中国草食动物科学2025，Vol.45Issue(6)：34-40,7.DOI:10.3969/j.issn.2095-3887.2025.00.034
基于SNP芯片分析灵丘青背山羊遗传多样性和群体遗传结构
Analysis of Genetic Diversity and Population Genetic Structure in Lingqiu Grayback Goat Based on SNP Chip
摘要
Abstract
This study aimed to provide a scientific basis for the identification of new breeding resources by analyzing the population genetic structure and genetic diversity of Lingqiu Grayback goat(to be identified).A total of 332 goats including Lingqiu Grayback goats,Taihang goats,Lüliang Black goats and Jining Gray goats were used as research ob-jects.Whole genome SNPs were detected using the"Zhongxin 1"65K SNP chip,and Plink(V1.90),VCFtools(v0.1.17),SNeP(v1.10),and PopLDdecay(v1.90)software were employed to analyze the genetic diversity of Lingqiu Grayback goats.And GCTA(v1.94),MEGA v11.0.13,Admixture(v1.30)software were employed to analyze the population genetic structure of Lingqiu Grayback goats.The results showed that a total of 59 727 SNPs were identified,and 51 819 SNPs remained after quality control.The principle component analysis(PCA)and phylogenetic tree analysis revealed Lingqiu Grayback goats separate clustering distinguishable from the other three populations.Population structure analysis of an-cestral components showed that when K=5,it is optimal cluster number,and Lingqiu Grayback goats had a proportion of unique ancestral components.The linkage disequilibrium(LD)decay plot showed that the decay of Lingqiu Gray-back goats was between that of Lüliang Black goat and Taihang goat,and the degree of genomic selection was mode-rate.Genetic diversity analysis showed the effective group content(Ne),expected heterozygosity(He),observed heterozy-gosity(Ho),proportion of polymorphic markers(PN)and nucleotide polymorphism(Pi)of Lingqiu Grayback goat were 16.4,0.381 7,0.382 6,0.899 0,and 0.384 0 respectively.The group differentiation index(FST)showed the population differentiation indices between Lingqiu Grayback goat and Jining Gray goat,Lüliang Black goat,and Taihang goat were 0.047 9,0.032 8,and 0.021 7 respectively,revealed the low population differentiation degree.Kinship analysis showed that most individuals of Lingqiu Grayback goats had a relatively far away genetic relationship,indicated low degree of close intercourse.In summary,this study found Lingqiu Grayback goat was clustered independently from the other three groups,and exhibited a certain genetic diversity,and low inbreeding degree in its poputation,and it could be determined as a potentially new genetic resource.关键词
灵丘青背山羊/SNP芯片/遗传多样性/群体遗传结构Key words
Lingqiu Grayback goat/SNP chip/genetic diversity/population genetic structure分类
农业科技引用本文复制引用
程彩虹,刘巧霞,杨建军,王政坤,周胜花,杨子森,杨帅,程俐芬..基于SNP芯片分析灵丘青背山羊遗传多样性和群体遗传结构[J].中国草食动物科学,2025,45(6):34-40,7.基金项目
山西省现代农业产业技术体系建设专项资金 （）
2022年省级乡村振兴资金计划(现代种业发展项目) （现代种业发展项目）
