福建农业学报2023，Vol.38Issue(11)：1312-1320,9.DOI:10.19303/j.issn.1008-0384.2023.11.007
浦市黑猪保种群体基于SNP芯片的遗传结构分析
Genetics of Preserved Pushi Black Pigs Analyzed Using SNP Chip
摘要
Abstract
[Objective]Genetic diversity and family structure of a preserved population of Pushi black pig were analyzed using the SNP bead chip for resource conservation.[Method]SNPs of 79 adult Pushi black pigs consisting of 10 boars and 69 sows were determined using Porcine 50K SNP Beadchips.Software,including Plink,Gmatix,and Mega X,was used to analyze the genetic diversity and phylogenetic relationships to construct phylogenetic structure of the pig population.[Result]A total of polymorphic 57466 SNP loci were found with an average genotype detection rate of 99.15%.The population showed evidence of inbreeding as the effective Ne was merely 1.5 and the average observed heterozygosity slightly below the expected level.The average distance of IBS was(0.2949±0.0726)and that for the boars(0.277 1±0.091 8).A total of(29.60±16.12)ROHs were detected with 40.5%of them between 0 and 100 Mb in length.The average inbreeding coefficient based on ROH was 0.108.The analysis on IBS distance matrix,G matrix,and population ROHs indicated a close genetic relationship among the individual animals.Based on the evolutionary tree,the population was divided into two families containing boars and one without.[Conclusion]The population of Pushi black pigs under study had only a few families,which varied greatly in number of members in each family and showed a high degree of inbreeding.Consequently,introducing or creating new lineages to expand the gene pool and reduce inbreeding coefficient for the population seemed imperative.关键词
浦市黑猪/保种群体/SNP芯片/遗传多样性/亲缘关系Key words
Pushi black pig/preserved population/SNP chip/genetic diversity/phylogenetic relationship分类
农业科技引用本文复制引用
邓缘,喻国均,陈晨,彭英林,崔清明,陈四海,左剑波,刘莹莹,朱吉,任慧波,胡雄贵,李华丽..浦市黑猪保种群体基于SNP芯片的遗传结构分析[J].福建农业学报,2023,38(11):1312-1320,9.基金项目
湖南省自然科学基金项目(2021JJ30386) （2021JJ30386）
湖南省创新平台与人才计划项目(2021NK1009) （2021NK1009）
湖南省重点研发计划项目(2020NK2024、2019NK2193) （2020NK2024、2019NK2193）
湖南省重点实验室开放研究基金项目(2017TP1030) （2017TP1030）
