Genome Wide Association Study Reveals Novel Loci Controlling Agronomic Traits in Tomato (Solanum lycopersicum L.)

The genetic basis of agronomic traits is critical for enhancing yield, quality, and disease resistance in tomato. In this study, genome-wide association study (GWAS) was performed on a diverse panel of 72 tomato accessions to identify genomic regions linked to 18 agronomic, processing, and disease resistance traits. Phenotypic data were collected over two growing seasons, and genotyping was conducted using genotyping-by-sequencing (GBS) on the Illumina platform. A total of 78,828 high-quality single nucleotide polymorphisms (SNPs) were identified, primarily located in intergenic (54.66%), upstream (15.46%), downstream (14.35%), intronic (10.73%), and exonic (2.90%) regions. After stringent filtering, 7751 SNPs were retained for GWAS, leading to the identification of 47 significant quantitative trait loci (QTLs) associated with 13 traits. Fruit length exhibited the highest number of QTLs (23), while chromosomes 1 and 4 contained the most QTLs (9 each). Several candidate genes were identified for key traits, including F-box protein CPR1-like and transcription factor bHLH162-like for fruit weight, F-box protein At5g49610 for fruit length, transcription factor TGA9 for fruit diameter, F-box protein CPR1-like and Beta-D-xylosidase 2 for fruit yield, Cinnamoyl-CoA reductase-like SNL6 and UDP-glucosyltransferase, as well as stress-induced protein KIN2-like and serine/threonine-protein kinase BLUS1 for ToLCV resistance. Population structure and phylogenetic analyses indicated variation among ancestral populations (K = 3). These findings provide valuable genomic resources and identify candidate genes for key traits, supporting genomics-driven breeding in tomato.