Skip to main content

Advertisement

SpringerLink
Log in

Tomato near isogenic lines to unravel the genetic diversity of S. pimpinellifolium LA0722 for fruit quality and shelf life breeding

  • Published:
Euphytica Aims and scope Submit manuscript

Abstract

The introgression of genes from the wild species S. pimpinellifolium has the potential to improve tomato commercial varieties for numerous fruit quality traits. One of particular interest for fresh-market tomatoes is long shelf life (SL). Twenty-two near isogenic lines (NILs) were developed in three to four backcrosses using S. pimpinellifolium accession LA0722 as the donor parent, based on phenotypic selection for long SL and using a set of 28 SSRs for marker assisted selection. A total of 30 QTLs for fruit quality were found and 18 were subsequently validated in previous generations. A two year trial of the NILs homozygous for the LA0722 introgressions showed several novel QTLs. Fruit quality QTLs revealed an increased effect promoted by LA0722 alleles. A SL QTL was found on chromosome 9 and was consistent both years. A wild introgression on chromosome 3 showed a stable QTL for increased firmness and for yellow fruits. Therefore, the wild introgressions provide a source of variation with positive effects in fruit traits of commercial value. While obtaining new varieties, this strategy provided an effective method that integrates the QTL analysis and the prediction of positive alleles in wild germplasm.

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

Access this article

Log in via an institution

Subscribe and save

Springer+ Basic
$34.99 /Month
  • Get 10 units per month
  • Download Article/Chapter or eBook
  • 1 Unit = 1 Article or 1 Chapter
  • Cancel anytime
Subscribe now

Buy Now

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4

Similar content being viewed by others

Availability of data and material

Data supporting the findings of this work are available within this published article and its Electronic Supplementary Material.

References

  • Barrantes W, López-Casado G, García-Martínez S et al (2016) Exploring new alleles involved in tomato fruit quality in an introgression line library of Solanum pimpinellifolium. Front Plant Sci 7:1172

    PubMed  PubMed Central  Google Scholar 

  • Bates D, Mächler M, Bolker B, Wlaker S (2015) Fitting linear mixed-effects models using lme4. J Stat Softw 67:1–48

    Google Scholar 

  • Bauchet G, Causse M (2012) Genetic diversity in tomato (Solanum lycopersicum) and its wild relatives. In: Caliskan M (ed) Genetic diversity in plants. Intech, Rijeka, pp 133–162

    Google Scholar 

  • Bauchet G, Grenier S, Samson N et al (2017) Identification of major loci and genomic regions controlling acid and volatile content in tomato fruit: implications for flavor improvement. New Phytol 215:624–641

    CAS  PubMed  Google Scholar 

  • Bernacchi D, Beck-Bunn T, Emmatty D et al (1998) Advanced backcross QTL analysis of 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 97:170–180

    CAS  Google Scholar 

  • Blanca J, Montero-Pau J, Sauvage C et al (2015) Genomic variation in tomato, from wild ancestors to contemporary breeding accessions. BMC Genomics 16:257

    PubMed  PubMed Central  Google Scholar 

  • Brummell DA, Harpster MH (2001) Cell wall metabolism in fruit softening and quality and its manipulation in transgenic plants. Plant Mol Biol 47:311–340

    CAS  PubMed  Google Scholar 

  • Cambiaso V, Gimenez M, Pereira da Costa J et al (2019) Selected genome regions for fruit weight and shelf life in tomato RILs discernible by markers based on genomic sequence information. Breed Sci 69:447–454

    PubMed  PubMed Central  Google Scholar 

  • Casals J, Rivera A, Sabat J et al (2019) Cherry and fresh market tomatoes: differences in chemical, morphological, and sensory traits and their implications for consumer acceptance. Agronomy 9:9

    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

    CAS  Google Scholar 

  • Causse M, Duffe P, Gomez M et al (2004) A genetic map of candidate genes and QTLs involved in tomato fruit size and composition. J Exp Bot 55:1671–1685

