Skip to main content

Knowledge on the Genomes of Wild Tomato Species is the Key to Unlocking Their Breeding Potential

  • Chapter
  • First Online:
The Wild Solanums Genomes

Part of the book series: Compendium of Plant Genomes ((CPG))

  • 646 Accesses

Abstract

Wild tomato species are characterized by wide genetic variability and phenotypic diversity that might be recovered to reintroduce favorable ‘wild’ genes/alleles back into the ‘domesticated’ genomes. Within this context, the assessment of the genetic diversity of wild tomato species is gaining momentum and an ever-growing number of genomic resources are now available. The latter provide novel opportunities to broaden the genetic basis of cultivated tomatoes and exploit the overwhelming inter‐species genetic variability via ‘introgression’ breeding and/or new plant breeding techniques to address emerging challenges. This chapter describes the main genomic resources developed so far for wild tomato species; emphasizes that they are an important reservoir of favorable alleles for biotic and abiotic stress tolerance and fruit quality traits and, finally, recalls the concepts of ‘introgressomics’ and ‘rewilding’ as founding elements of future breeding strategies.

This is a preview of subscription content, log in via an institution to check access.

Access this chapter

Chapter
USD 29.95
Price excludes VAT (USA)
  • Available as PDF
  • Read on any device
  • Instant download
  • Own it forever
eBook
USD 169.00
Price excludes VAT (USA)
  • Available as EPUB and PDF
  • Read on any device
  • Instant download
  • Own it forever
Softcover Book
USD 219.99
Price excludes VAT (USA)
  • Compact, lightweight edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info
Hardcover Book
USD 219.99
Price excludes VAT (USA)
  • Durable hardcover edition
  • Dispatched in 3 to 5 business days
  • Free shipping worldwide - see info

Tax calculation will be finalised at checkout

Purchases are for personal use only

Institutional subscriptions

References

  • Aliberti A, Olivieri F, Graci S, Rigano MM, Barone A, Ruggieri V (2020) Genomic dissection of a wild region in a superior solanum pennellii introgression sub-line with high ascorbic acid accumulation in tomato fruit. Genes (basel) 11(8):847. https://doi.org/10.3390/genes11080847

    Article  CAS  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(10):536–538

    Article  CAS  Google Scholar 

  • Alseekh S, Tohge T, Wendenberg R, Scossa F, Omranian N, Li J, Kleessen S, Giavalisco P, Pleban T, Mueller-Roeber B, Zamir D, Nikoloski Z, Fernie AR (2015) Identification and mode of inheritance of quantitative trait loci for secondary metabolite abundance in tomato. Plant Cell 27(3):485. https://doi.org/10.1105/tpc.114.132266

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Andersen MM, Landes X, Xiang W, Anyshchenko A, Falhof J, Østerberg JT, Olsen LI, Edenbrandt AK, Vedel SE, Thorsen BJ, Sandøe P, Gamborg C, Kappel K, Palmgren MG (2015) Feasibility of new breeding techniques for organic farming. Trends Plant Sci 20(7):426–434. https://doi.org/10.1016/j.tplants.2015.04.011

    Article  CAS  PubMed  Google Scholar 

  • Ashrafi H, Kinkade M, Foolad MR (2009) A new genetic linkage map of tomato based on a Solanum lycopersicum× S. pimpinellifolium RIL population displaying locations of candidate pathogen response genes. Genome 52(11):935–956

    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(1):549–567

    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  Google Scholar 

  • Ballester A-R, Tikunov Y, Molthoff J, Grandillo S, Viquez-Zamora M, de Vos R, de Maagd RA, van Heusden S, Bovy AG (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). https://doi.org/10.3389/fpls.2016.01428

  • Bergau N, Bennewitz S, Syrowatka F, Hause G, Tissier A (2015) The development of type VI glandular trichomes in the cultivated tomato Solanum lycopersicum and a related wild species S. habrochaites. BMC Plant Biol 15(1):289. https://doi.org/10.1186/s12870-015-0678-z

