Google Scholar 

  • Liu J, Van Eck J, Cong B, Tanksley SD (2002) A new class of regulatory genes underlying the cause of pear-shaped tomato fruit. Proc Natl Acad Sci USA 99:13302–13306

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Liu HJ, Yan J (2019) Crop genome-wide association study: a harvest of biological relevance. Plant J 97:8–18

    Article  CAS  PubMed  Google Scholar 

  • Liu H, Yu C, Li H, Ouyang B, Wang T, Zhang J et al (2015) Overexpression of SHDHN, a dehydrin gene from Solanum habrochaites enhances tolerance to multiple abiotic stresses in tomato. Plant Sci 231:198–211

    Article  CAS  PubMed  Google Scholar 

  • Liu M, Yu H, Zhao G et al (2017) Profiling of drought-responsive microRNA and mRNA in tomato using high-throughput sequencing. BMC Genomics 18:481

    Google Scholar 

  • Liu Y, Zhou T, Ge H, Pang W, Gao L, Ren L et al (2016a) SSR mapping of QTLs conferring cold tolerance in an interspecific cross of tomato. Intl J Genom 2016:1–6

    Article  CAS  Google Scholar 

  • Lobit P, Génard M, Soing P, Habib R (2006) Modelling malic acid accumulation in fruits: relationships with organic acids, potassium, and temperature. J Exp Bot 57:1471–1483

    Article  CAS  PubMed  Google Scholar 

  • Lobit P, Génard M, Wu BH, Soing P, Habib R (2003) Modelling citrate metabolism in fruits: responses to growth and temperature. J Exp Bot 54:2489–2501

    Article  CAS  PubMed  Google Scholar 

  • Lü P, Yu S, Zhu N, Chen Y-R, Zhou B, Pan Y, Tzeng D, Fabi JP, Argyris J, Garcia-Mas J et al. (2018) Genome encode analyses reveal the basis of convergent evolution of fleshy fruit ripening. Nat Plants 1

    Google Scholar 

  • Luo J (2015) Metabolite-based genome-wide association studies in plants. Curr Opin Plant Biol 24:31–38

    Article  CAS  PubMed  Google Scholar 

  • Maayan Y, Pandaranayaka EPJ, Srivastava DA, Lapidot M, Levin I, Dombrovsky A, Harel A (2018) Using genomic analysis to identify tomato Tm-2 resistance-breaking mutations and their underlying evolutionary path in a new and emerging tobamovirus. Arch Virol 163:1863–1875

    Article  CAS  PubMed  Google Scholar 

  • Mackay IJ, Bansept-Basler P, Barber T, Bentley AR, Cockram J, Gosman N, Greenland AJ, Horsnell R, Howells R, O’Sullivan DM et al (2014) An eight-parent multiparent advanced generation inter-cross population for winter-sown wheat: creation, properties, and validation. G3: GenesGenomGenet 4: 1603–1610

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Madhavi DL, Salunkhe DK (1998) Handbook of vegetable science and technology. In: Salunkhe DK, Kadam SS (eds) Production, composition, storage, and processing, New York, USA. https://doi.org/10.1201/9781482269871

    Book  Google Scholar 

  • Malundo TMM, Shewfelt RL, Scott JW (1995) Flavor quality of fresh tomato (Lycopersicon esculentum Mill.) as affected by sugar and acid levels. Postharv BiolTechnol 6:103–110

    Article  CAS  Google Scholar 

  • Manavella PA, Hagmann J, Ott F, Laubinger S, Franz M, Macek B, Weigel D (2012) Fast-forward genetics identifies plant CPL phosphatases as regulators of miRNA processing factor HYL1. Cell 151:859–870

    Article  CAS  PubMed  Google Scholar 

  • Mangin B, Rincent R, Rabier CE, Moreau L, Goudemand-Dugue E (2019) Training set optimization of genomic prediction by means of EthAcc. PLoS ONE 14:e0205629

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Mangin B, Thoquet P, Olivier J, Grimsley NH (1999) Temporal and multiple quantitative trait loci analyses of resistance to bacterial wilt in tomato permit the resolution of linked loci. Genetics 151:1165–1172

    CAS  PubMed  PubMed Central  Google Scholar 

  • Manning K, Tör M, Poole M, Hong Y, Thompson AJ, King GJ, Giovannoni JJ, Seymour GB (2006) A naturally occurring epigenetic mutation in a gene encoding an SBP-box transcription factor inhibits tomato fruit ripening. Nat Genet 38:948–952

    Article  CAS  PubMed  Google Scholar 

  • Mao L, Begum D, Chuang H, Budiman MA, Szymkowiak EJ, Irish EE, Wing RA (2000) JOINTLESS is a MADS-box gene controlling tomato flower abscissionzone development. Nature 406:910–913

    Article  CAS  PubMed  Google Scholar 

  • Marchini J, Howie B (2010) Genotype imputation for genome-wide association studies. Nat Rev Genet 11:499–511

    Article  CAS  PubMed  Google Scholar 

  • Marques de Carvalho L, Benda ND, Vaughan MM, Cabrera AR, Hung K, Cox T, Abdo Z, Allen LH, Teal PE (2015) Mi-1-mediated nematode resistance in tomatoes is broken by short-term heat stress but recovers over time. J Nematol 47:133–140

    CAS  PubMed  PubMed Central  Google Scholar 

  • Marschner H (1983) General introduction to the mineral nutrition of plants. In: Lauchli A, Bieleski R (eds) Inorganic plant nutrition. Springer, Berlin, pp 5–60

    Chapter  Google Scholar 

  • Martin GB, Brommonschenkel SH, Chunwongse J, Frary A, Ganal MW, Spivey R, Wu T, Earle ED, Tanksley SD, Sipvey R et al (1993) Map-based cloning of a protein kinase gene conferring disease resistance in tomato. Science (80-) 262:1432–1436

    Article  CAS  PubMed  Google Scholar 

  • Martin GB, Frary A, Wu T, Brommonschenkel S, Chunwongse J, Earle ED, Tanksley SD (1994) A member of the tomato Pto gene family confers sensitivity to fenthion resulting in rapid cell death. Plant Cell 6:1543–1552

    CAS  PubMed  PubMed Central  Google Scholar 

  • Martre P, Bertin N, Salon C, Génard M (2011) Modelling the size and composition of fruit, grain and seed by process-based simulation models. New Phytolt Tansley Review 191:601–618

    Article  CAS  Google Scholar 

  • Martre P, Quilot-Turion B, Luquet D, Ould-Sidi M-M, Chenu K, Debaeke P (2015) Model-assisted phenotyping and ideotype design. In: Sadras V, Calderini D (eds) Crop physiology: applications for genetic improvement and agronomy. Academic Press, London, pp 349–373

    Chapter  Google Scholar 

  • Mazzucato A, Cellini F, Bouzayen M, Zouine M, Mila I, Minoia S, Petrozza A, Picarella ME, Ruiu F, Carriero F (2015) A TILLING allele of the tomato Aux/IAA9 gene offers new insights into fruit set mechanisms and perspectives for breeding seedless tomatoes. Mol Breed 35:22

    Article  Google Scholar 

  • Mazzucato A, Papa R, Bitocchi E, Mosconi P, Nanni L, Negri V, Picarella ME, Siligato F, Soressi GP, Tiranti B et al (2008) Genetic diversity, structure and marker-trait associations in a collection of Italian tomato (Solanum lycopersicum L.) landraces. Theor Appl Genet 116:657–669

    Article  PubMed  Google Scholar 

  • Mboup M, Fischer I, Lainer H, Stephan W (2012) Trans-species polymorphism and Allele-Specific expression in the CBF gene family of wild tomatoes. Mol Biol Evol 29:3641–3652

    Article  CAS  PubMed  Google Scholar 

  • McCormick S, Niedermeyer J, Fry J, Barnason A, Horsch R, Fraley R (1986) Leaf disc transformation of cultivated tomato (L. esculentum) using Agrobacterium tumefaciens. Plant Cell Rep 5(2):81–84

    Article  CAS  PubMed  Google Scholar 

  • McCouch SR, Wright MH, Tung C-W, Maron LG, McNally KL, Fitzgerald M, Singh N, DeClerck G, Agosto-Perez F, Korniliev P et al (2016) Open access resources for genome-wide association mapping in rice. Nat Commun 7:10532

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • McGlasson WB, Last JH, Shaw KJ, Meldrum SK (1987) Influence of the non-ripening mutant rin and nor on the aroma of tomato fruits. HortScience 22:632–634

    CAS  Google Scholar 

  • Meena YK, Khurana DS, Singh K (2018) Towards enhanced low temperature stress tolerance in tomato : an approach. J Environ Biol. https://doi.org/10.22438/jeb/39/4/MRN-590

    Article  Google Scholar 

  • Megraw M, Baev V, Rusinov V, Jensen ST, Kalantidis K, Hatzigeorgiou AG (2006) MicroRNA promoter element discovery in Arabidopsis. RNA 12:1612–1619

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Menda N, Semel Y, Peled D, Eshed Y, Zamir D (2004) Insilico screening of a saturated mutation library of tomato. Plant J 38:861–872

    Article  CAS  PubMed  Google Scholar 

  • Menda N, Strickler SR, Edwards JD, Bombarely A, Dunham DM, Martin GB, Mejia L, Hutton SF, Havey MJ, Maxwell DP et al (2014) Analysis of wild-species introgressions in tomato inbreds uncovers ancestral origins. BMC Plant Biol 14:287

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Mendell JT, Olson EN (2012) MicroRNAs in stress signaling and human disease. Cell 148:1172–1187

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Meng C, Yang D, Ma X, Zhao W, Liang X, Ma N, Meng Q (2016) Suppression of tomato SlNAC1 transcription factor delays fruit ripening. J Plant Physiol 193:88–96

    Article  CAS  PubMed  Google Scholar 

  • Meng FJ, Xu XY, Huang FL, Li JF (2010) Analysis of genetic diversity in cultivated and wild tomato varieties in Chinese market by RAPD and SSR. Agri Sci China 9:1430–1437

