Genome-Wide Association Study and Whole-Genome Prediction in Tomato F1 Varieties in Japan by using Custom 50K SNP Genotyping Array

In Japanese tomato varieties, high sugar content has been the primary breeding objective, while high yield performance has also been an important trait in recent breeding programs. However, there is a negative correlation between sugar content and yield performance. In this study, we examined the potential use of genome-wide association studies (GWAS) and whole-genome prediction (WGP) in genetic improvement of these traits using a custom 50k SNP genotyping array. We used 96 large-fruit fresh market F₁ varieties from Japan that were phenotyped for sugar content based on degrees of Brix, total fruit yield, and other yield- and quality-related traits. In WGP, several linear and non-linear models were evaluated using cross validation. WGP was accurate at a high level for both Brix (>0.7) and total fruit weight (>0.5). In addition, we detected several loci related to physiological disorders of fruit such as blossom end rot and irregular shaped fruits based on GWAS. These results suggest that WGP and GWAS can be used for breeding programs in Japanese tomato.