High-density genetic map construction and quantitative trait loci analysis of the stony hard phenotype in peach based on restriction-site associated DNA sequencing

Abstract

BackgroundPeach (Prunus persica) is an important fruit crop that generally softens rapidly after harvest resulting in a short shelf-life. By contrast, stony hard (SH) peach fruit does not soften and hardly produces ethylene. To explore the candidate genes responsible for the SH phenotype, a high-density genetic map was constructed by restriction-site associated DNA sequencing technology.ResultsIn the present study, the linkage map consisted of 1310 single nucleotide polymorphism markers, spanning 454.2 cM, with an average marker distance of 0.347 cM. The single nucleotide polymorphisms were able to anchor eight linkage groups to their corresponding chromosomes. Based on this high-density integrated peach linkage map and two years of fruit phenotyping, two potential quantitative trait loci for the SH trait were identified and positioned on the genetic map. Additionally, Prupe.6G150900.1, a key gene in abscisic acid (ABA) biosynthesis, displayed a differential expression profile identical to the ABA accumulation pattern: mRNA transcripts were maintained at a high level during storage of SH peaches but occurred at low levels in melting fruit.ConclusionThus Prupe.6G150900.1 might play a crucial role in the SH phenotype of peach in which ABA negatively regulates ethylene production. Also, this high-density linkage map of peach will contribute to the mapping of important fruit traits and quantitative trait loci identification.Electronic supplementary materialThe online version of this article (10.1186/s12864-018-4952-y) contains supplementary material, which is available to authorized users.

Construction of a high-density genetic map and QTL mapping of leaf traits and plant growth in an interspecific F1 population of Catalpa bungei × Catalpa duclouxii Dode

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Genome‐wide analysis of PmTCP4 transcription factor binding sites by ChIP‐Seq during pistil abortion in Japanese apricot

“…RT‐qPCR was performed using the ABI‐7300 Real‐Time PCR system (Applied Biosystems, Foster City, CA, USA) and SYBR Green Master Mix (Toyobo, Osaka, Japan). The experiment was performed using the method described by (Guo et al., 2018a; Iqbal et al., 2020; Wu et al., 2019). Three technical repeats were performed for each biological repeat.…”

Comprehensive transcriptome profiling to identify genes involved in pistil abortion of Japanese apricot

“…Primers were designed using Beacon Designer software (Premier Biosoft, version 7.0). The RT-qPCR was performed according to the method followed by Guo and Iqbal (Guo et al 2018;Iqbal et al 2020a;Shi, 2020). Using RPII as a reference internal genes, each sample was taken thrice for biological repeat and the expression was calculated using the 2 -44CT method (Livak and Schmittgen 2001).…”