    Article  CAS  Google Scholar 

  • Messeguer R, Ganal M, de Vicente MC, Young ND, Bolkan H, Tanksley SD (1991) High resolution RFLP map around the root knot nematode resistance gene (Mi) in tomato. Theor Appl Genet 82:529–536

    Article  CAS  PubMed  Google Scholar 

  • Meuwissen THE, Hayes BJ, Goddard ME (2001) Prediction of total genetic value using genome-wide dense marker maps. Genetics 157:1819–1829

    CAS  PubMed  PubMed Central  Google Scholar 

  • Migault V, Pallas B, Costes E (2017) Combining genome-wide information with a functional structural plant model to simulate 1-year-old apple tree architecture. Front Plant Sci. https://doi.org/10.3389/fpls.2016.02065

    Article  PubMed  PubMed Central  Google Scholar 

  • Miller JC, Tanksley SD (1990) RFLP analysis of phylogenetic relationships and genetic variation in the genus Lycopersicon. Theor Appl Genet 80:437–448

    Article  CAS  PubMed  Google Scholar 

  • Milligan SB, Bodeau J, Yaghoobi J, Kaloshian I, Zabel P, Williamson VM (1998) The root knot nematode resistance gene Mi from tomato is a member of the leucine zipper, nucleotide binding, leucine-rich repeat family of plant genes. Plant Cell 10:1307–1319

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Milner S et al (2011) Bioactivities of glycoalkaloids and their aglycones from Solanum species. J Agri Food Chem 59:3454–3484

    Article  CAS  Google Scholar 

  • Minamikawa MF, Nonaka K, Kaminuma E, Kajiya-Kanegae H, Onogi A, Goto S, Yoshioka T, Imai A, Hamada H, Hayashi T et al (2017) Genome-wide association study and genomic prediction in citrus: Potential of genomics-assisted breeding for fruit quality traits. Sci Rep 7:4721

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Minoïa S, Bendahmane A, Piron F, Salgues A, Moretti A, Caranta C, Piednoir E, Nicolaï M, Zamir D (2010) An induced mutation in tomato eIF4E leads to immunity to two potyviruses. PLoS ONE 5:e11313

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Minoia S, Cellini F, Bendahmane A, D’Onofrio O, Petrozza A, Carriero F, Piron F, Mosca G, Sozio G (2010) A new mutant genetic resource for tomato crop improvement by TILLING technology. BMC Res Notes. https://doi.org/10.1186/1756-0500-3-69

    Article  PubMed  PubMed Central  Google Scholar 

  • Mirnezhad M, Romero-Gonzalez RR, Leiss KA, Choi YH, Verpoorte R, Klinkhamer PG (2010) Metabolomic analysis of host plant resistance to thrips in wild and cultivated tomatoes. Phytochem Analys 21(1):110–117

    Article  CAS  Google Scholar 

  • Mirouze M, Paszkowski J (2011) Epigenetic contribution to stress adaptation in plants. Curr Opin Plant Biol 14:267–274

    Article  CAS  PubMed  Google Scholar 

  • Mitchell J, Shennan C, Grattan S (1991) Developmental-changes in tomato fruit composition in response to water deficit and salinity. Physiol Plant 83:177–185

    Article  CAS  Google Scholar 

  • Mohorianu I, Schwach F, Jing R, Lopez-Gomollon S, Moxon S, Szittya G, Sorefan K, Moulton V, Dalmay T (2011) Profiling of short RNAs during fleshy fruit development reveals stage-specific sRNAome expression patterns. Plant J 67:232–246

    Article  CAS  PubMed  Google Scholar 

  • Molgaard P, Ravn H (1988) Evolutionary aspects of caffeoyl ester distribution in dicotyledons. Phytochemistry 27:2411–2421

    Article  CAS  Google Scholar 

  • Monforte AJ, Asíns MJ, Carbonell EA (1996) Salt tolerance in Lycopersicon species. IV. Efficiency of marker-assisted selection for salt tolerance improvement. Theor Appl Genet 93–93:765–772

    Article  Google Scholar 

  • Monforte AJ, Asíns MJ, Carbonell EA (1997a) Salt tolerance in Lycopersicon species VI. Genotype-by-salinity interaction in quantitative trait loci detection: constitutive and response QTLs. Theor Appl Genet 95:706–713

    Article  Google Scholar 

  • Monforte AJ, Asíns MJ, Carbonell EA (1997b) Salt tolerance in Lycopersicon species. V. Does genetic variability at quantitative trait loci affect their analysis? Theor Appl Genet 95:284–293

    Article  CAS  Google Scholar 

  • Monforte AJ, Tanksley SD (2000) Fine mapping of a quantitative trait locus (QTL) from Lycopersicon hirsutum chromosome 1 affecting fruit characteristics and agronomic traits: breaking linkage among QTLs affecting different traits and dissection of heterosis for yield. Theor Appl Genet 100:471–479

    Article  CAS  Google Scholar 

  • Montesinos-López OA, Montesinos-López A, Crossa J, Toledo FH, Pérez-Hernández O, Eskridge KM, Rutkoski J (2016) A genomic Bayesian MULTI-TRAIT AND MULTI-ENVIRONMENT MODEL. G3: GenesGenomGenet 6: 2725–2744

    Article  PubMed  PubMed Central  Google Scholar 

  • Moxon S, Jing R, Szittya G, Schwach F, Rusholme Pilcher RL, Moulton V, Dalmay T (2008) Deep sequencing of tomato short RNAs identifies microRNAs targeting genes involved in fruit ripening. Genome Res 18:1602–1609

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Mu Q, Huang Z, Chakrabarti M, Illa-Berenguer E, Liu X, Wang Y, Ramos A, van der Knaap E (2017) Fruit weight is controlled by cell size regulator encoding a novel protein that is expressed in maturing tomato fruits. PLoS Genet 13:e1006930

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Muir SR, Collins GJ, Robinson S, Hughes S, Bovy A, Ric De Vos CH, van Tunen AJ, Verhoeyen ME (2001) Overexpression of petunia chalcone isomerase in tomato results in fruit containing increased levels of flavonols. Nat Biotechnol 19:470–474

    Article  CAS  PubMed  Google Scholar 

  • Mueller LA, Tanksley SD, Giovannoni JJ, van Eck J, Stack S, Choi D, Kim BD, Chen M, Cheng Z, Li C, Ling H, Xue Y, Seymour G, Bishop G, Bryan G, Sharma R, Khurana J, Tyagi A, Chattopadhyay D, Singh NK, Stiekema W, Lindhout P, Jesse T, Lankhorst RK, Bouzayen M, Shibata D, Tabata S, Granell A, Botella MA, Giuliano G, Frusciante L, Causse M, Zamir D (2005) The tomato sequencing project, the first cornerstone of the International Solanaceae Project (SOL). Comp Funct Genomics 6(3):153–158

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Müller BSF, Neves LG, de Almeida Filho JE, Resende MFR, Muñoz PR, dos Santos PET, Filho EP, Kirst M, Grattapaglia D (2017) Genomic prediction in contrast to a genome-wide association study in explaining heritable variation of complex growth traits in breeding populations of Eucalyptus. BMC Genom 18:524

    Article  Google Scholar 

  • Munns R, Gilliham M (2015) Salinity tolerance of crops - what is the cost? New Phytol 208:668–673

    Article  CAS  PubMed  Google Scholar 

  • Munns R, Tester M (2008) Mechanisms of salinity tolerance. Annu Rev Plant Biol 59:651–681

    Article  CAS  PubMed  Google Scholar 

  • Muños S, Ranc N, Botton E, Bérard A, Rolland S, Duffé P, Carretero Y, Le Paslier MC, Delalande C, Bouzayen M, Brunel D, Causse M (2011) Increase in tomato locule number is controlled by two single-nucleotide polymorphisms located near WUSCHEL. Plant Physiol 156(4):2244–2254

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Mutshinda CM, Sillanpää MJ (2010) Extended Bayesian LASSO for multiple quantitative trait loci mapping and unobserved phenotype prediction. Genetics 186:1067–1075

    Article  PubMed  PubMed Central  Google Scholar 

  • Nadeem M, Li J, Wang M, Shah L, Lu S, Wang X, Ma C, Nadeem M, Li J, Wang M et al (2018) Unraveling field crops sensitivity to heat stress: mechanisms, approaches, and future prospects. Agronomy 8:128

    Article  CAS  Google Scholar 

  • Nakazato T, Warren DL, Moyle LC (2010) Ecological and geographic modes of species divergence in wild tomatoes. Amer J Bot 97:680–693

    Article  Google Scholar 

  • Navarro JM, Flores P, Carvajal M, Martinez V (2005) Changes in quality and yield of tomato fruit with ammonium, bicarbonate and calcium fertilisation under saline conditions. J Hort Sci Biotechnol 80:351–357

    Article  CAS  Google Scholar 

  • Naves ER, de Ávila Silva L, Sulpice R, Araújo WL, Nunes-Nesi A, Peres LE, Zsögön A (2019) Capsaicinoids: pungency beyond capsicum. Trends Plant Sci 24:109–120

    Article  CAS  PubMed  Google Scholar 

  • Nawaz MA, Imtiaz M, Kong Q, Cheng F, Ahmed W, Huang Y et al (2016) Grafting: a technique to modify ion accumulation in horticultural crops. Front Plant Sci 7:1457

    Google Scholar 

  • Nekrasov V, Wang C, Win J, Lanz C, Weigel D, Kamoun S (2017) Rapid generation of a transgene-free powdery mildew resistant tomato by genome deletion. Sci Rep 7:482

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Nesbitt TC, Tanksley SD (2002) Comparative sequencing in the genus Lycopersicon: implications for the evolution of fruit size in the domestication of cultivated tomatoes. Genetics 162:365–379