  • Bolger A, Scossa F, Bolger ME, Lanz C, Maumus F, Tohge T, Quesneville H, Alseekh S, Sørensen I, Lichtenstein G, Fich EA, Conte M, Keller H, Schneeberger K, Schwacke R, Ofner I, Vrebalov J, Xu Y, Osorio S, Aflitos SA, Schijlen E, Jiménez-Goméz JM, Ryngajllo M, Kimura S, Kumar R, Koenig D, Headland LR, Maloof JN, Sinha N, van Ham RCHJ, Lankhorst RK, Mao L, Vogel A, Arsova B, Panstruga R, Fei Z, Rose JKC, Zamir D, Carrari F, Giovannoni JJ, Weigel D, Usadel B, Fernie AR (2014) The genome of the stress-tolerant wild tomato species Solanum pennellii. Nat Genet 46(9):1034–1038. https://doi.org/10.1038/ng.3046

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Calafiore R, Aliberti A, Ruggieri V, Olivieri F, Rigano MM, Barone A (2019) Phenotypic and molecular selection of a superior solanum pennellii introgression sub-line suitable for improving quality traits of cultivated tomatoes. Front Plant Sci 10(190). https://doi.org/10.3389/fpls.2019.00190

  • Canady MA, Ji Y, Chetelat RT (2006) Homeologous recombination in solanum lycopersicoides introgression lines of cultivated tomato. Genetics 174(4):1775–1788. https://doi.org/10.1534/genetics.106.065144

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Caruso G, Gomez LD, Ferriello F, Andolfi A, Borgonuovo C, Evidente A, Simister R, McQueen-Mason SJ, Carputo D, Frusciante L, Ercolano MR (2016) Exploring tomato Solanum pennellii introgression lines for residual biomass and enzymatic digestibility traits. BMC Genet 17(1):56. https://doi.org/10.1186/s12863-016-0362-9

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Causse M, Desplat N, Pascual L, Le Paslier M-C, Sauvage C, Bauchet G, Bérard A, Bounon R, Tchoumakov M, Brunel D, Bouchet J-P (2013) Whole genome resequencing in tomato reveals variation associated with introgression and breeding events. BMC Genomics 14(1):791. https://doi.org/10.1186/1471-2164-14-791

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Chetelat RT, Pertuzé RA, Faúndez L, Graham EB, Jones CM (2009) Distribution, ecology and reproductive biology of wild tomatoes and related nightshades from the Atacama Desert region of northern Chile. Euphytica 167(1):77–93. https://doi.org/10.1007/s10681-008-9863-6

    Article  Google Scholar 

  • Chetelat RT, Qin X, Tan M, Burkart-Waco D, Moritama Y, Huo X, Wills T, Pertuzé R (2019) Introgression lines of Solanum sitiens, a wild nightshade of the Atacama Desert, in the genome of cultivated tomato. Plant J 100(4):836–850. https://doi.org/10.1111/tpj.14460

    Article  CAS  PubMed  Google Scholar 

  • Coneva V, Frank MH, Balaguer MAdL, Li M, Sozzani R, Chitwood DH (2017) Genetic Architecture and molecular networks underlying leaf thickness in desert-adapted tomato Solanum pennellii. https://doi.org/10.1104/pp.17.00790

  • D’Agostino N, Tripodi P (2017) NGS-based genotyping, high-throughput phenotyping and genome-wide association studies laid the foundations for next-generation breeding in horticultural crops. Diversity 9(3):38

    Article  Google Scholar 

  • Dariva FD, Copati MGF, Pessoa HP, Alves FM, Dias FdO, Picoli EAdT, da Cunha FF, Nick C (2020) Evaluation of anatomical and physiological traits of Solanum pennellii Cor. associated with plant yield in tomato plants under water-limited conditions. Sci Reports 10(1):16052. https://doi.org/10.1038/s41598-020-73004-4

  • Darwin SC, Knapp S, Peralta IE (2003) Taxonomy of tomatoes in the Galápagos Islands: native and introduced species of Solanum section Lycopersicon (Solanaceae). Syst Biodivers 1(1):29–53

    Article  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 <em>Solanum chmielewskii</em> introgression line population. Plant Physiol 154(3):1128. https://doi.org/10.1104/pp.110.163030

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Ercolano MR, Sacco A, Ferriello F, D’Alessandro R, Tononi P, Traini A, Barone A, Zago E, Chiusano ML, Buson G (2014) Patchwork sequencing of tomato San Marzano and Vesuviano varieties highlights genome-wide variations. BMC Genomics 15(1):138

