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

doi:10.16431/j.cnki.1671-7236.2024.08.023

Abstract

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 (F_ROH) was 0.099641,the F_ROH 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 F_ROH more than 0.125 to prevent inbreeding depression,and reasonable exchange of breeding rams should be carried out according to different breeding objectives.

Key words: Yunshang Black goats main mating rams; genotyping-by-sequencing (GBS); genetic relationship; inbreeding coefficient

CLC Number:

S813.3

LI Zijian, JIANG Yanting, LAN Rong, ZHU Lan, YE Langhui, GONG Xiang, OUYANG Yina. Genetic Relationship and Inbreeding Coefficients of Yunshang Black Goats Main Mating Rams Using Genotyping-by-Sequencing[J]. China Animal Husbandry and Veterinary Medicine, 2024, 51(8): 3447-3460.

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Genetic Relationship and Inbreeding Coefficients of Yunshang Black Goats Main Mating Rams Using Genotyping-by-Sequencing

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