Theoretical and Applied Genetics

, Volume 130, Issue 5, pp 875–889 | Cite as

Use of modern tomato breeding germplasm for deciphering the genetic control of agronomical traits by Genome Wide Association study

  • Guillaume Bauchet
  • Stéphane Grenier
  • Nicolas Samson
  • Julien Bonnet
  • Laurent Grivet
  • Mathilde Causse
Original Article

Abstract

Key message

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.

Abstract

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.

Supplementary material

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Supplementary material 1 (XLSX 50 KB)
122_2017_2857_MOESM2_ESM.pptx (20.2 mb)
Supplementary material 2 (PPTX 20643 KB)

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Copyright information

© Springer-Verlag Berlin Heidelberg 2017

Authors and Affiliations

  • Guillaume Bauchet
    • 1
    • 2
    • 3
  • Stéphane Grenier
    • 1
  • Nicolas Samson
    • 1
  • Julien Bonnet
    • 1
  • Laurent Grivet
    • 1
  • Mathilde Causse
    • 2
  1. 1.Syngenta SeedsSaint SauveurFrance
  2. 2.INRA, UR1052, Centre de Recherche PACA, GAFLMontfavet CedexFrance
  3. 3.Boyce Thompson InstituteCornell UniversityIthacaUSA

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