A major focus in plant breeding has been the improvement of crops through various traits that affect disease resistance and yield. However, the focus on productivity has led to an inattentiveness to other traits that specifically affect produce quality. An example of a critical fruit quality trait is its flavor, contributing to our perception of aromatic volatiles. Even at nanomolar concentrations, aromatic volatiles can be perceived by the olfactory system and influence the liking of the fruit. The focus of this study was to investigate the genetic aspect of the branched-chain amino acid (BCAA) volatiles, derived from L-valine, L-isoleucine and L-leucine, in tomato fruits. It is generally considered that these BCAA-derived volatiles contribute positively to overall liking, because these are essential amino acids required by the human diet. To identify quantitative trait loci (QTLs) affecting the biosynthetic pathway for 11 BCAA-derived volatiles, a Genome-Wide Association Study (GWAS) was conducted using a diverse and unique panel of 167 tomato accessions. The GWAS was run using the FarmCPU model in GAPIT-R, with a total of 21,893,681 SNPs, 2,735,297 INDELs, and 154 structural variants across the genome. Furthermore, a weighted gene co-expression network analysis (WGCNA) was conducted in parallel to identify modules of co-expressed genes that cluster with known genes that affect the BCAA-derived volatile pathway. A total of 113 QTLs were identified from GWAS and 3024 co-expressed genes were identified from the WGCNA. Candidate genes were screened based on annotated biochemical function, overlap within the GWAS QTLs, and gene expression in the red-ripe fruits. This led to the identification of two candidate genes, one on the long arm of chromosome 1 and another on the long arm of chromosome 11. These genes are being knocked-out using CRISPR-Cas9, and current progress is aimed to confirm the validity and function of these genes in the near-future.