    Article  Google Scholar 

  • Eshed Y, Zamir D (1995) An introgression line population of Lycopersicon pennellii in the cultivated tomato enables the identification and fine mapping of yield-associated QTL. Genetics 141(3):1147–1162

    Article  CAS  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 U S A 97(9):4718–4723. https://doi.org/10.1073/pnas.97.9.4718

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Fridman E, Liu Y, 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 Genomics 266(5):821–826. https://doi.org/10.1007/s00438-001-0599-4

    Article  CAS  PubMed  Google Scholar 

  • Fridman E, Carrari F, Liu Y-S, Fernie AR, Zamir D (2004) Zooming in on a quantitative trait for tomato yield using interspecific introgressions. Science 305(5691):1786. https://doi.org/10.1126/science.1101666

    Article  CAS  PubMed  Google Scholar 

  • Gao L, Gonda I, Sun H, Ma Q, Bao K, Tieman DM, Burzynski-Chang EA, Fish TL, Stromberg KA, Sacks GL, Thannhauser TW, Foolad MR, Diez MJ, Blanca J, Canizares J, Xu Y, van der Knaap E, Huang S, Klee HJ, Giovannoni JJ, Fei Z (2019) The tomato pan-genome uncovers new genes and a rare allele regulating fruit flavor. Nat Genet 51(6):1044–1051. https://doi.org/10.1038/s41588-019-0410-2

    Article  CAS  PubMed  Google Scholar 

  • Gonda I, Ashrafi H, Lyon DA, Strickler SR, Hulse-Kemp AM, Ma Q, Sun H, Stoffel K, Powell AF, Futrell S, Thannhauser TW, Fei Z, Van Deynze AE, Mueller LA, Giovannoni JJ, Foolad MR (2019) Sequencing-based bin map construction of a tomato mapping population, facilitating high-resolution quantitative trait loci detection. Plant Genome 12(1):180010. https://doi.org/10.3835/plantgenome2018.02.0010

    Article  CAS  Google Scholar 

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

    Article  PubMed  PubMed Central  Google Scholar 

  • Igic B, Smith W, Robertson K, Schaal B, Kohn J (2007) Studies of self-incompatibility in wild tomatoes: I. S-allele diversity in solanum chilense Dun.(Solanaceae). Heredity 99(5):553–561

    Google Scholar 

  • Kilambi HV, Manda K, Rai A, Charakana C, Bagri J, Sharma R, Sreelakshmi Y (2017) Green-fruited solanum habrochaites lacks fruit-specific carotenogenesis due to metabolic and structural blocks. J Exp Bot 68(17):4803–4819. https://doi.org/10.1093/jxb/erx288

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Kim HT, Lee JM (2018) Organellar genome analysis reveals endosymbiotic gene transfers in tomato. PLoS ONE 13(9):e0202279–e0202279. https://doi.org/10.1371/journal.pone.0202279

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Lin T, Zhu G, Zhang J, Xu X, Yu Q, Zheng Z, Zhang Z, Lun Y, Li S, Wang X, Huang Z, Li J, Zhang C, Wang T, Zhang Y, Wang A, Zhang Y, Lin K, Li C, Xiong G, Xue Y, Mazzucato A, Causse M, Fei Z, Giovannoni JJ, Chetelat RT, Zamir D, Städler T, Li J, Ye Z, Du Y, Huang S (2014) Genomic analyses provide insights into the history of tomato breeding. Nat Genet 46(11):1220–1226. https://doi.org/10.1038/ng.3117

    Article  CAS  PubMed  Google Scholar 

  • Lin Y-P, Lu C-Y, Lee C-R (2020) The climatic association of population divergence and future extinction risk of Solanum pimpinellifolium. AoB Plants 12(2):plaa012

    Google Scholar 

  • Lippman ZB, Semel Y, Zamir D (2007) An integrated view of quantitative trait variation using tomato interspecific introgression lines. Curr Opin Genet Dev 17(6):545–552. https://doi.org/10.1016/j.gde.2007.07.007

