基于靶向测序技术的菜豆SNP液相芯片开发及验证
The Development and Verification of SNP Lquid Chips for Common Bean Based on Targeted Sequencing Technology
袁娜 1徐勤圆 1徐照龙 1周玲 1刘晓庆 2陈新 2杜建厂1
作者信息
- 1. 江苏省农业科学院种质资源与生物技术研究所,南京 210014
- 2. 江苏省农业科学院经济作物研究所,江苏省高效园艺作物遗传改良重点实验,南京 210014
- 折叠
摘要
根据公开发表的菜豆基因组和重测序数据,利用生物信息学的方法筛选出61 950个高质量SNP位点,通过对目标位点进行探针设计评估,最终设计开发出分别包含40 352、20 855和10 486个SNP位点的40K、20K和10K液相芯片.利用10K液相芯片,对89份菜豆品种进行靶向测序基因分型检测,结果显示菜豆的平均多态性信息含量值和基因多样性值分别为0.35和0.29.STRUCTURE和聚类分析将89份菜豆划分为2个品种群,该分类结果显示同一地域的菜豆品种遗传背景和果实性状大都较为相似.基于选择信号分析,共鉴定到103个处于强烈选择状态的区域,这些区域中的位点可为后续功能基因研究提供候选.
Abstract
A total of 61 950 high-quality SNP loci were identified based on published common bean genome and resequencing data using bioinformatic methods.By evaluating the target loci for probe design,40K,20K and 10K liquid chips containing 40 352,20 855 and 10 486 SNP loci were finally designed and developed,respectively.Using the 10K liquid chip,89 common bean varieties were genotyped by targeted sequencing.The results showed that the mean polymorphic information content and genetic diversity values of 89 common bean varieties were 0.35 and 0.29,respectively.The 89 common bean varieties were classified into two genetic subgroups by STRUCTURE and cluster analysis,which showed that the genetic background and fruit traits of common bean varieties in the same region were mostly similar.Based on selection signal analysis,a total of 103 regions subject to strong selective pressure were identified,and the loci in these regions will provide candidates for subsequent functional gene studies.
关键词
菜豆/单核苷酸多态性/靶向测序/遗传多样性Key words
common bean/single nucleotide polymorphism(SNP)/genotyping by target sequencing(GBTS)/genetic diversity引用本文复制引用
基金项目
江苏省农业科技自主创新项目(CX203099)
出版年
2024
NETL
NSTL
万方数据