GWAS Characterization of the Genetic Regions Associated with Nine Important Agronomic Traits in Tomato (Solanum lycopersicum L.)

Understanding the genetic background of elite cultivated tomato germplasm resources in crossbreeding and revealing the genetic basis of complex traits are vital for better-targeted germplasm expansion and the creation of strong hybrids. Here, we obtained approximately 21 million single-nucleotide polymorphisms (SNPs) based on the sequencing of 212 cultivated tomato accessions and the population structure of which was revealed. More importantly, we found that target genes distributed on chromosomes 1, 5, 9, and 11 may be actively selected in breeding. In particular, the significant signals related to soluble sugar content (chr1_94170222, chr1_96273188, chr9_4167512, and chr11_55592768), fruit firmness (chr5_4384919 and chr5_5111452) and gray leaf spot resistance (chr11_8935252 and chr11_9707993) were also detected on the corresponding chromosomes, respectively. Overall, we reported 28 significant association signals for nine agronomic traits based on a mixed linear model (MLM), including 114 genes. Among these signals, 21 contained potential novel genes for six fruit traits. These novel candidate genes located in genomic regions without previously known loci or on different chromosomes explained approximately 16% of the phenotypic variance on average in cultivated tomatoes. These findings could accelerate the identification and validation of novel and known candidate genes and QTLs, improving the understanding of the genetic structure of complex quantitative traits. These results also provide a basis for tomato breeding and improvement.