    Article  CAS  PubMed  Google Scholar 

  • Muir CD, Pease JB, Moyle LC (2014) Quantitative genetic analysis indicates natural selection on leaf phenotypes across wild tomato species (&lt;em&gt;Solanum&lt;/em&gt; sect. &lt;em&gt;Lycopersicon&lt;/em&gt;; Solanaceae). Genetics 198(4):1629. https://doi.org/10.1534/genetics.114.169276

  • Palmgren MG, Edenbrandt AK, Vedel SE, Andersen MM, Landes X, Østerberg JT, Falhof J, Olsen LI, Christensen SB, Sandøe P, Gamborg C, Kappel K, Thorsen BJ, Pagh P (2015) Are we ready for back-to-nature crop breeding? Trends Plant Sci 20(3):155–164. https://doi.org/10.1016/j.tplants.2014.11.003

    Article  CAS  PubMed  Google Scholar 

  • Peralta IE, Knapp S, Spooner DM (2005) New species of wild tomatoes (solanum section Lycopersicon: Solanaceae) from Northern Peru. Syst Bot 30(2):424–434

    Article  Google Scholar 

  • Powell AF, Courtney LE, Schmidt MHW, Feder A, Vogel A, Xu Y, Lyon DA, Dumschott K, McHale M, Sulpice R, Bao K, Duhan A, Hallab A, Denton AK, Mueller LA, Alseekh S, Lie J, Martin C, Fernie AR, Hind SR, Martin GB, Fei Z, Giovannoni JJ, Strickler SR, Usadel B (2020) A &lt;em&gt;Solanum lycopersicoides&lt;/em&gt; reference genome facilitates biological discovery in tomato. bioRxiv:2020.2004.2016.039636. https://doi.org/10.1101/2020.04.16.039636

  • Prohens J, Gramazio P, Plazas M, Dempewolf H, Kilian B, Díez MJ, Fita A, Herraiz FJ, Rodríguez-Burruezo A, Soler S, Knapp S, Vilanova S (2017) Introgressiomics: a new approach for using crop wild relatives in breeding for adaptation to climate change. Euphytica 213(7):158. https://doi.org/10.1007/s10681-017-1938-9

    Article  Google Scholar 

  • Rambla JL, Medina A, Fernández-del-Carmen A, Barrantes W, Grandillo S, Cammareri M, López-Casado G, Rodrigo G, Alonso A, García-Martínez S, Primo J, Ruiz JJ, Fernández-Muñoz R, Monforte AJ, Granell A (2017) Identification, introgression, and validation of fruit volatile QTLs from a red-fruited wild tomato species. J Exp Bot 68(3):429–442. https://doi.org/10.1093/jxb/erw455

    Article  CAS  PubMed  Google Scholar 

  • Razali R, Bougouffa S, Morton MJL, Lightfoot DJ, Alam I, Essack M, Arold ST, Kamau AA, Schmöckel SM, Pailles Y, Shahid M, Michell CT, Al-Babili S, Ho YS, Tester M, Bajic VB, Negrão S (2018) The genome sequence of the wild tomato solanum pimpinellifolium provides insights into salinity tolerance. Front Plant Sci 9(1402). https://doi.org/10.3389/fpls.2018.01402

  • Ruggieri V, Sacco A, Calafiore R, Frusciante L, Barone A (2015) Dissecting a QTL into candidate genes highlighted the key role of pectinesterases in regulating the ascorbic acid content in tomato fruit. Plant Genome 8(2):plantgenome2014.2008.0038. https://doi.org/10.3835/plantgenome2014.08.0038

  • 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. https://doi.org/10.1007/s11032-012-9763-2

    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 Genomics 18(1):430. https://doi.org/10.1186/s12864-017-3822-3

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Schauer N, Semel Y, Roessner U, Gur A, Balbo I, Carrari F, Pleban T, Perez-Melis A, Bruedigam C, Kopka J, Willmitzer L, Zamir D, Fernie AR (2006) Comprehensive metabolic profiling and phenotyping of interspecific introgression lines for tomato improvement. Nat Biotechnol 24(4):447–454. https://doi.org/10.1038/nbt1192

