基于GBS技术的籼稻种质资源SNPs和Haplotype分析

SNPs and Haplotype Based on GBS in Indica Rice

利用GBS技术(NlaⅢ和MseⅠ分别酶切)对198份(112份恢复系,49份保持系和37份不明恢保关系材料)陕西省主要籼稻种质资源进行测序,MAF 0.05过滤,获得91421 SNPs,构建6981个Haplotype。采用MEGA5、PLINKv 1.07、TASSEL 5.0等生物学主流软件和R语言,进行籼稻群体的SNPs和Haplotype在全基因组的分布特点、群体遗传结构及全基因组KEGG分析。分布在籼稻12个连锁群上的SNPs和Haplotype的多态性及密度都不同。主成分、UPGMA及K聚类都表明198个籼稻的遗传基础较单一,样本间的遗传距离为0.01~0.60,平均遗传距离为0.28。籼稻全基因组注释基因主要参与核糖体、植物激素信号转导和内质网蛋白质加工信号通路。平均每4374 bp有1个SNP。198个籼稻组成的自然群体分层不明显,可以作为后续QTLs的定位群体。不同连锁群上编码的基因行使的主要生物学功能差异明显。

With the development of high-throughput sequencing technology,a large number of single nucleotide polymorphism(SNPs)data and haplotype construction based on SNPs are emerging,which are widely used in phylogeny,population structure,linkage mapping,quantitative trait locus(QTLs)mapping,genome-wide association and so on.This survey of genetic diversity provides a foundation for rice breeding,so as to resolve complex traits through genome-wide association studies.In this study,198 samples representing the main Indica rice germplasm resources in Shaanxi province,including 112 restorer lines,49 maintainer lines and 37 lines(unclear restoring and maintaining relationship)were selected for genotyping SNPs using GBS technology(NlaⅢand MseⅠdigestion,respectively),a total of 91421 SNPs(MAF≥0.05)were obtained and 6981 haplotypes were constructed.The SNPs characteristics of the number and density distribution,haplotype as well as genetic structure of population were analyzed by MEGA5,Plinkv 1.07,TASSEL 5.0 software and R package.The results showed that the polymorphism and density of SNPs and haplotypes on 12 linkage groups of Indica rice were different.The genetic basis of 198 samples was single,and the genetic distance between samples ranging from 0.01 to 0.60,and the average genetic distance was 0.28.The KEGG analysis showed that those genes of genome-wide annotated were mainly involved in ribosome,the plant hormone signal transduction and protein processing in endoplasmic reticulum.There was one SNP at average of 4734 bp.The natural population composed of 198 Indica rice had no obvious stratification,which could be used as a mapping population for subsequent QTLs.The main biological functions of the genes encoded on different linkage groups were significantly different.