    CAS  PubMed  Google Scholar 

  • Celik I, Gurbuz N, Uncu AT et al (2017) Genome-wide SNP discovery and QTL mapping for fruit quality traits in inbred backcross lines (IBLs) of Solanum pimpinellifolium using genotyping by sequencing. BMC Genomics 18:1

    PubMed  PubMed Central  Google Scholar 

  • Chaïb J, Lecomte L, Buret M, Causse M (2006) Stability over genetic backgrounds, generations and years of quantitative trait locus (QTLs) for organoleptic quality in tomato. Theor Appl Genet 112:934–944

    PubMed  Google Scholar 

  • Chen F, Foolad M, Hyman J et al (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

    CAS  Google Scholar 

  • Collard BCY, Jahufer MZZ, Brouwer JB, Pang ECK (2005) An introduction to markers, quantitative trait loci (QTL) mapping and marker-assisted selection for crop improvement: the basic concepts. Euphytica 142:169–196

    CAS  Google Scholar 

  • Cong B, Barrero L, Tanksley S (2008) Regulatory change in YABBY-like transcription factor led to evolution of extreme fruit size during tomato domestication. Nat Genet 40:800–804

    CAS  PubMed  Google Scholar 

  • Doganlar S, Frary A, Ku H, Tanksley S (2002) Mapping quantitative trait loci in inbred backcross lines of Lycopersicon pimpinellifolium (LA1589). Genome 45:1189–1202

    CAS  PubMed  Google Scholar 

  • Eshed Y, Zamir D (1994) Introgessions from Lycopersicon pennellii can improve the soluble solids yield of tomato hybrids. Theor Appl Genet 88:891–897

    CAS  PubMed  Google Scholar 

  • Eshed Y, Zamir D (1995) An introgression line population. Genetics 141:1147–1162

    CAS  PubMed  PubMed Central  Google Scholar 

  • Foolad MR, Sharma A (2005) Molecular markers as selection tools in tomato breeding. Acta Hortic 695:225–240

    Google Scholar 

  • Frary A, Doganlar S, Frampton A et al (2003) Fine mapping of quantitative trait loci for improved fruit characteristics from Lycopersicon chmielewskii chromosome 1. Genome 46:235–243

    CAS  PubMed  Google Scholar 

  • Fridman E, Carrari F, Liu Y et al (2004) Zooming in on a quantitative interspecific introgressions. Science 305:1786–1789

    CAS  PubMed  Google Scholar 

  • Fulton T, Beck-Bunn T, Emmatty D et al (1997) QTL analysis of an advanced backcross of Lycopersicon peruvianum to the cultivated tomato and comparisons with QTL found in other wild species. Theor Appl Genet 95:881–894

    CAS  Google Scholar 

  • Fulton T, Bucheli P, Voirol E et al (2002) Quantitative trait loci (QTL) affecting sugars, organic acids and other biochemical properties possibly contributing to flavor, identified in four advanced backcross populations of tomato. Euphytica 127:163–177

    CAS  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

    CAS  PubMed  Google Scholar 

  • Giovannoni J (2004) Genetic regulation of fruit development and ripening. Plant Cell 16:S170–S180

    CAS  PubMed  PubMed Central  Google Scholar 

  • Green G, Pereira da Costa J, Cambiaso V et al (2016) Single and joint effect of the basal region of chromosome 2 and centromeric region of chromosome 8 on morphological and fruit quality traits in tomato. Euphytica 210:327–339

    CAS  Google Scholar 

  • Hajjar R, Hodgkin T (2007) The use of wild relatives in crop improvement: a survey of developments over the last 20 years. Euphytica 156:1–13

    Google Scholar 

  • Hobson G, Grierson D (1993) Tomato. In: Seymour G, Taylor J, Tucker G (eds) Biochemistry of fruit ripening. Chapman and Hall, London, pp 405–442

