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

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. 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.

Multi-allelic APRR2 Gene is Associated with Fruit Pigment Accumulation in Melon and Watermelon

“…In order to test whether the expression level of the CmAPRR2 gene is associated with mature fruit pigmentation, we analyzed RNA-seq data and mature fruit flesh carotenoids on a different RILs population derived from a cross between DUL and an Indian phut snapmelon (Momordica group), PI414723 (hereafter called 414) (Galpaz et al , 2018). While 414 has a spotted rind (and not a clear light or dark phenotype), we assume based on testcrosses with some of the light rind accessions that, as DUL, it also carry a ‘dark’ allele of the CmAPRR2 .…”

“…Another layer of quantitative variation in flesh pigment content and color intensity exists within those color classes as defined by several QTL mapping studies (Monforte et al , 2004; Cuevas et al , 2008, 2009; Paris et al , 2008; Harel-Beja et al , 2010; Diaz et al , 2011). These include the recent fine-mapping to a candidate causative gene level of flesh carotenoids QTL using a recombinant inbred lines (RILs) population (Galpaz et al , 2018). Thus far, however, causative genes governing this quantitative variation have not been shown.…”

Genetic dissection of the gene coexpression network underlying photosynthesis in Populus

“…The direct integration of eQTNs with quantitative trait analyses has facilitated the functional interpretation of complex trait association signals in previous studies (Nica et al , ). Combined quantitative trait loci (QTL) and expression‐QTL (eQTL) mapping analysis was previously used to construct a genetic regulatory network affecting melon ( Cucumis melo ) fruit quality and to identify a candidate gene ( CmPPR1 ) controlling flesh colour intensity, supporting the notion that eQTN analysis is a powerful approach for identifying trait‐related regulatory factors (Galpaz et al , ).…”

Melon ethylene-mediated transcriptome and methylome dynamics provide insights to volatile production

“…Fruits were collected during development according to Table S1. Ethylene emission was measured as previously described (Galpaz et al, 2018).…”

“…Much of our knowledge of climacteric fleshy fruit ripening derives from studies in tomato. Melon is also widely studied as it exhibits extreme genotypic and phenotypic variation including in climacterism (Burger et al, 2010; Gur et al, 2017; Galpaz et al, 2018). In contrast to tomato, fruit carotenoid accumulation is ethylene independent in melon and controlled by a ‘golden’ SNP in the CmOr gene (Tzuri et al, 2015).…”