Abstract
BackgroundHigh-density genetic mapping is a valuable tool for mapping loci that control specific traits for perennial fruit trees. Peach is an economically important fruit tree and a model Rosaceae species for genomic and genetic research. In peach, even though many molecular markers, genetic maps and QTL mappings have been reported, further research on the improvement of marker numbers, map densities, QTL accuracy and candidate gene identification is still warranted.ResultsA high-density single nucleotide polymorphism (SNP)-based peach linkage map was constructed using specific locus amplified fragment sequencing (SLAF-seq). This genetic map consisted of 7998 SLAF markers, spanning 1098.79 cM with an average distance of 0.17 cM between adjacent markers. A total of 40 QTLs and 885 annotated candidate genes were detected for 10 fruit-related traits, including fruit weight (FW), fruit diameter (FD), percentage of red skin colour (PSC), eating quality (EQ), fruit flavour (FV), red in flesh (RF), red around pit (RP), adherence to pit (AP), fruit development period (FDP) and fruit fibre content (FFC). Eighteen QTLs for soluble solid content (SSC) were identified along LGs 1, 4, 5, and 6 in 2015 and 2016, and 540 genes were annotated in QTL intervals. Thirty-two QTLs for fruit acidity content (FA) were detected on LG1, and 2, 4, 5, 6, and 1232 candidate genes were identified. The expression profiles of 2 candidate genes for SSC and 4 for FA were analysed in parents and their offspring.ConclusionsWe constructed a high-density genetic map in peach based on SLAF-seq, which may contribute to the identification of important agronomic trait loci. Ninety QTLs for 12 fruit-related traits were identified, most of which overlapped with previous reports, and some new QTLs were obtained. A large number of candidate genes for fruit-related traits were screened and identified. These results may improve our understanding of the genetic control of fruit quality traits and provide useful information in marker-assisted selection for fruit quality in peach breeding programmes.
Highlights
High-density genetic mapping is a valuable tool for mapping loci that control specific traits for perennial fruit trees
We constructed a high-density genetic map using single nucleotide polymorphism (SNP) markers which be developed through specific-locus amplified fragment sequencing (SLAFseq), and we identified stable quantitative trait loci (QTL) associated with 12 fruit quality traits for two years in an F1 population
fruit development period (FDP) was treated as a qualitative trait in the subsequent analysis
Summary
High-density genetic mapping is a valuable tool for mapping loci that control specific traits for perennial fruit trees. Peach is an important perennial fruit tree species with few chromosomes (2n = 2x = 16), a relatively small genome (~ 230 Mbp), and a short juvenile period (2–4 years) [1]. These traits make peach a model plant in Rosaceae fruit trees for genetic map construction, important agronomic trait location, and target candidate gene identification. Infante et al (2008) overviewed the fruit quality evaluation through physical, chemical and sensorial parameters, and the inheritance and molecular breeding of the main fruit quality traits in peach [2] Most of these quality traits are quantitatively inherited and controlled by multiple loci. The construction of genetic maps and quantitative trait loci (QTL) analysis are effective strategies for the identification of candidate genes associated with fruit quality traits [3]
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