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Phenotypic diversity and association mapping for fruit quality traits in cultivated tomato and related species

Jiaxin Xu 1, 2 Nicolas Ranc 1 Stephane Munos 1 Sophie Rolland 1 Jean-Paul Bouchet 1 Nelly Desplat 1 Marie-Christine Le Paslier 3, 4 Yan Liang 2 Dominique Brunel 3, 4 Mathilde Causse 1
1 GAFL - Génétique et Amélioration des Fruits et Légumes
2 Northwest A&F University
3 EPGV - Etude du Polymorphisme des Génomes Végétaux
4 CEA - Commissariat à l'énergie atomique et aux énergies alternatives
Abstract : Association mapping has been proposed as an efficient approach to assist in the identification of the molecular basis of agronomical traits in plants. For this purpose, we analyzed the phenotypic and genetic diversity of a large collection of tomato accessions including 44 heirloom and vintage cultivars (Solanum lycopersicum), 127 S. lycopersicum var. cerasiforme (cherry tomato) and 17 Solanum pimpinellifolium accessions. The accessions were genotyped using a SNPlex (TM) assay of 192 SNPs, among which 121 were informative for subsequent analysis. Linkage disequilibrium (LD) of pairwise loci and population structure were analyzed, and the association analysis between SNP genotypes and ten fruit quality traits was performed using a mixed linear model. High level of LD was found in the collection at the whole genome level. It was lower when considering only the 127 S. lycopersicum var. cerasiforme accessions. Genetic structure analysis showed that the population was structured into two main groups, corresponding to cultivated and wild types and many intermediates. The number of associations detected per trait varied, according to the way the structure was taken into account, with 0-41 associations detected per trait in the whole collection and a maximum of four associations in the S. lycopersicum var. cerasiforme accessions. A total of 40 associations (30 %) were co-localized with previously identified quantitative trait loci. This study thus showed the potential and limits of using association mapping in tomato populations.
Keywords : GENOME-WIDE ASSOCIATION SINGLE-NUCLEOTIDE POLYMORPHISMS FRESH-MARKET TOMATO LINKAGE DISEQUILIBRIUM ANALYSIS SOLANUM-LYCOPERSICON ARABIDOPSIS-THALIANA GENUS LYCOPERSICON
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https://hal.inrae.fr/hal-02651895
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Submitted on : Friday, May 29, 2020 - 5:51:21 PM
Last modification on : Tuesday, December 22, 2020 - 6:04:02 PM

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Jiaxin Xu, Nicolas Ranc, Stephane Munos, Sophie Rolland, Jean-Paul Bouchet, et al.. Phenotypic diversity and association mapping for fruit quality traits in cultivated tomato and related species. TAG Theoretical and Applied Genetics, Springer Verlag, 2013, 126 (3), pp.567 - 581. ⟨10.1007/s00122-012-2002-8⟩. ⟨hal-02651895⟩

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