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

(2018) PLANT JOURNAL. 94(1). p.169-191
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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 >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.
Keywords
next-generation sequencing, transcriptome, Cucumis melo, network analysis, pentatricopeptide repeat-containing protein, thiol acyltransferase, PENTATRICOPEPTIDE REPEAT PROTEINS, INBRED LINE POPULATION, FALSE DISCOVERY RATE, NON-MODEL PLANTS, CUCUMIS-MELO, L. FRUIT, BIOCHEMICAL CHARACTERISTICS, FUNCTIONAL-CHARACTERIZATION, NUCLEUS COMMUNICATION, ETHYLENE BIOSYNTHESIS

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Chicago
Galpaz, Navot, Itay Gonda, Doron Shem-Tov, Omer Barad, Galil Tzuri, Shery Lev, Zhangjun Fei, et al. 2018. “Deciphering Genetic Factors That Determine Melon Fruit-quality Traits Using RNA-Seq-based High-resolution QTL and eQTL Mapping.” Plant Journal 94 (1): 169–191.
APA
Galpaz, N., Gonda, I., Shem-Tov, D., Barad, O., Tzuri, G., Lev, S., Fei, Z., et al. (2018). Deciphering genetic factors that determine melon fruit-quality traits using RNA-Seq-based high-resolution QTL and eQTL mapping. PLANT JOURNAL, 94(1), 169–191.
Vancouver
1.
Galpaz N, Gonda I, Shem-Tov D, Barad O, Tzuri G, Lev S, et al. Deciphering genetic factors that determine melon fruit-quality traits using RNA-Seq-based high-resolution QTL and eQTL mapping. PLANT JOURNAL. 2018;94(1):169–91.
MLA
Galpaz, Navot, Itay Gonda, Doron Shem-Tov, et al. “Deciphering Genetic Factors That Determine Melon Fruit-quality Traits Using RNA-Seq-based High-resolution QTL and eQTL Mapping.” PLANT JOURNAL 94.1 (2018): 169–191. Print.
@article{8563192,
  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 {\textrangle}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 {\textrangle}12000 eQTL mapped for {\textrangle}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.},
  author       = {Galpaz, Navot and Gonda, Itay and Shem-Tov, Doron and Barad, Omer and Tzuri, Galil and Lev, Shery and Fei, Zhangjun and Xu, Yimin and Mao, Linyong and Jiao, Chen and Harel-Beja, Rotem and Doron-Faigenboim, Adi and Tzfadia, Oren and Bar, Einat and Meir, Ayala and Sa'ar, Uzi and Fait, Aaron and Halperin, Eran and Kenigswald, Merav and Fallik, Elazar and Lombardi, Nadia and Kol, Guy and Ronen, Gil and Burger, Yosef and Gur, Amit and Tadmor, Ya'akov and Portnoy, Vitaly and Schaffer, Arthur A and Lewinsohn, Efraim and Giovannoni, James J and Katzir, Nurit},
  issn         = {0960-7412},
  journal      = {PLANT JOURNAL},
  language     = {eng},
  number       = {1},
  pages        = {169--191},
  title        = {Deciphering genetic factors that determine melon fruit-quality traits using RNA-Seq-based high-resolution QTL and eQTL mapping},
  url          = {http://dx.doi.org/10.1111/tpj.13838},
  volume       = {94},
  year         = {2018},
}

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