基于SNP和InDel标记的余甘子群体遗传分析  

Population and genetic analysis of Phyllanthus emblica by SNP and InDel markers

作　　者：普天磊 金杰[1] 何璐[1] 瞿文林[1] 廖承飞[1] 袁建民[1] 罗会英[1] 赵琼玲[1] PU Tianei;JIN Jie;HE Lu;QU Wenin;LIAO Chengfei;YUAN Jianmin;LUO Huiying;ZHAO Qionging(Institute of Tropical Eco-agriculture Yunnan Academy of Agricultural Sciences/Yuanmou Dry-Hot Valley Botanical Garden,Yuanmou 651300,Yunnan,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

出　　处：《果树学报》2023年第5期875-883,共9页Journal of Fruit Science

基　　金：科技部重点研发计划(2017YFC0505106-1);金沙江干热河谷坝区生态综合治理及农业产业发展技术试验示范(2017YFC0505102);云南省重大科技专项(202002AA100007);云南省科技厅科技计划项目:余甘子良种筛选及产业化开发技术研究与示范(202204BP090017);云南省农业科学院热区生态农业研究所人才培养项目(2022RQS004)。

摘　　要：【目的】采用高通量测序技术解析余甘子种质资源的群体遗传结构和遗传多样性,为余甘子系统分类、遗传资源创新利用提供理论基础。【方法】利用ddRADseq技术对112份余甘子种质资源进行高通量简化基因组测序,利用Cutadapt和Trimmomatic软件对原始数据进行过滤,筛选得到高质量测序数据;使用MUNEAK软件进行多态性标记发掘,基于获得的SNP和InDel标记,进行群体结构分析、主成分分析、系统发育分析及遗传多样性分析。【结果】余甘子测序样品共获得8934个SNP和InDel标记,群体结构分析将余甘子种质分为2个类群,类群划分与种质来源地相关,该结果与主成分分析和系统发育分析相一致。余甘子各种质间遗传距离为0.027~0.459,平均遗传距离为0.248;云南地区的余甘子种质的期望杂合度、观测杂合度及多态性信息含量值最高,依次为0.267、0.184及0.218;余甘子群体间的Fst在0.080~0.266之间,群体遗传分化程度中等偏高。【结论】该测序技术可有效地解析余甘子种质的群体结构和遗传多样性,为余甘子种质资源的鉴定评价、系统分类及遗传多样性研究提供参考。【Objective】Based on SNP and InDel molecular markers,the high-throughput sequencing technology-ddRADseq was used to analyze the genetic background of 112 wild Phyllanthus emblica germplasms collected from different origins.The population genetic structure and genetic diversity of P.emblica germplasm resources were analyzed in order to provide a theoretical basis for the systematic classification and innovative utilization of genetic resources of P.emblica.【Methods】The leaves of 112 P.emblica germplasms from different origins were collected and preserved for future use.Among them,3 accessions were introduced from Fujian,9 accessions from Guangxi,11 accessions from Yun-nan.The genomic DNA of P.emblica leaves was extracted by the improved CTAB method.The purity and concentration of the genomic DNA were tested.The ddRADseq technology was used to perform high-throughput simplified genome sequencing on 112 P.emblica germplasm resources.The original da-ta were filtered by Cutadapt software and Trimmomatic software to obtain high-quality sequencing da-ta.The MUNEAK software was used to develop polymorphic markers.Based on the obtained SNP and InDel markers,the STRUCTURE software was used to analyze the population structure and calculate the value ofΔK.The most reasonable number of group number and the attribution of each sample were determined.The principal component analysis of each sample was carried out by Plink software.The scatter diagram of principal component analysis was drawn by R software.The MEGA 7 software was used for phylogenetic analysis to calculate the genetic distance of the tested materials,and then iTOL was used to draw the phylogenetic tree diagram.The PowerMarker software was used to evaluate the genetic diversity of the P.emblica population.The expected heterozygosity(He),observed heterozygosi-ty(Ho),polymorphism information content(PIC)and population differentiation index(Fst)of the popu-lation were calculated.【Results】The samples of P.emblica were constructed and sequenced,a total of

关 键 词：余甘子 SNP INDEL 群体结构 遗传多样性 

分 类 号：S667.5[农业科学—果树学]