Genome-Wide Association Study and Accuracy of Genomic Selection Models in Tomato F1 Varieties in Japan

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 genomic selection (GS) and genome-wide association study (GWAS) in genetic improvement of these traits. We used 96 large-sized 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 GS, several linear and non-parametric models were evaluated using cross validation. Genome wide predictions for GS were accurate at the 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 GS and GWAS can be used for breeding programs in Japanese tomato.