摘要
旨在基于SNP芯片信息分析通城猪保种群的群体结构和遗传多样性,对保种效果进行监测。本研究利用“中芯一号”50KSNP芯片对68头通城猪的全基因组SNP进行扫描,通过以下两方面评估保种效果:1)群体结构。通过群体分层、遗传距离、亲缘关系以及公猪基因组家系等分析,研究通城猪个体间的群体结构;2)遗传多样性。估算等位基因频率、有效等位基因数、多态信息含量、多态性标记比例、杂合度、核苷酸多样性等多态性和杂合性相关参数估计遗传多样性,分析有效群体含量和连续性纯合片段(runs of homozygosity,ROH),综合评估保种效果。结果显示:1)保种群无明显分层,遗传距离为0.27,亲缘系数为0.17;2)基因组等位基因频率为0.77,有效等位基因数为1.52,多态信息含量均值为0.31,多态性标记比例为88.28%,观测杂合度为0.32,期望杂合度为0.31;20世代前通城猪有效群体含量为105头,当前世代有效群体含量为94头;ROH共计有184个,平均ROH长度为23.71Mb,其中28.80%的长度在15~20Mb之间;基因组近交系数为0.04%,具较低水平的近交程度。通城猪保种群是一个没有分层的纯种群体,具有丰富的遗传多样性,得到了有效保护。
This study aimed to analyze the population structure and genetic diversity of Tongcheng pig conservation population based on SNP chip information and to monitor the conservation effect.In this study,"Zhongxin No.1"50KSNP chip was used to scan the whole genome SNPs of 68Tongcheng pigs,and the population conservation effect was evaluated from two aspects:1)Population structure.Based on the analysis of population stratification,genetic distance,kin ship,and boar genome family,the population structure among Tongcheng pigs were studied;2)Genetic diversity.Allele frequency,effective number of alleles,polymorphism information content,proportion of polymorphic loci,heterozygosity,nucleotide diversity,and other polymorphism and heterozygosity-related parameters were employed to estimate genetic diversity and to analyze effective population size and runs of homozygosity(ROH).Based on these parameters,comprehensive evaluation of population conservation effects was conducted.The results showed that:1)The conservation population exhibited no obvious stratification with the genetic distance of 0.27,and they had a medium kinship 0.17;2)The genome allele frequency was 0.77;the effective number of alleles was 1.52;the mean polymorphism information content was 0.31;the proportion of polymorphic markers was 88.28%;the observed heterozygosity was 0.32;and the expected heterozygosity was 0.31.The effective population size of Tongcheng pigs before the 20th generation was 105,and the effective population size of the current generation was 94.There were 184ROHs in total.The average ROH length was 23.71Mb,of which 28.80%was between 15and 20Mb in length.The genomic inbreeding coefficient was 0.04%,indicating a low level of inbreeding.Taken together,the results show that the conservation population of Tongcheng pigs is a pure breed without stratification,and Tongcheng pigs had rich genetic diversity with remarkable population conservation effect.
作者
袁娇
徐国强
周翔
徐三平
李胜
黎望明
刘榜
YUAN Jiao;XU Guoqiang;ZHOU Xiang;XU Sanping;LI Sheng;LI Wangming;LIU Bang(College of Animal Sciences&Technology,Huazhong Agricultural University,Wuhan 430070,China;Key Laboratory of Agricultural Animal Genetics,Breeding and Reproduction of Ministry of Education,Huazhong Agricultural University,Wuhan 430070,China;The Cooperative Innovation Center for Sustainable Pig Production,Wuhan 430070,China;The Engineering Technology Research Center of Hubei Province Local Pig Breed Improvement,Wuhan 430070,China;Agricultural and Rural Bureau of Tongcheng County,Tongcheng437400,China)
出处
《畜牧兽医学报》
CAS
CSCD
北大核心
2022年第8期2514-2523,共10页
ACTA VETERINARIA ET ZOOTECHNICA SINICA
基金
国家自然科学基金重点项目(31930104)。
关键词
通城猪
保种
群体结构
遗传多样性
Tongcheng pig
conservation
population structure
genetic diversity