基于GBS技术开展柚类资源群体遗传评价并发掘酸含量相关基因  

Population Genomic Structure of Pomelo Germplasm and Fruit Acidity Associated Genes Identification by Genotyping-by-Sequencing Technology

作　　者：江东[1] 王旭 李仁静 赵晓东 戴祥生 柳正葳[3] JIANG Dong;WANG Xu;LI RenJing;ZHAO XiaoDong;DAI XiangSheng;LIU ZhengWei(Citrus Research Institute,Southwest University,Chongqing 400712;Jinggangshan Agricultural Science and Technology Park Management Committee,Ji’an 343016,Jiangxi;Jianggangshan University,Ji’an 343016,Jiangxi)

机构地区：[1]西南大学柑橘研究所,重庆400712 [2]井冈山农业科技园管理委员会,江西吉安343016 [3]井冈山大学,江西吉安343016

出　　处：《中国农业科学》2023年第8期1547-1560,共14页Scientia Agricultura Sinica

基　　金：国家重点研发计划(2018YFD1000101,2019YFD1001401);种质资源精准鉴定(19211142);江西科技计划项目(20161BBF60048)。

摘　　要：【目的】弄清我国柚类种质资源的起源与演化、群体遗传结构和多样性水平,高效利用柚类自然资源群体发掘与果实重要品质性状相关的基因,为柚类种质资源群体的遗传结构研究、起源演化和柚类种质创新提供重要的理论及实践依据。【方法】利用国家果树种质重庆柑橘资源圃中保存的具有广泛遗传多样性和不同地理来源的282份柚类资源作为材料,采用EcoR I限制性内切酶消化基因组DNA后构建GBS文库,然后进行Illumina HiSeq PE150二代测序获得短读序列,通过BWA软件将序列映射到柚参考基因组上,利用SAMTOOLS软件鉴定SNP位点。依据SNP的基因分型结果,进行主成分分析和群体结构分析,并采用邻接法构建系统演化树,分析亚群的遗传多样性水平。选择23个低酸种质和32个高酸种质构成两个群体进行Fst、XP-CLR分析,同时利用282个柚类种质的基因型数据与果实可滴定酸含量的表型数据进行GWAS全基因组关联分析。【结果】利用GBS简化基因组测序技术对282份柚类种质进行测序,获得201.66 Gb的原始测序数据,每个样本的平均测序数据量为0.72 Gb,经过测序深度为5×次要等位基因频率>0.01、Miss0.2的筛选条件过滤,最终获得121726个高质量的SNP位点。主成分分析、群体结构分析和聚类分析均表明282份柚类资源可被分为6个亚群,其中柚与‘清见’杂交群体、葡萄柚等橘柚杂种群体可明显区别于其他真正柚类种质。不同地理来源和特定类型的柚类种质在遗传水平上存在明显差异,来源于泰国、越南等东南亚国家的柚类资源形成了较为独特的类群,与国内的沙田柚类、文旦柚类、垫江柚类等群体能够明显区分开。在中国南方的大部分柚类种质中有来自于越南柚的基因渗入,表明越南是柚的原始起源中心。另外,一些来源不清的柚类种质也通过GBS技术得以准确鉴定。Fst、XP-CLR选择性清除�【Objective】To reveal the phylogeny,population genetic structure and diversity level of pomelo(Citrus grandis(L.)Osbeck)germplasm,and to efficiently utilize them to explore genes related to important fruit quality traits,this research provided an insight into the population genetic structure and phylogeny of pomelo germplasm and facilitated the pomelo varieties innovation.【Method】A total of 282 pomelo accessions including landraces from different geographical regions and hybrid offspring of kiyomi tangor and pomelo were contained in this study.GBS library was constructed with genomic DNAs digested by EcoR I restriction endonuclease and sequenced on Illumina HiSeq PE150 platform,the clean short reads were then mapped to pomelo reference genome by BWA,and SNPs were called out with SAMTOOLS pipeline.Based on 121726 SNPs genotyping data,principal component analysis(PCA)and population genetic structure analysis were carried out and phylogenetic trees were constructed with Neighbor-joining method.Furthermore,two sub-populations containing high-acid accessions(32)and low-acid accessions(23)were used to identify candidate genes related to fruit acidity by Fst and XP-CLR selective sweeping analysis.Meanwhile,the genotype data of 282 pomelo accessions and the phenotypic data of titratable acid content in fruit were used for GWAS.【Result】A total of 201.66 Gb original reads were generated from 282 pomelo germplasm by GBS approach,in average each sample produced 0.72 Gb reads.After the screening conditions of sequencing depth of dp5,the miss less than 0.2 and minor alleles frequency(MAF)>0.01,and a total of 121726 SNPs were selected out for subsequent analysis.The PCA,structure and phylogenetic analysis all supported that the 282 pomelo germplasm could be divided into 6 subgroups,among which pomelo and kiyomi hybrid population,grapefruits and other pomelo hybrid populations could be obviously different from true-to-type pomelo populations,pomelos originated from different geographical region displayed unique geneti

关 键 词：GBS 柚系统演化 果实酸度调控基因 GWAS 

分 类 号：S666.3[农业科学—果树学]