基于ddRADseq的马铃薯品种遗传多样性分析  

Analysis on Genetic Diversity of Potato Varieties Based on ddRADseq

作　　者：单建伟 索海翠[1] 王丽[1] 安康[1] 刘计涛 李成晨 白建明[2] 李小波[1] SHAN Jianwei;SUO Haicui;WANG Li;AN Kang;LIU Jitao;LI Chengchen;BAI Jianming;LI Xiaobo(Crops Research Institute,Guangdong Academy of Agricultural Sciences/Guangdong Key Laboratory of Crops Genetics&Improvement,Guangzhou 510640,China;Industrial Crops Institute,Yunnan Academy of Agricultural Sciences,Kunming 650000,China)

机构地区：[1]广东省农业科学院作物研究所/广东省农作物遗传改良重点实验室,广东广州510640 [2]云南省农业科学院经济作物研究所,云南昆明650000

出　　处：《广东农业科学》2021年第12期120-128,共9页Guangdong Agricultural Sciences

基　　金：广东省农业科学院作物研究所所长基金(201904);广东省农作物遗传改良重点实验室开放基金(201904);广东省科技计划项目(2017B020232002);广东省现代农业产业技术体系创新团队项目(2021KJ111)。

摘　　要：【目的】收集国内外马铃薯品种(系)资源,研究马铃薯种质群体结构和遗传多样性,开发SNP分子标记,为马铃薯品种鉴定、分子标记辅助选择育种奠定基础。【方法】提取马铃薯嫩芽基因组DNA,利用限制性内切酶MseI和SacI进行双酶切建库,质量检测合格后用Illumina HiSeq平台进行双末端测序,用BWA软件将测序数据与马铃薯参考基因组进行比对,采用GATK软件进行SNP和InDel变异位点检测,利用ANNOVAR软件进行变异注释,并基于上述变异信息对群体结构进行Structure分析、主成分分析(PCA)和遗传多样性分析。【结果】通过简化基因组测序共获得7.50×10^(8)条测序reads和2.04×10^(11)个碱基,共检测到39038个变异位点,其中SNP位点36267个,InDel位点2771个;基于上述变异位点的Structure和PCA分析均将研究群体划分为两个亚群,群体系统发生分析表明,G2亚群中的个体聚类在一起,亲缘关系较近,但与其他个体相比G2亚群中的分枝距离中心较远,积累了更多的变异量;群体的平均多态性信息含量PIC=0.3107,期望杂合度He=0.3932,观测杂合度Ho=0.1852,群体自交系数Fis=0.553,表明马铃薯品种(系)间遗传多样性较低;开发了覆盖马铃薯12条染色体且包含120个SNP标记的SNP-Panel,并选取其中的60个标记在46个样品中进行了验证。【结论】研究结果为马铃薯遗传多样性研究、分子标记辅助选择育种、分子身份证开发、遗传图谱构建奠定了一定基础。【Objectice】The present research aimed to collect potato variety(strain)resources,study the population structure and genetic diversity of potato germplasm and develop SNP molecular markers,with a view to providing theoretical foundation for potato variety identification and molecular marker-assisted selection breeding.【Method】Genome DNA of potato tender shoots was extracted and digested with restriction enzymes MseI and SacI.After quality verification,Paired-end sequencing was carried out on Illumina HiSeq platform,sequencing data was aligned to potato reference genome with BWA software,SNP and InDel variation sites were detected and annotated with GATK and ANNOVAR respectively,and population structure analysis,principal component analysis and genetic diversity analysis were conducted based on the SNPs.【Result】By simplifying genome sequencing,7.50×108 sequencing reads and 2.04×1011 bases were obtained.A total of 39038 variation sites were detected,of which 36267 were SNP sites and the other 2771 sites were InDel.Based on the Structure analysis and PCA analysis,the 185 samples were divided into 2 subgroups.Population phylogenetic analysis showed that the individuals in G2 subgroup were clustered together with close genetic relationship,but the branches in G2 subgroup were far from the center and accumulated more variations than other individuals.PIC,He,Ho and Fis were 0.3107,0.3932,0.1852 and 0.553 respectively,which indicated that the genetic diversity of potato varieties(strains)was poor,SNP-Panel with 120 SNPs distributing on all the 12 potato chromosomes was developed and 60 SNPs of 46 samples were verified.【Conclusion】The research results laid a foundation for the study of potato genetic diversity,molecular marker-assisted selection breeding,development of molecular identity card and construction of genetic map.

关 键 词：马铃薯 遗传多样性 群体结构 SNP标记 ddRADseq 

分 类 号：S532.032[农业科学—作物学]