Ultra-High Resolution QTL Mapping of Fruit Quality Traits in Melon

Single-gene resolution QTL mapping was achieved using 81 Recombinant Inbred Lines (RIL) of melon (Cucumis melo L.). Genotyping was conducted using almost 60,000 SNPs obtained by Illumina RNA-seq of the flesh tissue of the mature fruit of 81 RI lines and their parents. Phenotyping and metabolic profiling included over 100 fruit quality traits affecting 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 the previously identified genes that underlie them. This clearly demonstrates the high resolution and accuracy of the mapping strategy. Novel candidate genes for fruit quality traits that were identified and functionally analyzed will be discussed. Supportive information for several candidate genes was obtained by high resolution QTL analysis of additional melon segregating population at F_2-3, using genotyping by sequencing (GBS) methodology. Mapping at the single-gene resolution, as reported here, highlights the potential for implementation of detected QTLs in precise Marker Assisted Breeding.