Abstract
BackgroundPeach (Prunus persica L.) is a diploid species and model plant of the Rosaceae family. In the past decade, significant progress has been made in peach genetic research via DNA markers, but the number of these markers remains limited.ResultsIn this study, we performed a genome-wide DNA markers detection based on sequencing data of six distantly related peach accessions. A total of 650,693~1,053,547 single nucleotide polymorphisms (SNPs), 114,227~178,968 small insertion/deletions (InDels), 8386~12,298 structure variants (SVs), 2111~2581 copy number variants (CNVs) and 229,357~346,940 simple sequence repeats (SSRs) were detected and annotated. To demonstrate the application of DNA markers, 944 SNPs were filtered for association study of fruit ripening time and 15 highly polymorphic SSRs were selected to analyze the genetic relationship among 221 accessions.ConclusionsThe results showed that the use of high-throughput sequencing to develop DNA markers is fast and effective. Comprehensive identification of DNA markers, including SVs and SSRs, would be of benefit to genetic diversity evaluation, genetic mapping, and molecular breeding of peach.
Highlights
Peach (Prunus persica L.) is a diploid species and model plant of the Rosaceae family
We detected a large number of putative polymorphic markers, including Single nucleotide polymorphism (SNP), InDels, Structure variant (SV), Copy number variant (CNV) and Simple sequence repea (SSR) by performing high-depth wholegenome re-sequencing of six peach accessions
944 SNPs were filtered for association study of fruit ripening time and 15 highly polymorphic SSRs were selected to analyze the genetic relationship among 221 accessions
Summary
Peach (Prunus persica L.) is a diploid species and model plant of the Rosaceae family. The development of molecular markers for use in plant genetic research has become essential for geneticists and breeders. Via next-generation sequencing (NGS) technology, entire genomes have been resequenced efficiently and economically to identify many polymorphic DNA markers, including single nucleotide polymorphisms (SNPs), small insertion/deletions (InDels), Guan et al BMC Genetics (2019) 20:101. With the rapid development of NGS technologies, whole-genome sequencing provides large amounts of DNA markers information in many plant species. A total of 4,980,259 SNPs, 1,026,375 INDELs and 159,330 SVs were identified through whole genome resequencing of 480 peach accessions [11]. We detected a large number of putative polymorphic markers, including SNPs, InDels, SVs, CNVs and SSRs by performing high-depth wholegenome re-sequencing of six peach accessions. The present study provides a large set of polymorphic markers among landraces and improved varieties of peach, and our results may facilitate peach molecular breeding in the future
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