    CAS  PubMed  PubMed Central  Google Scholar 

  • Nombela G, Williamson VM, Muniz M (2003) The root-knot nematode resistance gene Mi-1.2 of tomato is responsible for resistance against the whitefly Bemisia tabaci. Mol Plant-Microbe Interact 16:645–649

    Article  CAS  PubMed  Google Scholar 

  • Nuruddin MM, Madramootoo CA, Dodds GT (2003) Effects of water stress at different growth stages on greenhouse tomato yield and quality. HortScience 38:1389–1393

    Article  Google Scholar 

  • Ofner I, Lashbrooke J, Pleban T, Aharoni A, Zamir D (2016) Solanum pennellii backcross inbred lines (BILs) link small genomic bins with tomato traits. Plant J 87:151–160

    Article  CAS  PubMed  Google Scholar 

  • Ohlson EW, Ashrafi H, Foolad MR (2018) Identification and mapping of late blight resistance quantitative trait loci in tomato accession PI 163245. Plant Genome 11

    Google Scholar 

  • Ohlson EW, Foolad MR (2016) Genetic analysis of resistance to tomato late blight in Solanum pimpinellifolium accession PI 163245. Plant Breed 135:391–398

    Article  CAS  Google Scholar 

  • Okabe Y, Asamizu E, Saito T, Matsukura C, Ariizumi T, Brès C, Rothan C, Mizoguchi T, Ezura H (2011) Tomato TILLING technology: development of a reverse genetics tool for the efficient isolation of mutants from Micro-Tom mutant libraries. Plant Cell Physiol 52:1994–2005

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Okello RCO, Heuvelink E, de Visser PHB, Struik PC, Marcelis LFM (2015) What drives fruit growth? Funct Plant Biol 42:817–827

    Article  PubMed  Google Scholar 

  • Oliver JE, Whitfield AE (2016) The genus tospovirus: emerging bunyaviruses that threaten food security. In: Enquist LW (ed) Annu Rev Virol 3:101–124

    Google Scholar 

  • Ongom PO, Ejeta G (2017) Mating design and genetic structure of a multi-parent advanced generation intercross (MAGIC) population of Sorghum (Sorghum bicolor (L.) Moench). G3 Genes|Genomes|Genetics 8:331–341

    Article  PubMed Central  CAS  Google Scholar 

  • Ori N, Eshed Y, Paran I, Presting G, Aviv D, Tanksley S, Zamir D, Fluhr R (1997) The I2C family from the wilt disease resistance locus I2 belongs to the nucleotide binding, leucine-rich repeat superfamily of plant resistance genes. Plant Cell (The) 9:521–532

    CAS  PubMed  PubMed Central  Google Scholar 

  • Osorio S, Ruan Y-L, Fernie AR (2014) An update on source-to-sink carbon partitioning in tomato. Front Plant Sci 5:516

    Article  PubMed  PubMed Central  Google Scholar 

  • Ould-Sidi M-M, Lescourret F (2011) Model-based design of innovative cropping systems: state of the art and new prospects. AgronSustain Dev 31(3):571–588

    Google Scholar 

  • Overy SA, Walker HJ, Malone S, Howard TP, Baxter CJ, Sweetlove LJ, Hill SA, Quick WP (2004) Application of metabolite profiling to the identification of traits in a population of tomato introgression lines. J Exp Bot 56:287–296

    Article  PubMed  CAS  Google Scholar 

  • Pailles Y, Ho S, Pires IS, Tester M, Negrão S, Schmöckel SM (2017) Genetic diversity and population structure of two tomato species from the Galapagos Islands. Front Plant Sci 8:138

    Article  PubMed  PubMed Central  Google Scholar 

  • Panthee DR, Piotrowski A, Ibrahem R (2017) Mapping Quantitative Trait Loci (QTL) for resistance to late blight in tomato. Int J Mol Sci 18 (7). pii: E1589. https://doi.org/10.3390/ijms18071589

  • Papadopoulos I, Rendig VV (1983) Interactive effects of salinity and nitrogen on growth and yield of tomato plants. Plant Soil 73:47–57

    Article  CAS  Google Scholar 

  • Paran I, Goldman I, Tanksley SD, Zamir D (1995) Recombinant inbred lines for genetic mapping in tomato. Theor Appl Genet 90:542–548

    Article  CAS  PubMed  Google Scholar 

  • Park T, Casella G (2008) The Bayesian lasso. J Amer Stat Assoc 103:681–686

    Article  CAS  Google Scholar 

  • Park YH, West MA, St. Clair DA (2004) Evaluation of AFLPs for germplasm fingerprinting and assessment of genetic diversity in cultivars of tomato (Lycopersicon esculentum L.). Genome 47:510–518

    Article  CAS  PubMed  Google Scholar 

  • Pasaniuc B, Rohland N, McLaren PJ, Garimella K, Zaitlen N, Li H, Gupta N, Neale BM, Daly MJ, Sklar P et al (2012) Extremely low-coverage sequencing and imputation increases power for genome-wide association studies. Nat Genet 44:631–635

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • De Pascale S, Maggio A, Fogliano V, Ambrosino P, Ritieni A (2001) Irrigation with saline water improves carotenoids content and antioxidant activity of tomato. J Hort Sci Biotechnol 76:447–453

    Article  Google Scholar 

  • Pascual L, Desplat N, Huang BE, Desgroux A, Bruguier L, Bouchet JP, Le QH, Chauchard B, Verschave P, Causse M (2015) Potential of a tomato MAGIC population to decipher the genetic control of quantitative traits and detect causal variants in the resequencing era. Plant Biotechnol J 13:565–577

    Article  CAS  PubMed  Google Scholar 

  • Patanè C, Cosentino SL (2010) Effects of soil water deficit on yield and quality of processing tomato under a mediterranean climate. Agri Water Manag 97:131–138

    Article  Google Scholar 

  • Paterson AH, Damon S, Hewitt JD, Zamir D, Rabinowitch HD, Loncoln SE, Lander ES, Tanksley SD (1991) Mendelian factors underlying quantitative traits in tomato: comparison across species, generations, and environments. Genetics 127:181–197

    CAS  PubMed  PubMed Central  Google Scholar 

  • Paterson AH, DeVerna JW, Lanini B, Tanksley SD (1990) Fine mapping of quantitative trait loci using selected overlapping recombinant chromosomes, in an interspecies cross of tomato. Genetics 124:735–742

    CAS  PubMed  PubMed Central  Google Scholar 

  • Paterson AH, Lander ES, Hewitt JD, Peterson S, Lincoln SE, Tanksley SD (1988) Resolution of quantitative traits into Mendelian factors by using a complete linkage map of restriction fragment length polymorphisms. Nature 335:721–726

    Article  CAS  PubMed  Google Scholar 

  • Pattison RJ, Csukasi F, Zheng Y, Fei Z, van der Knaap E, Catalá C (2015) Comprehensive tissue-specific transcriptome analysis reveals distinct regulatory programs during early tomato fruit development. Plant Physiol 168(4):1684–1701

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Peralta IE, Knapp S, Spooner DM (2005) New species of wild tomatoes (Solanum Section Lycopersicon: Solanaceae) from Northern Peru. Syst Bot 30:424–434

    Article  Google Scholar 

  • Pertuzé RA, Ji Y, Chetelat RT (2003) Comparative linkage map of the Solanum lycopersicoides and S. sitiens genomes and their differentiation from tomato. Genome 45:1003–1012

    Article  Google Scholar 

  • Petró-Turza M (1986) Flavor of tomato and tomato products. Food Rev Intl 2:309–351

    Article  Google Scholar 

  • Pettigrew WT (2008) Potassium influences on yield and quality production for maize, wheat, soybean and cotton. Physiol Plant 133:670–681

    Article  CAS  PubMed  Google Scholar 

  • Philouze J (1991) Description of isogenic lines, except for one, or two, monogenically controlled morphological traits in tomato, Lycopersicon esculentum Mill. Euphytica 56:121–131

    Article  Google Scholar 

  • Pillen K, Ganal MW, Tanksley SD (1996) Construction of a high-resolution genetic map and YAC-contigs in the tomato Tm-2a region. Theor Appl Genet 93:228–233

    Article  CAS  PubMed  Google Scholar 

  • Piron F, Nicolai M, Minoia S, Piednoir E, Moretti A, Salgues A, Zamir D, Caranta C, Bendahmane A (2010) An induced mutation in tomato eIF4E leads to immunity to two potyviruses. PloS One 5

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Pnueli L, Carmel-Goren L, Hareven D, Gutfinger T, Alvarez J, Ganal M, Zamir D, Lifschitz E (1998) The SELF-PRUNING gene of tomato regulates vegetative to reproductive switching of sympodial meristems and is the ortholog of CEN and TFL1. Development 125(11):1979–1989

    CAS  PubMed  Google Scholar 

  • Poiroux-Gonord F, Bidel LPR, Fanciullino A-L, Gautier H, Lauri-Lopez F, Urban L (2010) Health benefits of vitamins and secondary metabolites of fruits and vegetables and prospects to increase their concentrations by agronomic approaches. J Agri Food Chem 58:12065–12082

    Article  CAS  Google Scholar 

  • Poland JA, Balint-Kurti PJ, Wisser RJ, Pratt RC, Nelson RJ (2009) Shades of gray: the world of quantitative disease resistance. Trends Plant Sci 14:21–29

    Article  CAS  PubMed  Google Scholar 

  • Prudent M, Lecomte A, Bouchet JP, Bertin N, Causse M, Génard M (2011) Combining ecophysiological modelling and quantitative trait loci analysis to identify key elementary processes underlying tomato fruit sugar concentration. J Exp Bot 62:907–919

    Article  CAS  PubMed  Google Scholar 

  • Qi LS, Larson MH, Gilbert LA, Doudna JA, Weissman JS, Arkin AP, Lim WA (2013) Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression. Cell 152(5):1173–1183

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Quadrana L, Almeida J, Asís R, Duffy T, Dominguez PG, Bermúdez L, Conti G, Corrêa da Silva JV, Peralta IE, Colot V et al (2014) Natural occurring epialleles determine vitamin E accumulation in tomato fruits. Nat Commun 5:4027

