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

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

来源：Plant Journal, 2018, 94(1): 169-191.

DOI：10.1111/tpj.13838

• next-generation sequencing
• transcriptome
• Cucumis melo
• network analysis
• pentatricopeptide repeat-containing protein
• thiol acyltransferase

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 >58000 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 invitro. 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 >12000 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.
Significance Statement Fruit-quality traits of melon were studied by linking genotypic, metabolic and transcriptomic data from a recombinant inbred line population. High resolution RNA-Seq-based quantitative trait loci and expression-QTL analyses enabled the identification of two genes that affect aroma and color.

• 出版日期2018-4