Use of modern tomato breeding germplasm for deciphering the genetic control of agronomical traits by Genome Wide Association study
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A panel of 300 tomato accessions including breeding materials was built and characterized with >11,000 SNP. A population structure in six subgroups was identified. Strong heterogeneity in linkage disequilibrium and recombination landscape among groups and chromosomes was shown. GWAS identified several associations for fruit weight, earliness and plant growth.
Genome-wide association studies (GWAS) have become a method of choice in quantitative trait dissection. First limited to highly polymorphic and outcrossing species, it is now applied in horticultural crops, notably in tomato. Until now GWAS in tomato has been performed on panels of heirloom and wild accessions. Using modern breeding materials would be of direct interest for breeding purpose. To implement GWAS on a large panel of 300 tomato accessions including 168 breeding lines, this study assessed the genetic diversity and linkage disequilibrium decay and revealed the population structure and performed GWA experiment. Genetic diversity and population structure analyses were based on molecular markers (>11,000 SNP) covering the whole genome. Six genetic subgroups were revealed and associated to traits of agronomical interest, such as fruit weight and disease resistance. Estimates of linkage disequilibrium highlighted the heterogeneity of its decay among genetic subgroups. Haplotype definition allowed a fine characterization of the groups and their recombination landscape revealing the patterns of admixture along the genome. Selection footprints showed results in congruence with introgressions. Taken together, all these elements refined our knowledge of the genetic material included in this panel and allowed the identification of several associations for fruit weight, plant growth and earliness, deciphering the genetic architecture of these complex traits and identifying several new loci useful for tomato breeding.
KeywordsLinkage Disequilibrium Genetic Group Fruit Weight Linkage Disequilibrium Decay Best Linear Unbiased Predictor
We thank the CRBLeg group in INRA for providing accessions and Stephane Deville and Sandrine Paulin for genotyping. Syngenta and Association Française pour la Recherche et la Technologie (ANRT) funded this work.
Compliance with ethical standards
Conflict of interest
Authors declared no conflict of interest in the authorship and publication of this document.
- Bastian M, Heymann S, Jacomy M (2009) Gephi: an open source software for exploring and manipulating networks. ICWSM 8:362Google Scholar
- Bates DM, Watts DG (2008) Nonlinear regression analysis and its applications. Wiley, HobokenGoogle Scholar
- Bauchet G, Causse M (2012) Genetic diversity in tomato (Solanum lycopersicum) and its wild relatives. In: Genetic diversity in plants. PMC: InTechGoogle Scholar
- Chakrabarti M, Zhang N, Sauvage C, Munos S, Blanca J, Canizares J, Diez MJ, Schneider R, Mazurek M, McClead J, Causse M, van der Knaap E (2013) A cytochrome P450 CYP78A regulates a domestication trait in tomato (Solanum lycopersicum). Proc Natl Acad Sci USA PNAS 110(42):17125–17130PubMedCrossRefGoogle Scholar
- Chen A-L, Liu C-Y, Chen C-H, Wang J-F, Liao Y-C, Chang C-H, Tsai M-H, Hwu K-K, Chen K-Y (2014) Reassessment of QTLs for late blight resistance in the tomato accession L3708 using a restriction site associated DNA (RAD) linkage map and highly aggressive isolates of Phytophthora infestans. PLoS One 9(5):e96417PubMedPubMedCentralCrossRefGoogle Scholar
- Fernandez-Pozo N, Menda M, Edwards JD, Saha S, Tecle IY, Strickler SR, Bombarely A, Fisher-York T, Pujar A, Foerster H, Yan A, Mueller LA (2014) The Sol Genomics Network (SGN)—from genotype to phenotype to breeding. Nucl Acids Res. doi: 10.1093/nar/gku1195 (first published online 26 Nov 2014) PubMedPubMedCentralGoogle Scholar
- Koenig D, Jiménez-Gómez JM, Kimura S, Fulop D, Chitwood DH, Headland LR, Kumar R, Covington MF, Devisetty UK, Tat AV, Tohge T, Bolger A, Schneeberger K, Ossowski S, Lanz C, Xiong G, Taylor-Teeples M, Brady SM, Pauly M, Weigel D, Usadel B, Fernie AR, Peng J, Sinha NR, Maloof JN (2013) Comparative transcriptomics reveals patterns of selection in domesticated and wild tomato. Proc Natl Acad Sci 110:2655–2662CrossRefGoogle Scholar
- Labate J, Grandillo S, Fulton T, Muños S, Caicedo A, Peralta I, Ji Y, Chetelat R, Scott JW, Gonzalo MJ, Francis D, Yang W, van der Knaap E, Baldo AM, Smith-White B, Mueller LA, Prince JP, Blanchard NE, Storey DB, Stevens MR, Robbins MD, Fen Wang J, Liedl BE, O’Connell MA, Stommel JR, Aoki K, Iijima Y, Slade, Hurst SR, Loeffler D, Steine MN, Vafeados D, McGuire C, Freeman C, Amen A, Goodstal J, Facciotti D, Van Eck J, Causse M (2007) 1 Tomato. In: Kole C (ed) Genome mapping and molecular breeding in plants, volume 5, vegetables. Springer-Verlag, Berlin, p 11–135Google Scholar
- Ranc N, Muños S, Xu J, Le Paslier MC, Chauveau A, Bounon R, Rolland S, Bouchet JP, Brunel D, Causse M (2012) Genome-wide association mapping in tomato (Solanum lycopersicum) is possible using genome admixture of Solanum lycopersicum var. cerasiforme. G3 2:853–864PubMedPubMedCentralCrossRefGoogle Scholar
- Rincent R, Moreau L, Monod H, Kuhn E, Melchinger AE, Malvar RA, Moreno-Gonzalez J, Nicolas S, Madur D, Combes V, Dumas F, Altmann T, Brunel D, Ouzunova M, Flament P, Dubreuil P, Charcosset A, Mary-Huard T (2014) Recovering power in association mapping panels with variable levels of linkage disequilibrium. Genetics 197(1):375–387PubMedPubMedCentralCrossRefGoogle Scholar
- Sarah G, Homa F, Pointet S, Contreras S, Sabot F, Nabholz B, Santoni S, Sauné L, Ardisson M, Chantret N, Sauvage C, Tregear J, Jourda C, Pot D, Vigouroux Y, Chair H, Scarcelli N, Billot C, Yahiaoui N, Bacilieri R, Khadari B, Boccara M, Barnaud A, Péros J-P, Labouisse J-P, Pham J-L, David J, Glémin S, Ruiz M (2016) A large set of 26 new reference transcriptomes dedicated to comparative population genomics in crops and wild relatives. Mol Ecol Resour. doi: 10.1111/1755-0998.12587 PubMedGoogle Scholar