Development of a 775 SNP array for peach based on whole-genome resequencing data, and assessment of the potential of its application

文献类型： 外文期刊

第一作者： Guan, Liping

作者： Guan, Liping;Cao, Ke;Li, Yong;Zhu, Gengrui;Fang, Weichao;Wang, Xinwei;Chen, Changwen;Guo, Jian;Wang, Qi;Zhao, Yalin;Wang, Lirong;Guan, Liping;Xu, Qiang

作者机构：

关键词： SNP; Genetic analysis; Association studies; Peach identification

期刊名称：SCIENTIA HORTICULTURAE （ 影响因子：3.463； 五年影响因子：3.672 ）

ISSN： 0304-4238

年卷期： 2021 年 276 卷

页码：

收录情况： SCI

摘要： Peach (Prunus persica L.) is an economically important fruit crop worldwide. Although a large number of DNA markers have been developed for peach, effective variety identification remains challenging. Single nucleotide polymorphisms (SNPs) are the most frequent form of DNA variation distribution along the entire genome, thus, they are recognized as highly efficient tools for germplasm identification. In this study, next-generation sequencing technologies and bioinformatic tools were used to identify a total of 16,658,391 SNPs in 360 peach accessions. By filtering out SNPs with minor allele frequency < 0.05, missing data = 0, sequencing depth < 10x, quality score < 1000, pi < 0.48, and allele number> 2, 775 high-quality SNP markers with high poly-morphism were obtained. Using these SNP makrers, we successfully explored the genetic diversity of the 360 peach accessions and performed association studies for flesh adhesion, flesh color, fruit hairiness, fruit flavor, fruit shape, and pollen fertility traits. Next, we developed a minimal number of SNP makrers for variety identification and identified population-specific SNPs for accessions from China, Japan and Korea, and the USA and Europe. In addition, we identified a genome region with the highest SNP density (79 SNPs in 1000 bp), which may be helpful for the further develpment of one PCR to differentiate all 360 peach accessions. Briefly, the newly developed 775 SNP markers may be useful for genetic diversity, linkage, and variety identification in peach.

分类号：

  • 相关文献
作者其他论文 更多>>

微信小程序