Abstract
BackgroundMelon shows a broad diversity in fruit morphology and quality, which is still underexploited in breeding programs. The knowledge of the genetic basis of fruit quality traits is important for identifying new alleles that may be introduced in elite material by highly efficient molecular breeding tools.ResultsIn order to identify QTLs controlling fruit quality, a recombinant inbred line population was developed using two commercial cultivars as parental lines: “Védrantais”, from the cantalupensis group, and “Piel de Sapo”, from the inodorus group. Both have desirable quality traits for the market, but their fruits differ in traits such as rind and flesh color, sugar content, ripening behavior, size and shape. We used a genotyping-by-sequencing strategy to construct a dense genetic map, which included around five thousand variants distributed in 824 bins. The RIL population was phenotyped for quality and morphology traits, and we mapped 33 stable QTLs involved in sugar and carotenoid content, fruit and seed morphology and major loci controlling external color of immature fruit and mottled rind. The median confidence interval of the QTLs was 942 kb, suggesting that the high density of the genetic map helped in increasing the mapping resolution. Some of these intervals contained less than a hundred annotated genes, and an integrative strategy combining gene expression and resequencing data enabled identification of candidate genes for some of these traits.ConclusionSeveral QTLs controlling fruit quality traits in melon were identified and delimited to narrow genomic intervals, using a RIL population and a GBS-based genetic map.
Highlights
Melon shows a broad diversity in fruit morphology and quality, which is still underexploited in breeding programs
The aim of this study was to identify Quantitative Trait Loci (QTL) and major loci related with fruit quality in narrow genomic intervals, using a high-density genetic map obtained with a recombinant inbred lines (RIL) population from a cantalupensis x inodorus cross
Some of these were considered as qualitative (Table 1), some variation in intensity was observed for Mottled rind (MOT), External color of immature fruit (ECOL) and yellowing of mature rind (YELL)
Summary
Melon shows a broad diversity in fruit morphology and quality, which is still underexploited in breeding programs. The knowledge of the genetic basis of fruit quality traits is important for identifying new alleles that may be introduced in elite material by highly efficient molecular breeding tools. The use of genomic resources to better understand fruit morphology and quality has been facilitated by the availability of a reference genome [13] and the rapid advances in Next-Generation Sequencing (NGS) technologies, such as RNA-seq [9] and Genotyping-By-Sequencing (GBS) [11, 14, 15]. The availability of high numbers of SNPs has increased the precision of Quantitative Trait Loci (QTL) mapping. Linkage maps have shown their effectiveness as a tool to study the genetic architecture of both monogenic and complex traits [21]. It has been demonstrated that a higher SNP density substantially increases the QTL mapping potential, affecting both the detection and the resolution of QTLs [10, 15]
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