Construction of a high-density SNP-based genetic map and identification of fruit-related QTLs and candidate genes in peach [Prunus persica (L.) Batsch]

Abstract

Background High-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. Results A 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. Conclusions We 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.

Multi-Locus Genome-Wide Association Studies Reveal Fruit Quality Hotspots in Peach Genome

“…The FW QTN qtnFW_2.1 and qtnFW_3.1 could be the FW QTLs mapped in an interspecific cross between peach and a wild relative Prunus davidiana (Quilot et al, 2004;Desnoues et al, 2016). On chromosome 4 qtnFW_4.1 was close to the FW QTL reported by da Silva Linge et al (2015) and qtnFW_4.2 was in the same genetic interval of the QTL identified by Shi et al (2020).…”

“…Moreover, we identified two QTNs on chromosome 1 (qtnBlush_1.1: 26.9 Mbp; qtnBlush_1.2: 2.5 Mbp). Analyzing an F1 peach population derived from the cross between "Shahong" and "Hongfurong, " Shi et al (2020) also observed a QTL associated with blush on chromosome 1. However, the genetic interval was approximately at 21.5 Mbp.…”

“…The qtnBlush_3.1, qtnBlush_3.2 and qtnBlush_3.3 were located within the genetic interval of the major QTL for blush on chromosome 3. QTL regions for blush on chromosome 4 were mapped approximately at 10.5 – 11.5 Mbp ( Rawandoozi et al, 2020b ); 11.2 – 14.1 Mbp ( Hernández Mora et al, 2017 ); and at 19.8 and 28.6 Mb ( Shi et al, 2020 ). The qtnBlush_4.1 was detected at 6.6 Mbp and accounted for the highest phenotypic variation observed.…”

“…Understanding the genetic control of fruit diameter and weight is an important goal of breeding programs due to the importance of these traits for the fresh market ( Yue et al, 2014 ). QTL regions associated with fruit diameter and weight have been detected in all chromosomes ( da Silva Linge et al, 2015 ; Fresnedo-Ramírez et al, 2016 ; Zeballos et al, 2016 ; Hernández Mora et al, 2017 ; Cao et al, 2019 ; Abdelghafar et al, 2020 ; Shi et al, 2020 ). In this study, we identified two reliable QTNs associated with FDIA ( qtnFDIA_7.1 and qtnFDIA_1.1 ).…”

Molecular Bases of Fruit Quality in Prunus Species: An Integrated Genomic, Transcriptomic, and Metabolic Review with a Breeding Perspective

“…These LGs have been also identified as key genome regions for fruit quality traits in other Prunus species including almonds [ 176 ], peaches [ 177 , 178 , 179 , 180 , 181 ], and Japanese plums [ 170 , 182 ]. The most significant QTLs are located in LG4 for soluble solid contents and ripening dates, as well as in LG3 for skin ground and flesh color in different analyzed Prunus species [ 183 , 184 , 185 , 186 ]. Flesh color around the stone, flower color, and other color have been mapped to LG 3, fruit skin color and leaf color have been mapped to LG6, blood flesh has been mapped to the top of LG4, and dominant blood flesh has been mapped to the top of LG5 [ 63 , 187 , 188 ].…”