摘要
旨在基于全基因组SNPs数据探讨井冈黑掌鹅(Jinggang black-palm goose,JGG)与中国不同地域地方鹅之间的系统发育关系,解析中国家鹅及JGG的遗传多样性和遗传结构,为中国家鹅资源的鉴定与保护提供理论基础。本研究基于81只井冈黑掌鹅和6个地方家鹅品种的120只个体的基因组重测序数据(12×),使用GATK和SnpEff软件对重测序基因组的单核苷酸多态性(single nucleotide polymorphism,SNP)进行检测与注释。基于常染色体SNP,构建系统进化树(neighbour-joining tree,NJ tree),进行主成分分析(principal component analysis,PCA)聚类和Admixture分析,评估中国家鹅的群体结构和遗传多样性。研究结果显示,JGG群体中检测到5955261个SNPs,变异主要富集在基因间区(46.39%)和内含子区(34.56%),外显子区(1.38%)变异较少。NJ tree、PCA和Admixture的结果显示,JGG种群单独聚类,其遗传分化受地理隔离、体型和羽色选育的驱动,显示出与兴国灰鹅、丰城灰鹅以及狮头鹅较近的亲缘关系。JGG的遗传多样性较低,常见SNP为3414168个,多肽位点比例(proportion of polypeptide sites,Pn)、期望杂合度(expected heterozygosity,He)、实际杂合度(observed heterozygosity,Ho)、近交系数(inbreeding coefficient,F)、种群内遗传距离(intra-population genetic distance,DST)以及纯合性片段长度(runs of homozygosity,ROH)分别为0.83、0.26、0.23、0.33±0.09、0.224±0.022和12.87±8.27。该研究结果系统解析了中国家鹅及井冈黑掌鹅的群体遗传结构和基因组特征,结果表明井冈黑掌鹅作为独立的地方品种鹅,其遗传分化主要受地理隔离和表型选育的影响,但其遗传多样较低,种群特征存在丧失的风险,亟需加强对该地方品种的保护与利用。
This study aimed to explore the phylogenetic relationships between the Jinggang black-palm goose(JGG)and various local goose breeds across China based on whole-genome SNP data,and to analyze the genetic diversity and genetic structure of Chinese geese and JGG,providing a theoretical foundation for the identification and conservation of Chinese goose resources.Genome resequencing data(12×coverage)from 81 Jinggang black-palm geese and 120 individuals of 6 local goose breeds were analyzed.Single nucleotide polymorphisms(SNPs)detection and annotation were conducted on autosomal regions using GATK and SnpEff softwares.A neighbor-joining(NJ)tree,principal component analysis(PCA),and Admixture analysis were performed to assess their population structure and genetic diversity.The JGG population harbored 5955261 SNPs,predominantly in intergenic(46.39%)and intronic regions(34.56%),with fewer in exonic regions(1.38%).Consistently,NJ tree,PCA,and Admixture analyses revealed distinct clustering of JGG,showing closer genetic affinity to Xingguo grey geese,Fengcheng grey geese,and Lionhead goose,driven by geographic isolation and artificial selection for body size and plumage traits.JGG exhibited low genetic diversity,with 3414168 common SNPs.Key parameters included:proportion of polymorphic sites(Pn=0.83),expected heterozygosity(He=0.26),observed heterozygosity(Ho=0.23),inbreeding coefficient(F=0.33±0.09),intra-population genetic distance(DST=0.224±0.022),and runs of homozygosity(ROH=12.87±8.27).This study systematically elucidates the population genetic structure and genomic characteristics of Chinese geese and JGG.As an independent local breed,JGG’s genetic differentiation is shaped by geographic isolation and phenotypic selection,yet its low genetic diversity poses a risk of trait loss,highlighting the imperative for enhanced conservation and utilization efforts.
作者
缪俊杰
张日泉
吴厚义
游新明
黄奕雯
黄小英
郭震洋
刘建林
肖卫华
郭田华
陈浩
康冬柳
MIAO Junjie;ZHANG Riquan;WU Houyi;YOU Xinming;HUANG Yiwen;HUANG Xiaoying;GUO Zhenyang;LIU Jianlin;XIAO Weihua;GUO Tianhua;CHEN Hao;KANG Dongliu(Ji’an Agricultural and Rural Industry Development Service Center,Ji’an 343000,China;College of Life Sciences,Jiangxi Normal University of Science and Technology,Nanchang 330013,China;Ji’an Livestock and Poultry Breeding Farm,Ji’an 343000,China;Wan’an County Agricultural Industry Development Service Center,Wan’an 343800,China;Qingyuan District Agricultural and Rural Bureau,Ji’an 343000,China;Suichuan County Agricultural Industry Development Service Center,Suichuan 343900,China)
出处
《畜牧兽医学报》
北大核心
2025年第7期3199-3209,共11页
ACTA VETERINARIA ET ZOOTECHNICA SINICA
基金
国家自然科学基金地区项目(32460141)
江西省自然科学基金面上项目(20232BAB205059)
江西科技师范大学青年拔尖人才项目(2023QNBJRC004)。
关键词
井冈黑掌鹅
中国家鹅
全基因组SNPs
遗传多样性
种质资源
Jinggang black-palm goose
Chinese domestic goose
whole-genome SNPs
genetic diversity
germplasm resources
