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

Navot Galpaz, Itay Gonda, Doron Shem-Tov, Omer Barad, Galil Tzuri, Shery Lev, Zhangjun Fei, Yimin Xu, Linyong Mao, Chen Jiao, Rotem Harel-Beja, Adi Doron-Faigenboim, Oren Tzfadia, Einat Bar, Ayala Meir, Uzi Sa'ar, Aaron Fait, Eran Halperin, Merav Kenigswald, Elazar FallikNadia Lombardi, Guy Kol, Gil Ronen, Yosef Burger, Amit Gur, Ya'akov Tadmor, Vitaly Portnoy, Arthur A Schaffer, Efraim Lewinsohn, James J Giovannoni, Nurit Katzir

Research output: Contribution to journalA1: Web of Science-articlepeer-review


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. CmPPR1 encodes a member of the pentatricopeptide protein family, involved in processing of RNA in plastids, where carotenoid and chlorophyll pigments accumulate. Network analysis of > 12 000 eQTL mapped for > 8000 differentially expressed fruit genes supported the role of CmPPR1 in determining the expression level of plastid targeted genes. 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.

Original languageEnglish
JournalPlant Physiology
Issue number1
Pages (from-to)169-191
Number of pages23
Publication statusPublished - 2018


  • Chromosome Mapping
  • Cucurbitaceae/genetics
  • Food Quality
  • Fruit/genetics
  • Genes, Plant/genetics
  • Genetic Linkage
  • Genome-Wide Association Study
  • Polymorphism, Single Nucleotide/genetics
  • Quantitative Trait Loci/genetics
  • Sequence Analysis, RNA


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