Genome-wide Association Analysis of Red Flesh Character Based on Resequencing Approach in Peach

Abstract

<jats:p>Anthocyanins are important molecules that are responsible for fruit color formation and are also beneficial to human health. To date, numerous structural and regulatory genes associated with anthocyanin biosynthesis in peach (<jats:italic>Prunus persica</jats:italic>) have been reported based on linkage analysis. In this study, we sought to identify further genes associated with anthocyanin content in peach by conducting a genome-wide association analysis of 129 peach accessions to detect markers associated with the trait. Significant association signals were detected when anthocyanin content was considered a qualitative character but not when it was considered a quantitative trait. We detected an association region located between 11.7 and 13.1 Mb in chromosome 1, a region in which only 133 of 146 genes have previously been functionally annotated. Gene ontology annotation of the genes in this region showed that membrane-associated genes (including one gene encoding a chloride channel protein and 17 sugar transport/carrier-associated genes) were significantly enriched, and we focused on these in subsequent analyses. Based on in vitro induction of anthocyanins in fruit flesh using different exogenously applied sugars and subsequent culture, we found that the expression level of 3 of the 18 membrane-associated genes, <jats:italic>Prupe.1G156300</jats:italic>, <jats:italic>Prupe.1G156900</jats:italic>, and <jats:italic>Prupe.1G157000</jats:italic>, increased during induction treatment. Furthermore, during the fruit development period of a white-fleshed and a red-fleshed peach cultivar, the expression of one gene encoding a transmembrane sugar transport protein was observed to be positively correlated with anthocyanin biosynthesis. These results will facilitate understanding of the molecular mechanism of anthocyanin biosynthesis in peach.</jats:p>

Inheritance of Fruit Red-Flesh Patterns in Peach

“…In the SDF2 population, in addition to the major gene in G5, we identified another QTL at the top of G1 between markers SNP_IGA_19514 and SNP_IGA_67137 (6.872.054 and 20.219.128 pb). In a GWAS study with a panel of 129 Chinese accessions, this same genomic region (between 11,7 and 13.1 Mbp) was associated with anthocyanin content codified as presence or absence, but not as a quantitative trait [ 24 ]. A QTL was also reported in this region in a BC2 population derived from an interspecific cross between peach and P. davidiana [ 25 ].…”

Down-regulation of NCED leads to the accumulation of carotenoids in the flesh of F1 generation of peach hybrid

“…Chlorophyll, carotenoids and anthocyanins are main compounds determining the flesh color of fruits ( Liu et al., 2022 ; Wu et al., 2022 ). White-fleshed peach has less pigment; and carotenoids and anthocyanins are the main pigments of yellow-fleshed and red-fleshed peach, respectively ( Bai et al., 2016 ; Liu et al., 2019 ; Zhu et al., 2020 ). Compared with white-fleshed peach, yellow-fleshed peach contains a higher level of carotene.…”

Phenological phases of introduced peach varieties

“…Huihui Liu et al (2019) performed GWAS (genome-wide association study) screening and candidate gene screening to identify a candidate gene regulating anthocyanin content of peach fruits and first identified an association signal ranging from 11.7 to 13.1 Mb in the chromosome 1 (Chr. 1) region.…”