    Article  CAS  Google Scholar 

  • Quilot B, Kervella J, Genard M, Lescourret F (2005) Analysing the genetic control of peach fruit quality through an ecophysiological model combined with a QTL approach. J Exp Bot 56:3083–3092

    Article  CAS  PubMed  Google Scholar 

  • Quilot-Turion B, Génard M, Valsesia P, Memmah M-M (2016) Optimization of allelic combinations controlling parameters of a Peach quality model. Front Plant Sci 7:1873

    Article  PubMed  PubMed Central  Google Scholar 

  • Quilot-Turion B, Ould-Sidi M-M, Kadrani A, Hilgert N, Génard M, Lescourret F (2012) Optimization of parameters of the ‘Virtual Fruit’ model to design peach genotype for sustainable production systems. Eur J Agron 42:34–48

    Article  Google Scholar 

  • Quinet M, Kinet J-M, Lutts S (2011) Flowering response of the uniflora: blind: self-pruning and jointless: uniflora: self-pruning tomato (Solanum lycopersicum) triple mutants. Physiol Plant 141:166–176

    Article  CAS  PubMed  Google Scholar 

  • Rached M, Pierre B, Yves G, Matsukura C, Ariizumi T, Ezura H et al (2018) Differences in blossom-end rot resistance in tomato cultivars is associated with total ascorbate rather than calcium concentration in the distal end part of fruits per se Hortic J 87:372–381

    Google Scholar 

  • Rajasekaran LR, Aspinall D, Paleg LG (2000) Physiological mechanism of tolerance of Lycopersicon spp. exposed to salt stress. Can J Plant Sci 80:151–159

    Article  Google Scholar 

  • Rajewsky N (2006) microRNA target predictions in animals. Nat Genet 38:S8–S13

    Article  CAS  PubMed  Google Scholar 

  • Rambla JL, Tikunov YM, Monforte AJ, Bovy AG, Granell A (2014) The expanded tomato fruit volatile landscape. J Exp Bot 65:4613–4623

    Article  CAS  PubMed  Google Scholar 

  • Ramstein GP, Jensen SE, Buckler ES (2018) Breaking the curse of dimensionality to identify causal variants in Breeding 4. Theor Appl Genet 132:559–567

    Article  PubMed  PubMed Central  Google Scholar 

  • Ranc N, Muños S, Xu J, Le Paslier M-C, Chauveau A, Bounon R, Rolland S, Bouchet J-P, Brunel D, Causse M (2012) Genome-wide association mapping in tomato (Solanum lycopersicum) is possible using genome admixture of Solanum lycopersicum var. cerasiforme. G3: GenesGenomesGenet 2: 853–864

    Google Scholar 

  • Ranjan A, Budke JM, Rowland SD, Chitwood DH, Kumar R, Carriedo L et al (2016) eQTL regulating transcript levels associated with diverse biological processes in tomato. Plant Physiol 172(1):328–340

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Rao ES, Kadirvel P, Symonds RC, Ebert AW (2013) Relationship between survival and yield related traits in Solanum pimpinellifolium under salt stress. Euphytica 190:215–228

    Article  Google Scholar 

  • Rasmussen S, Barah P, Suarez-Rodriguez MC, Bressendorff S, Friis P, Costantino P, Bones AM, Nielsen HB, Mundy J (2013) Transcriptome responses to combinations of stresses in arabidopsis. Plant Physiol 161:1783–1794

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Rengel Z (1992) The role of calcium in salt toxicity. Plant Cell Environ 15:625–663

    Article  CAS  Google Scholar 

  • Reymond M, Muller B, Leonardi A, Charcosset A, Tardieu F (2003) Combining quantitative trait loci analysis and an ecophysiological model to analyze the genetic variability of the responses of maize leaf growth to temperature and water deficit. Plant Physiol 131:664–675

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Rick CM, Chetelat RT (1995) Utilization of related wild species for tomato improvement. In: FernandezMunoz R, Cuartero J, GomezGuillamon ML (eds) First international symposium on solanaceae for fresh market. Acta Hort 412:21–38

    Google Scholar 

  • Ripoll J, Urban L, Brunel B, Bertin N (2016) Water deficit effects on tomato quality depend on fruit developmental stage and genotype. J Plant Physiol 190:26–35

    Article  CAS  PubMed  Google Scholar 

  • Ripoll J, Urban L, Staudt M, Lopez-Lauri F, Bidel LPR, Bertin N (2014) Water shortage and quality of fleshy fruits—making the most of the unavoidable. J Exp Bot 65:4097–4117

    Article  CAS  PubMed  Google Scholar 

  • Rivero RM, Mestre TC, Mittler R, Rubio F, Garcia-Sanchez F, Martinez V (2014) The combined effect of salinity and heat reveals a specific physiological, biochemical and molecular response in tomato plants. Plant Cell Environ 37:1059–1073

    Article  CAS  PubMed  Google Scholar 

  • Robbins MD, Masud MAT, Panthee DR, Gardner RG, Francis DM, Stevens MR (2010) Marker-assisted selection for coupling phase resistance to Tomato spotted wilt virus and Phytophthora infestans (Late Blight) in tomato. HortScience 45:1424–1428

    Article  Google Scholar 

  • Robert VJM, West MAL, Inai S, Caines A, Arntzen L, Smith JK, St Clair DA (2001) Marker-assisted introgression of blackmold resistance QTL alleles from wild Lycopersicon cheesmanii to cultivated tomato (L. esculentum) and evaluation of QTL phenotypic effects. Mol Breed 8:217–233

    Article  CAS  Google Scholar 

  • Rodríguez GR, Muños S, Anderson C, Sim S-C, Michel A, Causse M, Gardener BBM, Francis D, van der Knaap E (2011) Distribution of SUN, OVATE, LC, and FAS in the tomato germplasm and the relationship to fruit shape diversity. Plant Physiol 156:275–285

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Rodríguez-Leal D, Lemmon ZH, Man J, Bartlett ME, Lippman ZB (2017) Engineering quantitative trait variation for crop improvement by genome editing. Cell 171:470–480

    Article  PubMed  CAS  Google Scholar 

  • Rogers K, Chen X (2013) Biogenesis, turnover, and mode of action of plant MicroRNAs. Plant Cell 25:2383–2399

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ronen G, Cohen M, Zamir D, Hirschberg J (1999) Regulation of carotenoid biosynthesis during tomato fruit development: expression of the gene for lycopene epsilon-cyclase is down-regulated during ripening and is elevated in the mutant Delta. Plant J17:341–351

    Google Scholar 

  • Rosales MA, Rubio-Wilhelmi MM, Castellano R, Castilla N, Ruiz JM, Romero L (2007) Sucrolytic activities in cherry tomato fruits in relation to temperature and solar radiation. Sci Hort (Amsterdam) 113:244–249

    Article  Google Scholar 

  • Rosental L, Perelman A, Nevo N, Toubiana D, Samani T, Batushansky A, Sikron N, Saranga Y, Fait A (2016) Environmental and genetic effects on tomato seed metabolic balance and its association with germination vigor. BMC Genom 17:1047

    Article  CAS  Google Scholar 

  • Rossi M, Goggin FL, Milligan SB, Kaloshian I, Ullman DE, Williamson VM (1998) The nematode resistance gene Mi of tomato confers resistance against the potato aphid. Proc Natl Acad Sci USA 95:9750–9754

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Rothan C, Diouf I, Causse M (2019) Trait discovery and editing in tomato. Plant J 97:73–90

    Article  CAS  PubMed  Google Scholar 

  • Rousseaux MC, Jones CM, Adams D, Chetelat R, Bennett A, Powell A (2005) QTL analysis of fruit antioxidants in tomato using Lycopersicon pennellii introgression lines. Theor Appl Genet 111:1396–1408

    Article  CAS  PubMed  Google Scholar 

  • Ruan Y-L, Patrick JW, Bouzayen M, Osorio S, Fernie AR (2012) Molecular regulation of seed and fruit set. Trends Plant Sci 17:656–665

    Article  CAS  PubMed  Google Scholar 

  • Ruffel S, Gallois JL, Lesage ML, Caranta C (2005) The recessive potyvirus resistance gene pot-1 is the tomato orthologue of the pepper pvr2-eIF4E gene. Mol Genet Genom 274:346–353

    Article  CAS  Google Scholar 

  • Ruggieri V, Francese G, Sacco A, Alessandro AD, Rigano MM, Parisi M, Milone M, Cardi T, Mennella G, Barone A (2014) An association mapping approach to identify favourable alleles for tomato fruit quality breeding. BMC Plant Biol 14:1–15

    Article  CAS  Google Scholar 

  • Sacco A, Di Matteo A, Lombardi N, Trotta N, Punzo B, Mari A, Barone A (2013) Quantitative trait loci pyramiding for fruit quality traits in tomato. Mol Breed 31(1):217–222

    Article  CAS  PubMed  Google Scholar 

  • Sahu KK, Chattopadhyay D (2017) Genome-wide sequence variations between wild and cultivated tomato species revisited by whole genome sequence mapping. BMC Genom 18:430

    Article  CAS  Google Scholar 

  • Sainju UM, Dris R, Singh B (2003) Mineral nutrition of tomato. Food Agri Environ 1:176–183

    CAS  Google Scholar 

  • Saliba-Colombani V, Causse M, Langlois D, Philouze J, Buret M (2001) Genetic analysis of organoleptic quality in fresh market tomato: 1. Mapping QTLs for physical and chemical traits. Theor Appl Genet 102:259–272

    Article  CAS  Google Scholar 

  • Sallam A, Martsch R (2015) Association mapping for frost tolerance using multi-parent advanced generation inter-cross (MAGIC) population in faba bean (Vicia faba L.). Genetica 143:501–514

