Systems Approach for Unraveling the Genetic Components ‎that Underlie Fruit Quality Traits in Melon

Fruit quality is determined by numerous genetic factors that affect taste, aroma, ‎color, texture, nutritional value and shelf life. The major goal of the research was to identify novel genes/loci that are involved in, or that regulate, the metabolic pathways that underlie these traits. We utilized a population of 94 Recombinant Inbred (RI) lines (PI414723x'Dulce') that differ in fruit ripening and quality traits. Phenotypic and genotypic data collection included: (1) RNA-seq of mature fruit from all 94 RI lines and their parents (Illumina platform); (2) Phenotypic and metabolic profiling of the same samples using targeted (sugars, organic acids, carotenoids, volatiles) and non-targeted metabolomic analyses. Genome-wide association study (GWAS) and correlation analyses were performed. GWAS, using 46000 Single Nucleotide Polymorphism (SNP) markers developed in the project, resulted in high resolution Quantitative Trait Loci (QTL) detection. The analysis of >100 statistically significant fruit QTLs including aroma, carotenoids and sugars is described. Traits for which previously cloned and functionally analyzed genes served for QTL validation. QTLs for fruit pH, fruit length and volatile levels were located within 1-5 genes from known genes that control them, demonstrating the high resolution and accuracy of the mapping strategy. Novel candidate genes for fruit quality traits were identified and are being validated and functionally analyzed. Several of these were also identified by association patterns of metabolites versus genes. Clusters of QTLs that control various fruit quality traits were mapped to chromosomes 5 and 8, suggesting a genetically controlled co-regulation of quality traits during fruit ripening in melon.