Transcriptome-Based Ultra-High Resolution QTL Analysis of Fruit Quality Traits in Melon

Fruit quality is determined by taste, aroma, ‎color, texture, nutritional value and shelf life. The major goal of the research was to identify the genetic factors that affect the metabolic pathways that underlie these traits in melon (Cucumis melo L.). Single-gene resolution QTL mapping was achieved using 81 Recombinant Inbred Lines (RIL) of the melon 414 x Dul population. Genotyping was conducted using ca 60,000 SNPs, obtained by Illumina RNA-seq from flesh tissue of mature fruits from all RI lines and their parents. Phenotyping and metabolic profiling included over 100 fruit quality traits of taste, aroma, color and appearance. Anova-based QTL analysis revealed nearly 250 QTLs for the above traits and over 12,000 expression QTLs (eQTL).

QTLs for fruit pH, fruit length and volatile levels were located to within 1-9 genes of previously identified genes that underlie them. This clearly demonstrates the high resolution and accuracy of the mapping strategy. Novel candidate genes, controlling fruit aroma and color that were identified and functionally analyzed will be discussed. Mapping at the single-gene resolution as reported here highlights the potential for implementation of detected QTLs in precise Marker Assisted Breeding.