    Article  PubMed  Google Scholar 

  • Salmeron JM, Oldroyd GE, Rommens CM, Scofield SR, Kim H-S, Lavelle DT, Dahlbeck D, Staskawicz BJ (1996) Tomato Prf is a member of the leucine-rich repeat class of plant disease resistance genes and lies embedded within the Pto Kinase gene cluster. Cell 86:123–133

    Article  CAS  PubMed  Google Scholar 

  • Sanei M, Chen X (2015) Mechanisms of microRNA turnover. Curr Opin Plant Biol 27:199–206

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sarlikioti V, de Visser PHB, Buck-Sorlin GH, Marcelis LFM (2011) How plant architecture affects light absorption and photosynthesis in tomato: towards an ideotype for plant architecture using a functional–structural plant model. Ann Bot 108(6):1065–1073

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sato S, Tabata S, Hirakawa H et al (2012) The tomato genome sequence provides insights into fleshy fruit evolution. Nature 485:635–641

    Article  CAS  Google Scholar 

  • Sauvage C, Rau A, Aichholz C, Chadoeuf J, Sarah G, Ruiz M, Santoni S, Causse M, David J, Glémin S (2017) Domestication rewired gene expression and nucleotide diversity patterns in tomato. Plant J 91:631–645

    Article  CAS  PubMed  Google Scholar 

  • Sauvage C, Segura V, Bauchet G, Stevens R, Do PT, Nikoloski Z, Fernie AR, Causse M (2014) Genome-wide association in tomato reveals 44 candidate loci for fruit metabolic traits. Plant Physiol 165:1120–1132

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Schachtman DP, Shin R (2007) Nutrient sensing and signaling: NPKS. Annu Rev Plant Biol 58:47–69

    Article  CAS  PubMed  Google Scholar 

  • Schaffer AA, Levin I, Oguz I, Petreikov M, Cincarevsky F, Yeselson Y, Shen S, Gilboa N, Bar M (2000) ADPglucose pyrophosphorylase activity and starch accumulation in immature tomato fruit: the effect of a Lycopersicon hirsutum-derived introgression encoding for the large subunit. Plant Sci 152:135–144

    Article  CAS  Google Scholar 

  • Schauer N, Semel Y, Roessner U, Gur A, Balbo I, Carrari F, Pleban T, Perez-Melis A, Bruedigam C, Kopka J et al (2006) Comprehensive metabolic profiling and phenotyping of interspecific introgression lines for tomato improvement. Nat Biotechnol 24:447–454

    Article  CAS  PubMed  Google Scholar 

  • Schauer N, Zamir D, Fernie AR (2005) Metabolic profiling of leaves and fruit of wild species tomato: a survey of the Solanum lycopersicum complex. J Exp Bot 56:297–307

    Article  CAS  PubMed  Google Scholar 

  • Scheben A, Batley J, Edwards D (2017) Genotyping-by-sequencing approaches to characterize crop genomes: choosing the right tool for the right application. Plant Biotechnol J 15:149–161

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Schijlen EG, de Vos CR, Martens S, Jonker HH, Rosin FM, Molthoff JW, Tikunov YM, Angenent GC, van Tunen AJ, Bovy AG (2007) RNA interference silencing of chalcone synthase, the first step in the flavonoid biosynthesis pathway, leads to parthenocarpic tomato fruits. Plant Physiol 144(3):1520–1530

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Scholberg JMS, Locascio SJ (1999) Growth response of snap bean and tomato as affected by salinity and irrigation method. HortScience 34:259–264

    Article  Google Scholar 

  • Segura V, Vilhjálmsson BJ, Platt A, Korte A, Seren Ü, Long Q, Nordborg M (2012) An efficient multi-locus mixed-model approach for genome-wide association studies in structured populations. Nat Genet 44:825–830

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Semel Y, Nissenbaum J, Menda N, Zinder M, Krieger U, Issman N, Pleban T, Lippman Z, Gur A, Zamir D (2006) Overdominant quantitative trait loci for yield and fitness in tomato. Proc Natl Acad Sci USA 103:12981–12986

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Semel Y, Schauer N, Roessner U, Zamir D, Fernie AR (2007) Metabolite analysis for the comparison of irrigated and non-irrigated field grown tomato of varying genotype. Metabolomics 3:289–295

    Article  CAS  Google Scholar 

  • Shahlaei A, Torabi S, Khosroshahli M (2014) Efficiacy of SCoT and ISSR marekers in assesment of tomato (Lycopersicum esculentum Mill.) genetic diversity. Intl J Biosci 5:14–22

    CAS  Google Scholar 

  • Shalit A, Rozman A, Goldshmidt A, Alvarez JP, Bowman JL, Eshed Y, Lifschitz E (2009) The flowering hormone florigen functions as a general systemic regulator of growth and termination. Proc Natl Acad Sci USA 106:8392–8397

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Shammai A, Petreikov M, Yeselson Y, Faigenboim A, Moy-Komemi M, Cohen S, Cohen D, Besaulov E, Efrati A, Houminer N et al (2018) Natural genetic variation for expression of a SWEET transporter among wild species of Solanum lycopersicum (tomato) determines the hexose composition of ripening tomato fruit. Plant J 96:343–357

    Article  CAS  PubMed  Google Scholar 

  • Sharada MS, Kumari A, Pandey AK, Sharma S, Sharma P, Sreelakshmi Y, Sharma R (2017) Generation of genetically stable transformants by Agrobacterium using tomato floral buds. Plant Cell Tiss Org Cult 129(2):299–312

    Article  CAS  Google Scholar 

  • Shimatani Z, Kashojiya S, Takayama M, Terada R, Arazoe T, Ishii H, Teramura H, Yamamoto T, Komatsu H, Miura K, Ezura H (2017) Targeted base editing in rice and tomato using a CRISPR-Cas9 cytidine deaminase fusion. Nature Biotechnol 35(5):441–443

    Article  CAS  Google Scholar 

  • Shinozaki Y, Nicolas P, Fernandez-Pozo N, Ma Q, Evanich DJ, Shi Y, Xu Y, Zheng Y, Snyder SI, Martin LBB et al (2018) High-resolution spatiotemporal transcriptome mapping of tomato fruit development and ripening. Nat Commun 9:364

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Sim S-C, Van Deynze A, Stoffel K, Douches DS, Zarka D, Ganal MW, Chetelat RT, Hutton SF, Scott JW, Gardner RG, et al. (2012a) High-density SNP genotyping of tomato (Solanum lycopersicum L.) reveals patterns of genetic variation due to breeding. PLoS One 7:e45520

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sim S-C, Durstewitz G, Plieske J, Wieseke R, Ganal MW, van Deynze A, Hamilton JP, Buell CR, Causse M, Wijeratne S et al (2012b) Development of a large snp genotyping array and generation of high-density genetic maps in tomato. PLoS One. https://doi.org/10.1371/journal.pone.0040563

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Sim S-C, Robbins MD, Van Deynze A, Agee M, Francis DM (2010) Population structure and genetic differentiation associated with breeding history and selection in tomato (Solanum lycopersicum L.). Heredity (Edinb) 106:927–935

    Article  CAS  Google Scholar 

  • Sim SC, Robbins MD, Wijeratne S, Wang H, Yang WC, Francis DM (2015) Association analysis for bacterial spot resistance in a directionally selected complex breeding population of tomato. Phytopathology 105:1437–1445

    Article  CAS  PubMed  Google Scholar 

  • Simons G, Groenendijk J, Wijbrandi J, Reijans M, Groenen J, Diergaarde P, Van der Lee T, Bleeker M, Onstenk J, de Both M, Haring M, Mes J, Cornelissen B, Zabeau M, Vos P (1998) Dissection of the Fusarium I2 gene cluster in tomato reveals six homologs and one active gene copy. Plant Cell (The) 10:1055–1068

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Smart CD, Tanksley SD, Mayton H, Fry WE (2007) Resistance to Phytophthora infestans in Lycopersicon pennellii. Plant Dis 91:1045–1049

    Article  PubMed  Google Scholar 

  • Smirnoff N, Wheeler GL (2000) Ascorbic acid in plants: biosynthesis and function. Crit Rev Biochem Mol Biol 35:291–314

    Article  CAS  PubMed  Google Scholar 

  • Smith DL, Abbott JA, Gross KC (2002) Down-regulation of tomato β-galactosidase 4 results in decreased fruit softening. Plant Physiol 129(4):1755–1762

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Soyk S, Lemmon ZH, Oved M et al (2017a) Bypassing negative epistasis on yield in tomato imposed by a domestication gene. Cell 169:1142–1155

    Article  CAS  PubMed  Google Scholar 

  • Soyk S, Müller NA, Park SJ, Schmalenbach I, Jiang K, Hayama R, Zhang L, Van Eck J, Jiménez-Gómez JM, Lippman ZB (2017b) Variation in the flowering gene SELF PRUNING 5G promotes day-neutrality and early yield in tomato. Nat Genet 49:162–168

    Article  CAS  PubMed  Google Scholar 

  • Spano R, Mascia T, Kormelink R, Gallitelli D (2015) Grafting on a non-transgenic tolerant tomato variety confers resistance to the infection of a Sw5-breaking strain of tomato spotted wilt virus via RNA silencing. PloS One 10

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Spindel J, Begum H, Akdemir D, Virk P, Collard B, Redoña E, Atlin G, Jannink JL, McCouch SR (2015) Genomic selection and association mapping in rice (Oryza sativa): effect of trait genetic architecture, training population composition, marker number and statistical model on accuracy of rice genomic selection in elite, tropical rice breeding lines. PLoS Genet 11:1–25

    Google Scholar 

  • Stamova BS, Chetelat RT (2000) Inheritance and genetic mapping of cucumber mosaic virus resistance introgressed from Lycopersicon chilense into tomato. TheorAppl Genet 101:527–537

    Article  CAS  Google Scholar 

  • Stevens MA (1986) Inheritance of tomato fruit quality components. Plant Breed Rev 4:273–311

