基于全基因组重测序的油莎豆InDel位点鉴定及分子标记开发  

InDel Locus Identification and Molecular Marker Development in Cyperus esculentus Based on Whole Genome Re-sequencing

作　　者：张向歌 程珊 陈晨 朱雅婧 李春鑫[1] 许欣然[1] 王树峰[1] 武林海 王会伟[1] ZHANG Xiangge;CHENG Shan;CHEN Chen;ZHU Yajing;LI Chunxin;XU Xinran;WANG Shufeng;WU Linhai;WANG Huiwei(Industrial Crop Research Institute,He'nan Academy of Agricultural Sciences,Zhengzhou 450002,China)

机构地区：[1]河南省农业科学院经济作物研究所,郑州450002

出　　处：《种子》2024年第8期52-59,共8页Seed

基　　金：河南省重大科技专项(211100110100);河南省科技攻关项目(232102110188、232102110261、242102110290)。

摘　　要：选取4种不同类型油莎豆种质资源进行全基因组重测序,以此全基因组水平鉴定油莎豆的InDel位点,并根据多态性InDel位点序列信息开发有效的分子标记。基于重测序数据与油莎豆参考基因组的序列比对,利用GATK和SAMtools软件共鉴定到321271个InDel位点,在油莎豆各个scaffold上呈现高密度分布,其中93%以上位点呈现出杂合类型。通过4种油莎豆种质间InDel位点的多态性分析,发现98%的InDel位点不具有多态性,最终鉴定出6036个多态性InDel位点。基于多态性InDel位点的插入/缺失序列长度分析,筛选出829个插入/缺失序列长度大于20 bp的多态性InDel位点,适用于开发可通过琼脂糖凝胶电泳检测的InDel分子标记。选择8个多态性位点进行InDel分子标记开发和琼脂糖凝胶电泳检验,结果表明,鉴定的多态性InDel位点真实可靠以及开发的InDel分子标记合适可用。本研究利用不同类型油莎豆种质鉴定出大量的多态性InDel位点,能够开发出适合、准确、有效的InDel分子标记,极大地丰富了油莎豆的分子标记资源,为油莎豆种质资源更加精确的评价、鉴定和利用提供可靠的技术支撑。Four different types of Cyperus esculentus germplasm resources were selected for whole genome resequencing,and Cyperus esculentus InDel sites were identified at the whole genome level,and effective molecular markers were developed according to the polymorphic InDel site sequence information.A total of 321271 InDel loci were identified by GATK and SAMtools based on the sequence comparison between the resequencing data and the reference genome of the Cyperus esculentus,showing high density distribution on each scaffold,and more than 93%of the loci showed heterozygous types.According to the polymorphism analysis of InDel sites among four Cyperus esculentus germplasm species,98%of InDel sites were found to be non-polymorphic,and 6036 polymorphic InDel sites were identified.Based on the insertion/deletion sequence length analysis of polymorphic InDel sites,829 polymorphic InDel sites with insertion/deletion sequence length greater than 20 bp were selected,which was suitable for the development of InDel molecular markers that could be detected by agarose gel electrophoresis.Eight polymorphic sites were selected for InDel molecular marker development and agarose gel electrophoresis test.The results showed that the identified polymorphic InDel sites were real and reliable,and the developed InDel molecular markers were suitable and available.In this study,a large number of polymorphic InDel sites were identified by different types of Cyperus esculentus germplasm,and suitable,accurate and effective InDel molecular markers could be developed,which greatly enriched the molecular marker resources of Cyperus esculentus germplasm,and provided reliable technical support for more accurate evaluation,identification and utilization of Cyperus esculentus germplasm resources.

关 键 词：油莎豆 种质资源 全基因组重测序 InDel位点 分子标记 

分 类 号：S565.9[农业科学—作物学]