    Article  CAS  PubMed  Google Scholar 

  • Schmidt MHW, Vogel A, Denton AK, Istace B, Wormit A, van de Geest H, Bolger ME, Alseekh S, Maß J, Pfaff C, Schurr U, Chetelat R, Maumus F, Aury J-M, Koren S, Fernie AR, Zamir D, Bolger AM, Usadel B (2017) De novo assembly of a new Solanum pennellii accession using nanopore sequencing. Plant Cell 29(10):2336. https://doi.org/10.1105/tpc.17.00521

  • Sifres A, Blanca J, Nuez F (2011) Pattern of genetic variability of Solanum habrochaites in its natural area of distribution. Genet Resour Crop Evol 58(3):347–360. https://doi.org/10.1007/s10722-010-9578-0

    Article  Google Scholar 

  • Spooner DM, Peralta IE, Knapp S (2005) Comparison of AFLPs with other markers for phylogenetic inference in wild tomatoes [Solanum L. section Lycopersicon (Mill.) Wettst.]. Taxon 54(1):43–61

    Google Scholar 

  • Stam R, Nosenko T, Hörger AC, Stephan W, Seidel M, Kuhn JMM, Haberer G, Tellier A (2019) The &lt;em&gt;de Novo&lt;/em&gt; reference genome and transcriptome assemblies of the wild tomato species &lt;em&gt;Solanum chilense&lt;/em&gt; highlights birth and death of NLR genes between tomato species. G3: Genes|Genomes|Genetics 9(12):3933. https://doi.org/10.1534/g3.119.400529

  • The 100 Tomato Genome Sequencing Consortium (2014) Exploring genetic variation in the tomato (Solanum section Lycopersicon) clade by whole-genome sequencing. Plant J 80(1):136–148

    Article  CAS  Google Scholar 

  • Tieman D, Zhu G, Resende MFR, Lin T, Nguyen C, Bies D, Rambla JL, Beltran KSO, Taylor M, Zhang B, Ikeda H, Liu Z, Fisher J, Zemach I, Monforte A, Zamir D, Granell A, Kirst M, Huang S, Klee H (2017) A chemical genetic roadmap to improved tomato flavor. Science 355(6323):391. https://doi.org/10.1126/science.aal1556

    Article  CAS  PubMed  Google Scholar 

  • Tomato Genome Consortium (2012) The tomato genome sequence provides insights into fleshy fruit evolution. Nature 485(7400):635

    Article  Google Scholar 

  • Tranchida-Lombardo V, Aiese Cigliano R, Anzar I, Landi S, Palombieri S, Colantuono C, Bostan H, Termolino P, Aversano R, Batelli G (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(2):149–160

    Article  CAS  Google Scholar 

  • Wang X, Gao L, Jiao C, Stravoravdis S, Hosmani PS, Saha S, Zhang J, Mainiero S, Strickler SR, Catala C, Martin GB, Mueller LA, Vrebalov J, Giovannoni JJ, Wu S, Fei Z (2020) Genome of Solanum pimpinellifolium provides insights into structural variants during tomato breeding. bioRxiv:2020.2006.2017.157859. https://doi.org/10.1101/2020.06.17.157859

  • Yang S, Yu Q, Wang B, Yang T, Li N, Tang Y, Aisimutuola P, Wang Q, Xu J, Gao J (2016) Identification of QTLs for red fruit firmness using the wild tomato species Solanum pennellii LA716 introgression lines. Plant Breed 135(6):728–734. https://doi.org/10.1111/pbr.12423

    Article  CAS  Google Scholar 

Download references

Author information

Authors and Affiliations

Authors

Corresponding author

Correspondence to Nunzio D’Agostino .

Editor information

Editors and Affiliations

Rights and permissions

Reprints and permissions

Copyright information

© 2021 Springer Nature Switzerland AG

About this chapter

Check for updates. Verify currency and authenticity via CrossMark

Cite this chapter

D’Agostino, N., Barone, A., Rigano, M.M. (2021). Knowledge on the Genomes of Wild Tomato Species is the Key to Unlocking Their Breeding Potential. In: Carputo, D., Aversano, R., Ercolano, M.R. (eds) The Wild Solanums Genomes. Compendium of Plant Genomes. Springer, Cham. https://doi.org/10.1007/978-3-030-30343-3_7

Download citation

Publish with us

Policies and ethics