    Google Scholar 

  • Stevens MA, Kader AA, Albright M (1979) Potential for increasing tomato flavor via increased sugar and acid content. J Amer Soc Hort Sci 104:40–42

    Google Scholar 

  • Stevens MA, Kader AA, Albright-Holton M (1977) Intercultivar variation in composition of locular and pericarp portions of fresh market tomatoes. J Amer Soc Hort Sci 102:689–692

    CAS  Google Scholar 

  • Stevens MR, Lamb EM, Rhoads DD (1995) Mapping the Sw-5 locus for tomato spotted wilt virus-resistance in tomatoes using RAPD and RFLP analyses. Theor Appl Genet 90:451–456

    Article  CAS  PubMed  Google Scholar 

  • Stikic R, Popovic S, Srdic M, Savic D, Jovanovic Z, Zdravkovic J (2003) Partial root drying (PRD): a new technique for growing plants that saves water and improves the quality of fruit. Bulg J Plant Physiol 164–171

    Google Scholar 

  • Stricker SH, Köferle A, Beck S (2017) From profiles to function in epigenomics. Nat Rev Genet 18:51–66

    Article  CAS  PubMed  Google Scholar 

  • Struik PC, Yin XY, de Visser P (2005) Complex quality traits: now time to model. Trends Plant Sci 10:513–516

    Article  CAS  PubMed  Google Scholar 

  • Suliman-Pollatschek S, Kashkush K, Shats H, Hillel J, Lavi U (2002) Generation and mapping of AFLP, SSRs and SNPs in Lycopersicon esculentum. Cell Mol Biol Lett 7:583–597

    CAS  PubMed  Google Scholar 

  • Sun J, Poland JA, Mondal S, Crossa J, Juliana P, Singh RP, Rutkoski JE, Jannink J-L, Crespo-Herrera L, Velu G et al (2019) High-throughput phenotyping platforms enhance genomic selection for wheat grain yield across populations and cycles in early stage. Theor Appl Genet 1–16

    Google Scholar 

  • Sun X, Gao Y, Li H, Yang S, Liu Y (2015) Over-expression of SlWRKY39 leads to enhanced resistance to multiple stress factors in tomato. J Plant Biol 58:52–60

    Article  CAS  Google Scholar 

  • Suzuki N, Rivero RM, Shulaev V, Blumwald E, Mittler R (2014) Abiotic and biotic stress combinations. New Phytol 203:32–43

    Article  PubMed  Google Scholar 

  • Tadmor Y, Fridman E, Gur A, Larkov O, Lastochkin E, Ravid U, Zamir D, Lewinsohn E (2002) Identification of malodorous, a wild species allele affecting tomato aroma that was selected against during domestication. J Agri Food Chem 50:2005–2009

    Article  CAS  Google Scholar 

  • Takken FLW, Thomas CM, Joosten M, Golstein C, Westerink N, Hille J, Nijkamp HJJ, De Wit P, Jones JDG (1999) A second gene at the tomato Cf-4 locus confers resistance to Cladosporium fulvum through recognition of a novel avirulence determinant. Plant J 20:279–288

    Article  CAS  PubMed  Google Scholar 

  • Takken FLW, Schipper D, Nijkamp HJJ, Hille J (1998) Identification and Ds-tagged isolation of a new gene at the Cf-4 locus of tomato involved in disease resistance to Cladosporium fulvum race 5. Plant J 14:401–411

    Article  CAS  PubMed  Google Scholar 

  • Tam SM, Mhiri C, Vogelaar A, Kerkveld M, Pearce SR, Grandbastien MA (2005) Comparative analyses of genetic diversities within tomato and pepper collections detected by retrotransposon-based SSAP, AFLP and SSR. Theor Appl Genet 110:819–831

    Article  CAS  PubMed  Google Scholar 

  • Tanksley SD (2004) The genetic, developmental, and molecular bases of fruit size in tomato and shape variation. Plant Cell 16:181–190

    Article  Google Scholar 

  • Tanksley SD, Ganal MW, Prince JP, De Vicente MC, Bonierbale MW, Broun P, Fulton TM, Giovannoni JJ, Grandillo S, Martin GB et al (1992) High density molecular linkage maps of the tomato and potato genomes. Genetics 132:1141–1160

    CAS  PubMed  PubMed Central  Google Scholar 

  • Tanksley SD, Grandillo S, Fulton TM, Zamir D, Eshed Y, Petiard V, Lopez J, Beck-Bunn T (1996) Advanced backcross QTL analysis in a cross between an elite processing line of tomato and its wild relative L. pimpinellifolium. Theor Appl Genet 92:213–224

    Article  CAS  PubMed  Google Scholar 

  • Tanksley SD, Nelson JC (1996) Advanced backcross QTL analysis: a method for the simultaneous discovery and transfer of valuable QTLs from unadapted germplasm into elite breeding lines. Theor Appl Genet 92:191–203

    Article  CAS  PubMed  Google Scholar 

  • Tardieu F (2003) Virtual plants: modelling as a tool for the genomics of tolerance to water deficit. Trends Plant Sci 8:9–14

    Article  CAS  PubMed  Google Scholar 

  • Tashkandi M, Ali Z, Aljedaani F, Shami A, Mahfouz MM (2018) Engineering resistance against Tomato yellow leaf curl virus via the CRISPR/Cas9 system in tomato. Plant Signal Behav 13

    Google Scholar 

  • Taudt A, Colomé-Tatché M, Johannes F (2016) Genetic sources of population epigenomic variation. Nat Rev Genet 17:319–332

    Article  CAS  PubMed  Google Scholar 

  • The 100 Tomato Genome Sequencing Consortium (2014) Exploring genetic variation in the tomato (Solanum section Lycopersicon) clade by whole-genome sequencing. Plant J 80:136–148

    Google Scholar 

  • The 100 Tomato Genome Sequencing Consortium (2014) Exploring genetic variation in the tomato (Solanum section Lycopersicon) clade by whole-genome sequencing. Plant J 80:136–148

    Google Scholar 

  • The 1000 Genomes Project Consortium (2010) A map of human genome variation from population-scale sequencing. Nature 467:1061–1073

    Google Scholar 

  • The 1001 Genomes Consortium (2016) 1,135 genomes reveal the global pattern of polymorphism in Arabidopsis thaliana. Cell 166: 481–491

    Google Scholar 

  • The 1001 Genomes Consortium (2016) 1,135 genomes reveal the global pattern of polymorphism in Arabidopsis thaliana. Cell 166: 481–491

    Google Scholar 

  • The 3000 rice genomes project (2014) The 3,000 rice genomes project. Gigascience 3: 7

    Google Scholar 

  • The UK10K Consortium (2015) The UK10K project identifies rare variants in health and disease. Nature 526:82–89

    Google Scholar 

  • Thoen MPM, Davila Olivas NH, Kloth KJ, Coolen S, Huang PP, Aarts MGM, Bac-Molenaar JA, Bakker J, Bouwmeester HJ, Broekgaarden C et al (2017) Genetic architecture of plant stress resistance: multi-trait genome-wide association mapping. New Phytol 213:1346–1362

    Article  CAS  PubMed  Google Scholar 

  • Tieman D, Bliss P, McIntyre LMM, Blandon-Ubeda A, Bies D, Odabasi AZZ, Rodríguez GRR, Van Der Knaap E, Taylor MGG, Goulet C et al (2012) The chemical interactions underlying tomato flavor preferences. Curr Biol 22:1035–1039

    Article  CAS  PubMed  Google Scholar 

  • Tieman D, Taylor M, Schauer N, Fernie AR, Hanson AD, Klee HJ (2006) Tomato aromatic amino acid decarboxylases participate in synthesis of the flavor volatiles 2-phenylethanol and 2-phenylacetaldehyde. Proc Natl Acad Sci USA 103:8287–8292

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Tieman D, Zhu G, Resende MFR, Lin T, Nguyen C, Bies D, Rambla JL, Beltran KSO, Taylor M, Zhang B et al (2017) A chemical genetic roadmap to improved tomato flavor. Science (80-) 355:391–394

    Article  CAS  PubMed  Google Scholar 

  • Tieman DM, Handa AK (1994) Reduction in pectin methylesterase activity modifies tissue integrity and cation levels in ripening tomato (Lycopersicon esculentum Mill.) fruits. Plant Physiol 106(2):429–36

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Tikunov Y, Lommen A, Vos CHR, de Verhoeven HA, Bino RJ, Hall RD, Bovy AG (2005) A novel approach for nontargeted data analysis for metabolomics. Large-scale profiling of tomato fruit volatiles. Plant Physiol 139:1125–1137

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Tikunov YM, Molthoff J, de Vos RCH, Beekwilder J, van Houwelingen A et al (2013) Non-smoky glycosyltransferase1 prevents the release of smoky aroma from tomato fruit. Plant Cell 25(8):3067–3078

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Tranchida-Lombardo V, Aiese Cigliano R, Anzar I, Landi S, Palombieri S, Colantuono C, Bostan H, Termolino P, Aversano R, Batelli G et al (2018) Whole-genome re-sequencing of two Italian tomato landraces reveals sequence variations in genes associated with stress tolerance, fruit quality and long shelf-life traits. DNA Res 25:149–160

    Article  CAS  PubMed  Google Scholar 

  • Tuna AL, Kaya C, Ashraf M, Altunlu H, Yokas I, Yagmur B (2007) The effects of calcium sulphate on growth, membrane stability and nutrient uptake of tomato plants grown under salt stress. Environ Exp Bot 59:173–178

    Article  CAS  Google Scholar 

  • Turina M, Kormelink R, Resende RO (2016) Resistance to tospoviruses in vegetable crops: epidemiological and molecular aspects. In: Leach JE, Lindow S (eds) Annu Rev Phytopathol 54:347–371

    Google Scholar 

  • Uluisik S, Chapman NH, Smith R, Poole M, Adams G, Gillis RB, Besong TM, Sheldon J, Stiegelmeyer S, Perez L, Samsulrizal N (2016) Genetic improvement of tomato by targeted control of fruit softening. Nature Biotechnol 34(9):950

