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

Abstract

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.

Association and Genetic Identification of Loci for Four Fruit Traits in Tomato Using InDel Markers

“…Third, we used a relatively high stringency for association analysis in this study. The p -values of 1.19–1.30 × 10 −4 used here were much lower than 0.005 used in other studies (Xu et al, 2013; Zhang et al, 2016; Bauchet et al, 2017), which could decrease the power of association analysis. Fourth, it has been reported that the genome of cherry tomato accessions is a mosaic composed of polymorphisms of S. pimpinellifolium and S. lycopersicum (Blanca et al, 2015), which might also cause the failure of association mapping.…”

“…cerasiforme , and 865.7 kb in S. lycopersicum accessions (Lin et al, 2014). A recent study analyzing 300 tomato accessions with 11000 SNPs suggests that the LD decay ranges from 0.2 cM (73 kb) to 49 cM (47 Mb) at chromosomal level (Bauchet et al, 2017). In this study, the LD decay range from 3.0 to 47.2 Mb on 12 chromosomes with an overall of 28.5 Mb in the whole genome, which is larger than previous reports.…”

“…The rates of LD decay on seven chromosomes were <6.5 Mb, ~8.7 cM based on the estimation of 1 cM equals ~750 kb (Tanksley et al, 1992), which is consistent with previous data (van Berloo et al, 2008; Robbins et al, 2011). The remaining five chromosomes 4, 5, 6, 9, and 11 with relatively large LD could be biased by chromosome fragments that have been introgressed from wild species in the past decades (van Berloo et al, 2008; Bauchet et al, 2017), e.g., fragments containing resistance genes on chromosomes 5, 9, and 11. However, all studies suggest that the LD is strong in tomato than in other species and association mapping is theoretically feasible with a small number of markers (van Berloo et al, 2008; Robbins et al, 2011; Lin et al, 2014).…”

“…The second strategy is to run large-scale genotyping of various collections of tomato accessions using the tomato array platform of Solanaceae Coordinated Agricultural Project (SolCAP) or Centre of BioSystems Genomics (CBSG) for association analysis. This approach has identified phenotype/genotype associations for over 20 fruit traits including fruit color, FW, SSC, and fruit shape (Ruggieri et al, 2014; Sauvage et al, 2014; Sacco et al, 2015; Bauchet et al, 2017). The third strategy is to genotype a collection of tomato accessions with a relatively small amount of markers for association, which has detected hundreds of genotype/phenotype associations for fruit traits (Xu et al, 2013; Zhang et al, 2015, 2016; Zhao et al, 2016).…”

“…Due to the abundance and wide distribution of single nucleotide polymorphisms (SNPs) in the whole genome and the availability of automatic large-scale genotyping platform, SNPs have been popularly used in association analysis in tomato (Robbins et al, 2011; Shirasawa et al, 2013; Lin et al, 2014; Ruggieri et al, 2014; Sauvage et al, 2014; Sacco et al, 2015; Sim et al, 2015; Bauchet et al, 2017). However, as the second abundant form of genetic variation in the whole genome (Yang et al, 2014), InDel markers have not been widely used in genetic study.…”