中国畜牧兽医2024，Vol.51Issue(8)：3447-3460,14.DOI:10.16431/j.cnki.1671-7236.2024.08.023
基于GBS测序技术分析云上黑山羊主配公羊亲缘关系及近交系数
Genetic Relationship and Inbreeding Coefficients of Yunshang Black Goats Main Mating Rams Using Genotyping-by-Sequencing
摘要
Abstract
[Objective]This study was aimed to explore the kinship and inbreeding coefficient of Yunshang Black goats main mating rams,construct an efficient joint breeding system for meat goats,and improve the production performance and sustainable development of Yunshang Black goats.[Method]100 main mating rams from 5 core breeding farms(XD,ZY,ML,SB and TJ)of Yunshang Black goats were sequenced by genotyping-by-sequencing(GBS)technology,and softwares such as BWA,SAMTOOLS,PLINK v 1.90,Gmatrix v 2 and Mega X were used for the identification of high-quality single nucleotide polymorphism(SNP)after quality control,principal component analysis(PCA),the construction of identical by state(IBS)and G matrix,phylogenetic tree analysis,calculation of kinship coefficient and estimation of inbreeding coefficient,respectively.[Result]215 926 high-quality SNPs were obtained after GBS and quality control,and 8 692 long runs of homozygosity(ROH)were detected ranging from 10.59 to 591.23 Mb in length with an average of 245.74 Mb.The average IBS genetic distance in Yunshang Black goats main mating rams population was 0.118±0.011,and the results of the kinship G-matrix were consistent with the results of IBS distance matrix.100 Yunshang Black goats main mating rams were divided into 3 branches and 28 families according to the phylogenetic tree and kinship analysis.There was only one ram in family 2,11,13,14,16,17,18,20,23,24 and 25.There were 18,10,8,5 and 8 families in XD,ZY,ML,SB and TJ nuclear breeding farms,respectively.The average inbreeding coefficient of population genome based on ROH(FROH)was 0.099641,the FROH of 29 rams was less than 0.0625,that of 39 rams was between 0.0625-0.125,and that of 32 rams was more than 0.125,which indicated that there was a large inbreeding accumulation.[Conclusion]In summary,100 Yunshang Black goats main mating rams were divided into 28 families,among which 11 families had only one ram.Breeding should be strengthened to prevent the loss of their bloodlines.In the formulation of breeding plan,attention should be paid to the individuals with FROH more than 0.125 to prevent inbreeding depression,and reasonable exchange of breeding rams should be carried out according to different breeding objectives.关键词
云上黑山羊主配公羊/简化基因组测序(GBS)/亲缘关系/近交系数Key words
Yunshang Black goats main mating rams/genotyping-by-sequencing(GBS)/genetic relationship/inbreeding coefficient分类
农业科技引用本文复制引用
李子健,江炎庭,兰蓉,朱兰,叶朗惠,龚翔,欧阳依娜..基于GBS测序技术分析云上黑山羊主配公羊亲缘关系及近交系数[J].中国畜牧兽医,2024,51(8):3447-3460,14.基金项目
云南省基础研究计划重点项目(202001AS070002) （202001AS070002）
云南省重大科技专项计划(202102AE090039) （202102AE090039）
云南省技术创新人才培养对象项目(202405AD350042) （202405AD350042）
云南省兴滇英才支持计划(YNWR-CYJS-2020-028) （YNWR-CYJS-2020-028）