    Article  CAS  Google Scholar 

  • Usadel B, Chetelat R, Koren S, Maumus F, Fernie AR, Aury J-M, Maß J, Schmidt MH-W, Denton AK, Wormit A et al (2017) De novo assembly of a new Solanum pennellii accession using nanopore sequencing. Plant Cell 29:2336–2348

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Vakalounakis DJ, Laterrot H, Moretti A, Ligoxigakis EK, Smardas K (1997) Linkage between Frl (Fusarium oxysporum f sp radicis-lycopersici resistance) and Tm-2 (tobacco mosaic virus resistance-2) loci in tomato (Lycopersicon esculentum). Ann Appl Biol 130:319–323

    Article  Google Scholar 

  • van Berloo R, Stam P (1998) Marker-assisted selection in autogamous RIL populations: a simulation study. Theor Appl Genet 96:147–154

    Article  Google Scholar 

  • van Berloo R, Stam P (1999) Comparison between marker-assisted selection and phenotypical selection in a set of Arabidopsis thaliana recombinant inbred lines. Theor Appl Genet 98:113–118

    Article  Google Scholar 

  • Van Berloo R, Zhu A, Ursem R, Verbakel H, Gort G, van Eeuwijk FA (2008) Diversity and linkage disequilibrium analysis within a selected set of cultivated tomatoes. Theor Appl Genet 117:89–101

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • van der Knaap E, Tanksley SD (2003) The making of a bell pepper-shaped tomato fruit: identification of loci controlling fruit morphology in Yellow Stuffer tomato. Theor Appl Genet 107:139–147

    Article  PubMed  CAS  Google Scholar 

  • van Eeuwijk Fred A, Bustos-Korts D, Millet EJ, Boer MP, Kruijer W, Thompson A et al (2019) Modelling strategies for assessing and increasing the effectiveness of new phenotyping techniques in plant breeding. Plant Sci 282:23–39

    Article  PubMed  CAS  Google Scholar 

  • Vargas-Ponce O, Pérez-Álvarez LF, Zamora-Tavares P, Rodríguez A (2011) Assessing genetic diversity in mexican husk tomato species. Plant Mol Biol Rep 29:733–738

    Article  Google Scholar 

  • Veillet F, Perrot L, Chauvin L, Kermarrec M-P, Guyon-Debast A, Chauvin J-E, Nogué F, Mazier M (2019) Transgene-free genome editing in tomato and potato plants using Agrobacterium-mediated delivery of a CRISPR/Cas9 cytidine base editor. Intl J Mol Sci 20(2):402

    Article  CAS  Google Scholar 

  • Venter F (1977) Solar radiation and vitamin C content of tomato fruits. Acta Hortic 58:121–127

    Google Scholar 

  • Verkerke W, Janse J, Kersten M (1998) Instrumental measurement and modelling of tomato fruit taste. Acta Hort 199–206

    Google Scholar 

  • Verlaan MG, Hutton SF, Ibrahem RM, Kormelink R, Visser RGF, Scott JW, Edwards JD, Bai YL (2013) The Tomato Yellow Leaf Curl Virus Resistance Genes Ty-1 and Ty-3 Are Allelic and Code for DFDGD-Class RNA-Dependent RNA Polymerases. PLoS Genetics 9

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Villalta I, Bernet GP, Carbonell EA, Asins MJ (2007) Comparative QTL analysis of salinity tolerance in terms of fruit yield using two solanum populations of F7 lines. Theor Appl Genet 114:1001–1017

    Article  CAS  PubMed  Google Scholar 

  • Víquez-Zamora M, Vosman B, van de Geest H, Bovy A, Visser RGF, Finkers R, van Heusden AW (2013) Tomato breeding in the genomics era: insights from a SNP array. BMC Genom 14:354

    Article  CAS  Google Scholar 

  • Vos P, Simons G, Jesse T, Wijbrandi J, Heinen L, Hogers R, Frijters A, Groenendijk J, Diergaarde P, Reijans M, Fierens-Onstenk J, de Both M, Peleman J, Liharska T, Hontelez J, Zabeau M (1998) The tomato Mi-1 gene confers resistance to both root-knot nematodes and potato aphids. Nat Biotechnol 16:1365–1369

    Article  CAS  PubMed  Google Scholar 

  • Vrebalov J, Ruezinsky D, Padmanabhan V, White R, Medrano D, Drake R, Schuch W, Giovannoni J (2002) A MADS-box gene necessary for fruit ripening at the tomato ripening-inhibitor (rin) locus. Science (80-) 296:343–346

    Article  CAS  PubMed  Google Scholar 

  • Wahid A, Gelani S, Ashraf M, Foolad MR (2007) Heat tolerance in plants: an overview. Environ Exp Bot 61:199–223

    Article  Google Scholar 

  • Wang D, Salah El-Basyoni I, Stephen Baenziger P, Crossa J, Eskridge KM, Dweikat I (2012) Prediction of genetic values of quantitative traits with epistatic effects in plant breeding populations. Heredity (Edinb) 109:313–319

    Article  CAS  Google Scholar 

  • Wang DR, Agosto-Pérez FJ, Chebotarov D, Shi Y, Marchini J, Fitzgerald M, McNally KL, Alexandrov N, McCouch SR (2018) An imputation platform to enhance integration of rice genetic resources. Nat Commun 9:3519

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Wang JF, Ho FI, Truong HTH, Huang SM, Balatero CH, Dittapongpitch V, Hidayati N (2013a) Identification of major QTLs associated with stable resistance of tomato cultivar ‘Hawaii 7996’ to Ralstonia solanacearum. Euphytica 190:241–252

    Article  CAS  Google Scholar 

  • Wang K, Li M, Hakonarson H (2010) ANNOVAR: Functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Res 38:e164

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Wang L, Song X, Gu L, Li X, Cao S, Chu C, Cui X, Chen X, Cao X (2013b) NOT2 proteins promote polymerase II-dependent transcription and interact with multiple MicroRNA biogenesis factors in Arabidopsis. Plant Cell 25:715–727

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Wang R, Tavano ECDR, Lammers M, Martinelli AP, Angenent GC, de Maagd RA (2019) Re-evaluation of transcription factor function in tomato fruit development and ripening with CRISPR/Cas9-mutagenesis. Sci Rep 8:1696

    Article  CAS  Google Scholar 

  • Wang Y, Wu W-H (2015) Genetic approaches for improvement of the crop potassium acquisition and utilization efficiency. Curr Opin Plant Biol 25:46–52

    Article  PubMed  CAS  Google Scholar 

  • Wang Z, Gerstein M, Snyder M (2009) RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet 10:57–63

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Waters AJ, Makarevitch I, Noshay J, Burghardt LT, Hirsch CN, Hirsch CD, Springer NM (2017) Natural variation for gene expression responses to abiotic stress in maize. Plant J 89:706–717

    Article  CAS  PubMed  Google Scholar 

  • Wells T, Ward JL, Corol DI, Baker JM, Gerrish C, Michael H, Seymour GB, Fraser PD and Bramley PM (2013) Metabolite profiling of introgression lines of Solanum habrochaites using targeted and non-targeted approaches reveals novel quantitative trait loci. PhD Max Planck Institute Postdam, Germany, 149 p

    Google Scholar 

  • Wilkins KA, Matthus E, Swarbreck SM, Davies JM (2016) Calcium-mediated abiotic stress signaling in roots. Front Plant Sci 7:1296

    Google Scholar 

  • Willits MG, Kramer CM, Prata RT, De Luca V, Potter BG, Steffens JC, Graser G (2005) Utilization of the genetic resources of wild species to create a nontransgenic high flavonoid tomato. J Agri Food Chem 53:1231–1236

    Article  CAS  Google Scholar 

  • Won SY, Yumul RE, Chen X (2014) Small RNAs in plants. Molecular biology. Springer, New York, pp 95–127

    Google Scholar 

  • Xiao H, Jiang N, Schaffner E, Stockinger EJ, van der Knaap E (2008) A retrotransposon-mediated gene duplication underlies morphological variation of tomato fruit. Science 319:1527–1530

    Article  CAS  PubMed  Google Scholar 

  • Xie Z, Allen E, Fahlgren N, Calamar A, Givan SA, Carrington JC (2005) Expression of Arabidopsis MIRNA genes. Plant Physiol 138:2145–2154

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Xu J, Driedonks N, Rutten MJM, Vriezen WH, de Boer GJ, Rieu I (2017a) Mapping quantitative trait loci for heat tolerance of reproductive traits in tomato (Solanum lycopersicum). Mol Breed 37:58

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Xu J, Ranc N, Muños S, Rolland S, Bouchet J-PP, Desplat N, Le Paslier M-CC, Liang Y, Brunel D, Causse M (2013) Phenotypic diversity and association mapping for fruit quality traits in cultivated tomato and related species. Theor Appl Genet 126:567–581

    Article  PubMed  Google Scholar 

  • Xu J, Wolters-Arts M, Mariani C, Huber H, Rieu I (2017b) Heat stress affects vegetative and reproductive performance and trait correlations in tomato (Solanum lycopersicum). Euphytica 213:156

    Article  Google Scholar 

  • Xu WF, Shi WM, Yan F (2012) Temporal and tissue-specific expression of tomato 14-3-3 gene family in response to phosphorus deficiency. Pedosphere 22:735–745

    Article  CAS  Google Scholar 

  • Yamaguchi H, Ohnishi J, Saito A, Ohyama A, Nunome T, Miyatake K, Fukuoka H (2018) An NB-LRR gene, TYNBS1, is responsible for resistance mediated by the Ty-2 Begomovirus resistance locus of tomato. Theoret Appl Genet 131:1345–1362

    Article  CAS  PubMed  Google Scholar 

  • Yamamoto E, Matsunaga H, Onogi A, Kajiya-Kanegae H, Minamikawa M, Suzuki A, Shirasawa K, Hirakawa H, Nunome T, Yamaguchi H et al (2016) A simulation-based breeding design that uses whole-genome prediction in tomato. Sci Rep 6:19454