    Google Scholar 

  • Ikeda H, Hiraga M, Shirasawa K et al (2013) Analysis of a tomato introgression line, IL8-3, with increased Brix content. Sci Hortic 153:103–108

    CAS  Google Scholar 

  • Ishii T, Araki M (2016) Consumer acceptance of food crops developed by genome editing. Plant Cell Rep 35:1507–1518

    CAS  PubMed  Google Scholar 

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

    CAS  PubMed  Google Scholar 

  • Koka C, Cerny R, Gardner R et al (2000) A putative role for the tomato genes DUMPY and CURL-3 in brassinosteroid biosynthesis and response. Plant Physiol 122:85–98

    CAS  PubMed  PubMed Central  Google Scholar 

  • Labate J, Grandillo S, Fulton T et al (2007) Tomato. In: Kole C (ed) Genome mapping and molecular breeding in plants. Springer, Berlin, pp 1–96

    Google Scholar 

  • Lippman Z, Tanksley S (2001) Dissecting the genetic pathway to extreme fruit size in tomato using a cross between the small-fruited wild species Lycopersicon pimpinellifolium and L. esculentum var. Giant Heirloom. Genetics 158:413–422

    CAS  PubMed  PubMed Central  Google Scholar 

  • Liu B (1998) Statistical genomics: linkage, mapping, and QTL analysis. CRC Press, Boca Raton

    Google Scholar 

  • Manning K, Tör M, Poole M et al (2006) A naturally occurring epigenetic mutation in a gene encoding an SBP-box transcription factor inhibits tomato fruit ripening. Nat Genet 38:948–952

    CAS  PubMed  Google Scholar 

  • Meli VS, Ghosh S, Prabha TN et al (2010) Enhancement of fruit shelf life by suppressing N-glycan processing enzymes. PNAS 107:2413–2418

    CAS  PubMed  Google Scholar 

  • Miedes E, Lorences EP (2009) Xyloglucan endotransglucosylase/hydrolases (XTHs) during tomato fruit growth and ripening. J Plant Physiol 166:489–498

    CAS  PubMed  Google Scholar 

  • Monforte A, Tanksley S (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

    CAS  Google Scholar 

  • Mu Q, Huang Z, Chakrabarti M et al (2017) Fruit weight is controlled by Cell Size Regulator encoding a novel protein that is expressed in maturing tomato fruits. PLoS Genet 13:e1006930

    PubMed  PubMed Central  Google Scholar 

  • Nakano H, Sasaki K, Mine Y et al (2016) Quantitative trait loci (QTL) controlling plant architecture traits in a Solanum lycopersicum × S. pimpinellifolium cross. Euphytica 211:353–367

    CAS  Google Scholar 

  • Peralta I, Spooner D, Knapp S (2008) Taxonomy of wild tomatoes and their relatives (Solanum sect. Lycopersicoides, sect. Juglandifolia, sect. Lycopersicon; Solanaceae). Syst Bot Monogr 84:1–186

    Google Scholar 

  • Pereira da Costa J, Rodríguez G, Pratta G et al (2013) QTL detection for fruit shelf life and quality traits across segregating populations of tomato. Sci Hortic 156:47–53

    Google Scholar 

  • Pratta G, Zorzoli R, Picardi LA (2003) Diallel analysis of production traits among domestic, exotic and mutant germplasms of Lycopersicon. Genet Mol Res 2:206–213

    PubMed  Google Scholar 

  • Pratta G, Rodríguez G, Zorzoli R et al (2011) Molecular markers detect stable genomic regions underlying tomato fruit shelf life and weight. Crop Breed Appl Biotechnol 11:157–164

    Google Scholar 

  • Priyadarshan P (2019) Backcross breeding. Plant breeding: classical to modern. Springer, Singapor, pp 203–221

