基于基因组重测序发掘金针菇InDel、SV及丰度SNP标记  

Exploitation of InDel,SV and abundance SNP markers in Flammulina filiformis based on genome resequencing

作　　者：贾定洪 王波 何晓兰 刘询 JIA Dinghong;WANG Bo;HE Xiaolan;LIU Xun(Sichuan Institute of Edible Fungi,Chengdu 610066,Sichuan,China)

机构地区：[1]四川省食用菌研究所,四川成都610066

出　　处：《菌物学报》2024年第7期39-50,共12页Mycosystema

基　　金：国家食用菌产业技术体系项目(CARS-20);国家重点研发计划(2022YFD1200603)。

摘　　要：以金针菇白色单核菌株wm14基因组为参考基因组,以双核菌株15W、16W、18W、19W、20Y、21Y、22Y和25Y基因组重测序数据为研究对象,以自备的4个金针菇基因组为blast检验数据库,采用VCFtools-0.1.16软件进行数据过滤,发掘可靠且多态性强的SNP、InDel及SV位点信息。使用Primer3软件设计引物,通过标记引物的blastn特异性及通用性检测,实验获得了InDel/SV标记26个;它们可以直接扩增,根据电泳条带的大小差异检测菌株的遗传差异,获得了丰度SNP标记区域63个,成功设计出通用性引物16对作为传统ITS、Rpb2、Ef1α等靶标序列的有益补充。本研究拟开发更多可用于金针菇遗传分析的分子标记,希望可以从全基因组扫描明晰研究菌株的遗传背景,为后续金针菇分子辅助育种、功能基因发掘与机理探索等研究提供助力。Using the genome of white-coloured monokaryotic Flammulina filiformis wm14 as reference genome,resequencing data of dikaryotic strains 15W,16W,18W,19W,20Y,21Y,22Y,and 25Y as research objects,self-provided four genomes of F.filiformis as blast verification database,and VCFtools-0.1.16 software for data filtering,reliable and highly polymorphic SNP,InDel,and SV site informations were exploited.Primer3 software was used for primer design.Through blastn specificity and universality testing of the marker primers,26 InDel/SV markers were obtained,which could be directly amplified to detect genetic differences among strains based on the size differences of electrophoresis bands.Altogether 63 regions with abundant SNP markers were obtained and 16 pairs of universal primers were successfully designed,which could be used as beneficial supplements to traditional ITS,Rpb2,Ef1α,and other target sequences.More molecular markers for genetic analysis of F.filiformis have need to develop,aiming to clarify the genetic background of the research strains through whole-genome scanning,and provide support for subsequent research on molecular-assisted breeding,functional gene discovery,and mechanism exploration of F.filiformis.

关 键 词：金针菇 插入与缺失标记 结构变异标记 单核苷酸多态性标记 引物设计 

分 类 号：S646.15[农业科学—蔬菜学]