Linkage disequilibrium and genome-wide association analysis for anthocyanin pigmentation and fruit color in eggplant

Abstract

BackgroundThe genome-wide association (GWA) approach represents an alternative to biparental linkage mapping for determining the genetic basis of trait variation. Both approaches rely on recombination to re-arrange the genome, and seek to establish correlations between phenotype and genotype. The major advantages of GWA lie in being able to sample a much wider range of the phenotypic and genotypic variation present, in being able to exploit multiple rounds of historical recombination in many different lineages and to include multiple accessions of direct relevance to crop improvement.ResultsA 191 accessions eggplant (Solanum melongena L.) association panel, comprising a mixture of breeding lines, old varieties and landrace selections originating from Asia and the Mediterranean Basin, was SNP genotyped and scored for anthocyanin pigmentation and fruit color at two locations over two years. The panel formed two major clusters, reflecting geographical provenance and fruit type. The global level of linkage disequilibrium was 3.4 cM. A mixed linear model appeared to be the most appropriate for GWA. A set of 56 SNP locus/phenotype associations was identified and the genomic regions harboring these loci were distributed over nine of the 12 eggplant chromosomes. The associations were compared with the location of known QTL for the same traits.ConclusionThe GWA mapping approach was effective in validating a number of established QTL and, thanks to the wide diversity captured by the panel, was able to detect a series of novel marker/trait associations.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-896) contains supplementary material, which is available to authorized users.

The historical role of species from the Solanaceae plant family in genetic research

“…First association mapping experiments have also been performed, which identified associations of SSR and SNP markers with a number of fruit and plant characters. QTLs that have been detected previously by linkage mapping were confirmed, and novel QTL were also found (Cericola et al 2014; Ge et al 2013; Portis et al 2015). A draft genome sequence of the typical Asian eggplant cultivar ‘Nakate-Shinkuro’ was published recently (Hirakawa et al 2014).…”

Genome-Wide Association Analysis of the Anthocyanin and Carotenoid Contents of Rose Petals

“…(Jay et al, 2003; Grotewold, 2006; Tanaka et al, 2008). Although single loci influencing color variation have been identified, other researchers have described a quantitative inheritance of the anthocyanin content (Cardoso et al, 2012; Cericola et al, 2014; Henz et al, 2015). …”

Genomic Tools for the Enhancement of Vegetable Crops: A Case in Eggplant

“…A larger set of 191 accessions, including breeding lines, old varieties, and landraces from the Mediterranean basin and Asia, were investigated by Cericola et al (2014) based on genome-wide association (GWA) approach for anthocyanin pigmentation and fruit color at two locations over two years using 314 SNPs developed by Barchi et al (2011). A total of 56 associations were found between SNPs and anthocyanin content and fruit color-related traits, which were clustered into 12 groups and scattered over nine chromosomes, being eight of the groups overlapping with known QTL and demonstrating in that way the effectiveness of GWA approach.…”