Identification of loci associated with fruit traits using genome-wide single nucleotide polymorphisms in a core collection of tomato (Solanum lycopersicum L.)

Advances in sequencing technology have facilitated allele mining with high resolution for quantitative traits in crop species. In this study, a genome-wide association study (GWAS) was conducted to detect quantitative trait loci (QTL) for fruit traits in tomato. We developed a core collection of 192 tomato accessions representing contemporary breeding lines, vintage varieties, and wild species. Phenotypic variations in this collection were evaluated for six traits including fruit shape, fruit color, pericarp thickness, fruit weight, fruit height, and fruit width over two years in field trials. Genotyping by sequencing (GBS) detected a total of 140,072 SNPs in the core collection and 8,550 SNPs were selected based on missing data rate (<20%) and minor allele frequency (≥5%) for GWAS. The 192 accessions were divided into seven clusters and the resulting membership coefficient matrix was used to account for population structure. We identified two loci for fruit color, seven loci for fruit shape, 11 loci for pericarp thickness, 13 loci for fruit weight, seven loci for fruit height, and 10 loci for fruit width at P < 0.0001 using the compressed mixed linear model. These loci explained 7.11-37.64% of total phenotypic variance. We also found that nine loci on seven chromosomes showed significant associations with multiple traits, suggesting pleiotropic effects of QTL. A total of 41 loci associated with the six fruit traits in our study will be a useful resource for marker-assisted selection to improve fruit traits in tomato.