Deciphering genetic factors that determine melon fruit quality traits using RNA-seq based high-resolution QTL and eQTL mapping

Authors: GALPAZ, NAVOT - Agricultural Research Organization Of Israel; GONDA, ITAY - Boyce Thompson Institute; SHEM-TOV, DORON - Agricultural Research Organization Of Israel; BARAD, OMER - Agricultural Research Organization Of Israel; SHI, YANNA - Boyce Thompson Institute; TZURI, GALIL - Agricultural Research Organization Of Israel; LOMBARDI, NADIO - Boyce Thompson Institute; FEI, ZHANGJUN - Boyce Thompson Institute; Giovannoni, James; KATZIR, NURIT - Agricultural Research Organization Of Israel

Submitted to: Plant Journal
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/31/2018
Publication Date: 3/25/2018
Citation: Galpaz, N., Gonda, I., Shem-Tov, D., Barad, O., Shi, Y., Tzuri, G., Lombardi, N., Fei, Z., Giovannoni, J.J., Katzir, N. 2018. Deciphering genetic factors that determine melon fruit quality traits using RNA-seq based high-resolution QTL and eQTL mapping. Plant Journal. 94:169-191. doi.org/10.1111/tpj.13838
DOI: https://doi.org/10.1111/tpj.13838

Interpretive Summary: Numerous important agricultural traits are governed by quantitative trait loci (QTL). QTL analysis is a powerful tool for the detection of genomic regions that control a given trait, and can be further used for gene discovery and marker-assisted selection. In the past, QTL studies were based on a limited number of markers with constrained mapping resolution, resulting in the detection of QTL covering large genomic intervals harboring many candidate genes. As a result, expensive, laborious and time-consuming fine mapping and positional cloning strategies were frequently required to narrow down the boundaries of target loci and pinpoint the underlying genes. Moreover, direct application of QTL mapping to breeding programs was hindered because of the inherent linkage drag of deleterious alleles resulting from low-resolution mapping. Here, we applied a high-throughput transcriptome analysis of a melon population for the performance of high-resolution QTL mapping. Several causative genes were mapped at up to a single-gene resolution, and two undescribed genes that affect fruit aroma and flesh color were identified and functionally or genetically validated.

Technical Abstract: Combined quantitative trait loci (QTL) and expression-QTL (eQTL) mapping analysis was performed to identify genetic factors affecting melon (Cucumis melo) fruit quality, by linking genotypic, metabolic and transcriptomic data from a melon recombinant inbred line (RIL) population. RNA sequencing (RNA-Seq) of fruit from 96 RILs yielded a highly saturated collection of > 58 000 single-nucleotide polymorphisms, identifying 6636 recombination events that separated the genome into 3663 genomic bins. Bin-based QTL analysis of 79 RILs and 129 fruit-quality traits affecting taste, aroma and color resulted in the mapping of 241 QTL. Thiol acyltransferase (CmThAT1) gene was identified within the QTL interval of its product, S-methyl-thioacetate, a key component of melon fruit aroma. Metabolic activity of CmThAT1-encoded protein was validated in bacteria and in vitro. QTL analysis of flesh color intensity identified a candidate white-flesh gene (CmPPR1), one of two major loci determining fruit flesh color in melon. We highlight the potential of RNA-Seq-based QTL analysis of small to moderate size, advanced RIL populations for precise marker-assisted breeding and gene discovery. We provide the following resources: a RIL population genotyped with a unique set of SNP markers, confined genomic segments that harbor QTL governing 129 traits and a saturated set of melon eQTLs.