[目的]探究云上黑山羊主配公羊的亲缘关系及近交系数，构建肉羊高效联合育种体系，提升云上黑山羊生产性能和可持续发展力。[方法]采用简化基因组测序(genotyping-by-sequencing，GBS)技术对云上黑山羊5个核心育种场(XD、ZY、ML、SB、TJ)的100只主配公羊进行测序，并使用BWA、SAMTOOLS、PLINK v 1。90、Gmatrix v 2、Mega X等软件进行质控后高质量单核苷酸多态性(single nucleotide polymorphism，SNP)位点鉴定、主成分分析(PCA)、状态同源距离矩阵(identical by state，IBS)和G矩阵构建、群体进化树分析、亲缘系数计算及近交系数估计。[结果]GBS质控后共获得215 926个高质量SNPs位点;共检测到8 692条连续性纯合片段(runs of homozygosity，ROH)，长度在10。59～591。23 Mb之间，平均长度245。74 Mb。云上黑山羊主配公羊群体平均IBS遗传距离为0。118±0。011，亲缘关系G矩阵结果与IBS距离矩阵结果一致。结合群体进化树和亲缘关系分析，100只云上黑山羊被分为三大支和28个家系，其中家系2、11、13、14、16、17、18、20、23、24、25仅有1只公羊，XD、ZY、ML、SB、TJ核心育种场分别有18、10、8、5和8个家系;基于ROH的群体平均基因组近交系数为0。099641，29只公羊的近交系数＜0。0625，39只公羊的近交系数在0。0625～0。125之间，32只公羊近交系数＞0。125，存在较大的近交累积。[结论]100只云上黑山羊主配公羊被分为28个家系，其中11个家系仅有1只公羊，应加强繁育防止其血统的流失，配种方案制定中应关注近交系数＞0。125的个体，防止近交衰退，同时根据不同的育种目标合理进行种公羊的交换。
Genetic Relationship and Inbreeding Coefficients of Yunshang Black Goats Main Mating Rams Using Genotyping-by-Sequencing
[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.
Yunshang Black goats main mating ramsgenotyping-by-sequencing(GBS)genetic relationshipinbreeding coefficient
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