Genome-Wide Association Study for Horticultural Traits in a Core Collection of Tomato

Tomato is a major vegetable cultivated worldwide and a model plant for basic researches in the Solanaceae family. The reference genome assembly of tomato has led to the discovery of genome-wide single nucleotide polymorphisms (SNPs). High-throughput genotyping with these SNPs has provided an efficient tool for dissection of quantitative traits using association mapping approaches. In this study, a genome-wide association study (GWAS) was conducted to identify favorable alleles for horticultural traits using a core collection of 96 tomato varieties. We evaluated phenotypic variations of these varieties for seven traits (fruit shape, fruit weight, locule number, pericarp thickness, Brix, yield, and blossom end rot resistance). Genotyping by sequencing (GBS) detected a total of 7,814 single nucleotide polymorphisms (SNPs) in the core collection. Of them, 3,876 SNPs were selected based on missing data rate (≤ 10%) for GWAS. A total of 31 SNPs showed significant associations with the seven traits at P < 0.001 using the unified mixed model. Several associations were co-localized in the previously reported genes including ovate (fruit shape), fw11.3 (fruit weight), and lc and FAS (locule number). In addition, new candidate loci were identified on chromosomes 1, 3, 7, 9, 10, and 12 for pericarp thickness, fruit shape, Brix, yield, fruit weight, and blossom end rot resistance, respectively These results will facilitate development of breeder’s toolbox for marker-assisted selection for improving horticultural traits in tomato.