Abstract

Japanese plum is one of the most important stone fruit crops worldwide. Molecular markers are extremely useful tools in plant genetics and breeding. Currently, very few markers are available in Japanese plum hindering the implementation of Marker-Assisted Selection (MAS). Next-generation sequencing allows the study of genes involved in traits of interest, facilitating the development of strategies based on QTLs and GWAS conducted with data from genotyping-by-sequencing (GBS). RNA-seq is a accurate and sensitive tool for quantification of gene expression. Transcriptome studies facilitate the understanding of metabolic pathways, allowing the suggestion of transcription factors associated with traits of agronomic interest. They have also enabled the development of simple sequence repeats (EST-SSR) and single nucleotide polymorphism (SNPs) two of the most common markers used in MAS. Currently few studies have focused on developing EST-SSR markers considering both, genes expression levels and specific transcription factor from metabolic pathways. In this work, we report the first set of EST-SSR markers for P. salicina developed from specific genes associated to fruit color by anthocyanin accumulation. Our objectives were (i) to develop a set EST-SSR related to the synthesis and regulation of flavonoid pathway genes, (ii) determine the genetic structure in P. salicina germplasm using GBS, (iii) validate and evaluate the potential of EST-SSR as molecular markers for presence or absence of anthocyanins accumulation. Forty four of the fifty three markers developed amplified. Thirty seven were polymorphic. We identified three EST-SSR sequences of transcription factors described as key regulators in synthesis of anthocyanins. To assess their potential as molecular markers, we analyzed the genetic structure of 29 varieties of Japanese plum data using GBS, separating varieties into two groups. In comparison, genetic structure using 3 associated color EST-SSR separated accessions into 3 groups. Our results showed that EST-SSR markers better separate colored from non-colored varieties.