Identification of the Chromosomal Region Controlling Naringenin Chalcone Accumulation in Melon Rind by a Combination of RNA-Seq and Bulk Segregant Analysis

Major melon fruit pigments are carotenoids and chlorophylls. Recently we discovered that naringenin chalcone, a yellow flavonnoid, accumulates in ‘canary yellow‘ melon as the main fruit skin pigment or as an additional pigment in other melon fruit types. Accumulation of this chalcone segregates as monogenic trait. Analysis of candidate genes, controlling similar traits in other crops, could not identify this gene. We isolated RNA, at 10 DAP, 20 DAP and mature fruit, from the skins of developing fruit belonging to pools of F₃ families having either ‘yellow canary’ phenotype or white skin that do not accumulate detectable amounts of maringenin chalcone. We sequenced these RNA pools with Illumina/Solexa Genome Analyzer, assembled contigs, analyzed their expression patterns within and between the two pools at different fruit developmental stages and discovered SNPs that differentiate between the pools. We localized the contigs and the SNPs on the publicly available melon, cucumber and watermelon genomes. Most of the identified SNPs were localized to the same genomic region where contigs with significantly different expression patterns are co-localized. This indicates that the regulator gene for naringenin chalcone accumulation in melon skins is localized in this small region. Our next steps include cloning of this gene, exploring the network of genes that participate in naringenin chalcone accumulation, finding what limits the accumulation of flavonoids to fruit rind only and finding ways to exceed production of flavonoids to anthocyanins. This research could lead to the development of new pigmentation system in melon fruit that will be based on flavonoids.