חיפוש מתקדם
Plant Journal

D. Shem-Tov, O. Barad, Z. Fei, Y. Xu, L. Mao, C. Jiao, O. Tzfadia, A. Fait, E. Halperin, N. Lombardi, G. Kol, G. Ronen, J.J. Giovannoni

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.

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Deciphering genetic factors that determine melon fruit‐quality traits using RNA‐Seq‐based high‐resolution QTL and eQTL mapping
94

D. Shem-Tov, O. Barad, Z. Fei, Y. Xu, L. Mao, C. Jiao, O. Tzfadia, A. Fait, E. Halperin, N. Lombardi, G. Kol, G. Ronen, J.J. Giovannoni

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

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.

Scientific Publication
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