    Google Scholar 

  • R Core Team (2017) R: a language and environment for statistical computing. https://www.R-project.org/

  • Razifard H, Ramos A, Della Valle AL et al (2020) Genomic evidence for complex domestication history of the cultivated tomato in Latin America. Mol Biol Evol 37:1118–1132

    PubMed  PubMed Central  Google Scholar 

  • Rodríguez G, Pratta G, Zorzoli R, Picardi L (2006) Recombinant lines obtained from an interspecific cross between Lycopersicon species selected by fruit weight and fruit shelf life. J Am Soc Hortic Sci 131:651–656

    Google Scholar 

  • Rodríguez G, Liberatti D, Pratta G et al (2010) Inheritance of shelf life and other quality traits of tomato fruit estimated from F1’s, F2’s and backcross generations derived from standard cultivar, nor homozygote and wild cherry tomato. Euphytica 176:137–147

    Google Scholar 

  • Saladié M, Rose JKC, Cosgrove DJ, Catalá C (2006) Characterization of a new xyloglucan endotransglucosylase/hydrolase (XTH) from ripening tomato fruit and implications for the diverse modes of enzymic action. Plant J 47:282–295

    PubMed  Google Scholar 

  • Schaffer AA, Levin I, Oguz I et al (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

    CAS  Google Scholar 

  • Schauer N, Semel Y, Roessner U et al (2006) Comprehensive metabolic profiling and phenotyping of interspecific introgression lines for tomato improvement. Nat Biotechnol 24:447–454

    CAS  PubMed  Google Scholar 

  • Schmidt SM, Belisle M, Frommer WB (2020) The evolving landscape around genome editing in agriculture: many countries have exempted or move to exempt forms of genome editing from GMO regulation of crop plants. EMBO Rep 21:e50680

    CAS  PubMed  PubMed Central  Google Scholar 

  • Semel Y, Nissenbaum J, Menda N et al (2006) Overdominant quantitative trait loci for yield and fitness in tomato. Proc Natl Acad Sci USA 103:12981–12986

    CAS  PubMed  Google Scholar 

  • Seymour GB, Chapman NH, Chew BL, Rose JKC (2013) Regulation of ripening and opportunities for control in tomato and other fruits. Plant Biotechnol J 11:269–278

    CAS  PubMed  Google Scholar 

  • Shapiro S, Wilk M (1965) An analysis of variance test for normality (complete samples). Biometrika 52:591–611

    Google Scholar 

  • Song X, Xu L, Yu J et al (2019) Genome-wide characterization of the cellulose synthase gene superfamily in Solanum lycopersicum. Gene 688:71–83

    CAS  PubMed  Google Scholar 

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

    CAS  PubMed  Google Scholar 

  • Tanksley S (1993) Mapping polygenes. Annu Rev Genet 27:205–233

    CAS  PubMed  Google Scholar 

  • Tieman D, Zhu G, Resende MF et al (2017) A chemical genetic roadmap to improved tomato flavor. Science 355:391–394

    CAS  PubMed  Google Scholar 

  • Uluisik S, Chapman NH, Smith R et al (2016) Genetic improvement of tomato by targeted control of fruit softening. Nat Biotechnol 34:950–952

    CAS  PubMed  Google Scholar 

  • Vrebalov J, Ruezinsky D, Padmanabhan V et al (2002) A MADS-box gene necessary for fruit ripening at the tomato ripening-inhibitor (rin) locus. Science 296:343–346

    CAS  PubMed  Google Scholar 

  • Wang R, da Rocha Tavano EC, Lammers M et al (2019) Re-evaluation of transcription factor function in tomato fruit development and ripening with CRISPR/Cas9-mutagenesis. Sci Rep 9:1696

    PubMed  PubMed Central  Google Scholar 

  • Yang L, Huang W, Xiong F et al (2017) Silencing of SlPL, which encodes a pectate lyase in tomato, confers enhanced fruit firmness, prolonged shelf-life and reduced susceptibility to grey mould. Plant Biotechnol J 15:1544–1555