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Yamamoto E, Matsunaga H, Onogi A, Ohyama A, Miyatake K, Yamaguchi H, Nunome T, Iwata H, Fukuoka H (2017) Efficiency of genomic selection for breeding population design and phenotype prediction in tomato. Heredity (Edinb) 118:202–209

    Article  CAS  Google Scholar 

  • Yang D-Y, Li M, Ma N-N, Yang X-H, Meng Q-W (2017) Tomato SlGGP-LIKE gene participates in plant responses to chilling stress and pathogenic infection. Plant Physiol Biochem 112:218–226

    Article  CAS  PubMed  Google Scholar 

  • Yang X, Caro M, Hutton SF, Scott JW, Guo Y, Wang X, Rashid MH, Szinay D, de Jong H, Visser RGF et al (2014) Fine mapping of the tomato yellow leaf curl virus resistance gene Ty-2 on chromosome 11 of tomato. Mol Breed 34:749–760

    PubMed  PubMed Central  Google Scholar 

  • Yasmeen A, Mirza B, Inayatullah S, Safdar N, Jamil M, Ali S, Choudhry MF (2009) In planta transformation of tomato. Plant Mol Biol Rep 27(1):20–28

    Article  CAS  Google Scholar 

  • Ye J, Wang X, Hu T, Zhang F, Wang B, Li C, Yang T, Li H, Lu Y, Giovannoni JJ et al (2017) An InDel in the promoter of Al-ACTIVATED MALATE TRANSPORTER9 selected during tomato domestication determines fruit malate contents and aluminum tolerance. Plant Cell 29:2249–2268

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Yin X, Kropff MJ, Stam P (1999) The role of ecophysiological models in QTL analysis: the example of specific leaf area in barley. Heredity 82:415–421

    Article  PubMed  Google Scholar 

  • You C, Cui J, Wang H, Qi X, Kuo L-Y, Ma H, Gao L, Mo B, Chen X (2017) Conservation and divergence of small RNA pathways and microRNAs in land plants. Genome Biol 18:158

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Young ND, Tanksley SD (1989) RFLP analysis of the size of chromosomal segments retained around the Tm-2 locus of tomato during backcross breeding. Theor Appl Genet 77:353–359

    Article  CAS  PubMed  Google Scholar 

  • Yu B, Bi L, Zheng B, Ji L, Chevalier D, Agarwal M, Ramachandran V, Li W, Lagrange T, Walker JC et al (2008) The FHA domain proteins DAWDLE in Arabidopsis and SNIP1 in humans act in small RNA biogenesis. Proc Natl Acad Sci USA105: 10073–10078

    Article  CAS  Google Scholar 

  • Yu Y, Jia T, Chen X (2017) The ‘how’ and ‘where’ of plant microRNAs. New Phytol 216:1002–1017

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zamir D (2001) Improving plant breeding with exotic genetic libraries. Nat Rev Genet 2:3–9

    Article  Google Scholar 

  • Zanor MI, Rambla JL, Chaïb J, Steppa A, Medina A, Granell A, Fernie AR, Causse M (2009) Metabolic characterization of loci affecting sensory attributes in tomato allows an assessment of the influence of the levels of primary metabolites and volatile organic contents. J Exp Bot 60:2139–2154

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zegbe-Domı́nguez J, Behboudian M, Lang A, Clothier B (2003) Deficit irrigation and partial rootzone drying maintain fruit dry mass and enhance fruit quality in ‘Petopride’ processing tomato (Lycopersicon esculentum, Mill.). Sci Hort (Amsterdam) 98:505–510

    Article  Google Scholar 

  • Zhang B, Tieman DM, Chen J, Xu Y, Chen K, Fei Z, Giovannoni J, Klee HJ (2016) Loss of tomato flavor quality during chilling is associated with reduced expression of volatile biosynthetic genes and a transient alteration in DNA methylation. Proc Natl Acad Sci USA113:12580–12584

    Google Scholar 

  • Zhang C, Liu L, Wang X, Vossen J, Li G, Li T, Zheng Z, Gao J, Guo Y, Visser RGF et al (2014) The Ph-3 gene from Solanum pimpinellifolium encodes CC-NBS-LRR protein conferring resistance to Phytophthora infestans. Theor Appl Genet 127:1353–1364

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhang J, Zhao J, Liang Y, Zou Z (2016b) Genome-wide association-mapping for fruit quality traits in tomato. Euphytica 207:439–451

    Article  CAS  Google Scholar 

  • Zhang J, Zhao J, Xu Y, Liang J, Chang P, Yan F, Li M, Liang Y, Zou Z (2015a) Genome-wide association mapping for tomato volatiles positively contributing to tomato flavor. Front Plant Sci 6:1042

    PubMed  PubMed Central  Google Scholar 

  • Zhang S, Xie M, Ren G, Yu B (2013) CDC5, a DNA binding protein, positively regulates posttranscriptional processing and/or transcription of primary microRNA transcripts. Proc Natl Acad Sci USA 110:17588–17593

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhang Y, Butelli E, Alseekh S, Tohge T, Rallapalli G, Luo J, Kawar PG, Hill L, Santino A, Fernie AR, Martin C (2015b) Multi-level engineering facilitates the production of phenylpropanoid compounds in tomato. Nat Commun 6:8635

    Article  CAS  PubMed  Google Scholar 

  • Zhang Z, Guo X, Ge C, Ma Z, Jiang M, Li T, Koiwa H, Yang SW, Zhang X (2017) KETCH1 imports HYL1 to nucleus for miRNA biogenesis in Arabidopsis. Proc Natl Acad Sci USA 114:4011–4016

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Zhao C, Liu B, Piao S, Wang X, Lobell DB, Huang Y, Huang M, Yao Y, Bassu S, Ciais P et al (2017) Temperature increase reduces global yields of major crops in four independent estimates. Proc Natl Acad Sci USA114: 9326–9331

    Article  CAS  Google Scholar 

  • Zhao J, Sauvage C, Zhao J, Bitton F, Bauchet G, Liu D, Huang S, Tieman DM, Klee HJ, Causse M (2019) Meta-analysis of genome-wide association studies provides insights into genetic control of tomato flavor. Nat Commun 10:1534

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Zhao X, Liu Y, Liu X, Jiang J (2018) Comparative transcriptome profiling of two tomato genotypes in response to potassium-deficiency stress. Int J Mol Sci 19:2402

    Article  PubMed Central  CAS  Google Scholar 

  • Zhong S, Fei Z, Chen Y, Zheng Y, Huang M, Vrebalov J, McQuinn R, Gapper N, Liu B, Xiang J et al (2013) Single-base resolution methylomes of tomato fruit development reveal epigenome modifications associated with ripening. Nat Biotechnol 31:154–159

    Article  CAS  PubMed  Google Scholar 

  • Zhou R, Wu Z, Cao X, Jiang F (2015) Genetic diversity of cultivated and wild tomatoes revealed by morphological traits and SSR markers. Genet Mol Res 14:13868–13879

    Article  CAS  PubMed  Google Scholar 

  • Zhou R, Yu X, Ottosen C-O, Rosenqvist E, Zhao L, Wang Y, Yu W, Zhao T, Wu Z (2017) Drought stress had a predominant effect over heat stress on three tomato cultivars subjected to combined stress. BMC Plant Biol 17:24

    Article  PubMed  PubMed Central  CAS  Google Scholar 

  • Zhu G, Gou J, Klee H, Huang S (2019) Next-gen approaches to flavor-related metabolism. Ann Rev Plant Biol 70:187–212

    Article  CAS  Google Scholar 

  • Zhu G, Wang S, Huang Z, Zhang S, Liao Q et al (2018) Rewiring of the fruit metabolome in tomato breeding. Cell 172:249–261

    Article  CAS  PubMed  Google Scholar 

  • Zhuang K, Kong F, Zhang S, Meng C, Yang M, Liu Z, Wang Y, Ma N, Meng Q (2019) Whirly1 enhances tolerance to chilling stress in tomato via protection of photosystem II and regulation of starch degradation. New Phytol 221:1998–2012

    Article  CAS  PubMed  Google Scholar 

  • Zsögön A, Čermák T, Naves ER, Notini MM, Edel KH, Weinl S, Freschi L, Voytas DF, Kudla J, Peres LE (2018) De novo domestication of wild tomato using genome editing. Nat Biotechnol 36:1211–1216

    Article  CAS  Google Scholar 

  • Zsögön A, Cermak T, Voytas D, Pereira Peres LE (2017) Genome editing as a tool to achieve the crop ideotype and de novo domestication of wild relatives: case study in tomato. Plant Sci 256:120–130

    Article  PubMed  CAS  Google Scholar 

  • Zuo J, Fu D, Zhu Y, Qu G, Tian H, Zhai B, Ju Z, Gao C, Wang Y, Luo Y et al (2013) SRNAome parsing yields insights into tomato fruit ripening control. Physiol Plant 149:540–553

    Article  CAS  PubMed  Google Scholar 

  • Zuo J, Zhu B, Fu D, Zhu Y, Ma Y, Chi L, Ju Z, Wang Y, Zhai B, Luo Y (2012) Sculpting the maturation, softening and ethylene pathway: the influences of microRNAs on tomato fruits. BMC Genom 13:7

    Article  CAS  Google Scholar 

  • Zuriaga E, Blanca J, Nuez F (2009) Classification and phylogenetic relationships in Solanum section Lycopersicon based on AFLP and two nuclear gene sequences. Genet Resour Crop Evol 56:663–678

    Article  CAS  Google Scholar 

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Correspondence to Mathilde Causse .

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Causse, M. et al. (2020). Genomic Designing for Climate-Smart Tomato. In: Kole, C. (eds) Genomic Designing of Climate-Smart Vegetable Crops. Springer, Cham. https://doi.org/10.1007/978-3-319-97415-6_2

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