基于SNP标记的辣木群体遗传分析  

Analysis of Genetic of Moringa oleifera Population Based on SNP Markers

作　　者：普天磊 韩学琴[1] 罗会英[1] 邓红山[1] 邹枚伶[2] 金杰[1] 夏志强 王文泉 PU Tianlei;HAN Xueqin;LUO Huiying;DENG Hongshan;ZOU Meiling;JIN Jie;XIA Zhiqiang;WANG Wenquan(Institute of Tropical Eco-agriculture,Yunnan Academy of Agricultural Sciences/Yuanmou Dry-hot Valley Botanical Garden,Yuanmou,Yunnan 651300,China;Hainan University,Haikou,Hainan 570228,China)

机构地区：[1]云南省农业科学院热区生态农业研究所/元谋干热河谷植物园,云南元谋651300 [2]海南大学,海南海口570228

出　　处：《热带作物学报》2023年第9期1786-1793,共8页Chinese Journal of Tropical Crops

基　　金：国家现代农业产业技术体系项目(No.CARS-11-YNJJ);云南省重大科技专项“生物资源数字化开发应用”项目(No.202002AA100007);海南大学科研启动基金项目(No.KYQD(ZR)-20101)。

摘　　要：基于SNP标记对辣木亲本及其子代群体的杂合度、遗传结构及遗传多样性进行分析,研究其遗传变异特征。利用AFSM技术对96份辣木材料进行简化基因组测序,将获得的测序过滤数据比对至参考基因组,使用VCFtools和BCFtools软件检测并统计SNP和Indel位点信息。利用AWK语言分析杂合位点,并比对出子代与亲本的差异位点,以分析辣木的繁育类型。利用Plink软件对变异位点进行过滤,保留高质量的变异位点,再通过ADMIXTURE软件进行群体结构分析,根据交叉验证错误率确定最佳K值,同时采用GCTA软件进行主成分分析,构建系统进化树,解析辣木材料的群体结构。采用VCFtools计算遗传多样性指数及群体分化指数,分析该群体的遗传多样性。通过LDBlockShow软件进行连锁不平衡分析,得出位点间的连锁不平衡程度。结果显示,共检测出1187831个SNP位点,150861个Indel位点。将辣木子代基因与亲本比对后,发现辣木子代杂合的基因中,约有4.89%的基因为自身杂合基因,19.96%为外来遗传物质导致杂合的基因,基本表明辣木可通过自花和异花2种授粉方式繁衍后代。群体结构和主成分分析将辣木样品划分为3个亚群,与聚类分析的结果大概一致,即各亚群大致能聚在一起,且样品间有一定的交叉。辣木不同群体间的遗传分化指数(0.0049~0.0110)和遗传多样性指数(0.001)低,表明群体遗传分化弱,遗传多样性水平低。对检测到的136个scaffold的SNP进行统计并进行连锁不平衡分析后发现,scaffold1的SNP数目最多,为62225个,且其6748044~6748185位点之间具有强连锁不平衡关系。本研究通过对辣木及其子代的遗传分析,为辣木的杂交选育提供遗传学依据。The heterozygosity,population structure and genetic diversity of Moringa oleifera and its progeny were ana-lyzed using the SNP markers.The characteristics of genetic variation of M.oleifera and its progeny were studied.Sim-plified genome sequencing of 96 M.oleifera materials was performed by AFSM technology.The obtained sequencing filtering data were compared to the reference genome.SNP and Indel loci were detected and counted by using VCFtools and BCFtools.In order to analyze the reproduction types of M.oleifera,AWK language was used to analyze heterozy-gous loci,and compare the different loci of the progeny with the parents.The mutation sites were filtered by Plink software,and the high-quality mutation sites were reserved.The population structure was analyzed by ADMIXTURE software,and the optimal K value was determined according to the cross validation error rate.At the same time,GCTA software was used for principal component analysis,and the phylogenetic tree was constructed to analyze the population structure of the materials.VCFtools was used to calculate the genetic diversity index and population differentiation in-dex for analyzing the genetic polymorphism of the population.LDBlockShow software was used for linkage imbalance analysis,and the linkage imbalance degree between loci was obtained.The result showed that a total of 1187831 SNP sites and 150861 Indel sites were detected in this paper.We compared M.oleifera progeny genes with parents,which found that among the heterozygous genes in Moringa progeny,about 4.89%of the genes are self-heterozygous genes,and 19.96%of the heterozygous genes caused by foreign genetic materia.It indicates that M.oleifera produce offspring by the ways of self-pollination and cross-flowering.M.oleifera samples were divided into 3 subgroups by population structure and principal component analysis.The cluster analysis is roughly consistent with the above results.The subgroups can be clustered together,and there is a little crossover between the samples.The low genetic differen

关 键 词：辣木 SNP 杂合度 群体结构 遗传多样性 

分 类 号：S792.99[农业科学—林木遗传育种]