    CAS  PubMed  PubMed Central  Google Scholar 

  • Yu QH, Wang B, Li N et al (2017) CRISPR/Cas9-induced targeted mutagenesis and gene replacement to generate long-shelf life tomato lines. Sci Rep 7:11874

    PubMed  PubMed Central  Google Scholar 

  • Zorzoli R, Pratta G, Picardi L (2000) Variabilidad genética para la vida postcosecha y el peso de los frutos en tomate para familias F3 de un híbrido interespecífico. Pesqui Agropecu Bras 35:2423–2427

    Google Scholar 

Download references

Acknowledgements

This work was supported by Agencia Nacional de Promoción Científica y Tecnológica PICT2015-0424, Consejo Nacional de Investigaciones Científicas y Técnicas PIP008-2015-2017 GI and PUE0043. We thank the Tomato Genetic Resources Center, University of California, Davis, California, USA for kindly providing seeds of the wild accession LA0722 of S. pimpinellifolium and Estación Experimental Agropecuaria - Instituto Nacional de Tecnología Agropecuaria Cerrillos, Salta, Argentina for kindly providing seeds of the Caimanta cultivar. We thank Prof. Trad. Virginia Cattolica for the language editing.

Funding

This work was supported by Agencia Nacional de Promoción Científica y Tecnológica PICT2015-0424, Consejo Nacional de Investigaciones Científicas y Técnicas PIP008-2015-2017 GI and PUE0043.

Author information

Author notes

  1. Di Giacomo and Luciani did equal contribution to the manuscript.

Authors and Affiliations

  1. Instituto de Investigaciones en Ciencias Agrarias de Rosario (IICAR-CONICET-UNR), Campo Experimental Villarino, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Zavalla, S2125ZAA, Santa Fe, Argentina

    Melisa Di Giacomo, Marianela Dana Luciani, Vladimir Cambiaso, Gustavo Rubén Rodríguez & Javier Hernán Pereira da Costa

  2. Consejo de Investigaciones de la Universidad Nacional de Rosario CIUNR, Santa Fe, Argentina

    Roxana Zorzoli

  3. Cátedra de Genética, Facultad de Ciencias Agrarias, Universidad Nacional de Rosario, Zavalla, S2125ZAA, Santa Fe, Argentina

    Vladimir Cambiaso, Roxana Zorzoli, Gustavo Rubén Rodríguez & Javier Hernán Pereira da Costa

Authors
  1. Melisa Di Giacomo
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Marianela Dana Luciani
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Vladimir Cambiaso
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Roxana Zorzoli
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Gustavo Rubén Rodríguez
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Javier Hernán Pereira da Costa
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

Melisa Di Giacomo and Marianela D. Luciani: first draft of the manuscript, plant material development, molecular and phenotype characterization, formal analysis; Vladimir Cambiaso: review and editing, molecular and phenotype characterization; Roxana Zorzoli: review and editing, conception and design, formal analysis; Gustavo R. Rodríguez: review and editing, conception and design, formal analysis, funding acquisition; Javier H. Pereira da Costa: review and editing, plant material development, conception and design, formal analysis, funding acquisition.

Corresponding author

Correspondence to Javier Hernán Pereira da Costa.

Ethics declarations

Conflict of interest

The authors declare that they have no conflict of interest.

Additional information

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Electronic supplementary material

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Di Giacomo, M., Luciani, M.D., Cambiaso, V. et al. Tomato near isogenic lines to unravel the genetic diversity of S. pimpinellifolium LA0722 for fruit quality and shelf life breeding. Euphytica 216, 126 (2020). https://doi.org/10.1007/s10681-020-02649-z

Download citation

  • Received:

  • Accepted:

  • Published:

  • DOI: https://doi.org/10.1007/s10681-020-02649-z

Keywords

Search

Navigation