基于GBS简化基因组测序数据重建麦洼牦牛保种群系谱

doi:10.11843/j.issn.0366-6964.2023.09.012

摘要/Abstract

摘要： 旨在利用简化基因组测序技术(genotyping-by-sequencing,GBS)构建四川省龙日种畜场的3个麦洼牦牛保种群(全黑群、粉嘴群和弗洛群)系谱,为麦洼牦牛保种选育工作打下基础。本研究从3个保种群选取406头麦洼牦牛(全黑群211头、粉嘴群140头、弗洛群55头),采血提取DNA后进行GBS测序,利用获得的SNP对保种群亲缘关系展开研究,并初步构建系谱。结果:GBS测序后获得高质量SNP位点126 122个。PCA分析(principal component analysis,PCA)表明粉嘴群和全黑群有明显的分化趋势,弗洛群与全黑群、粉嘴群部分个体聚类紧密。本研究共计算出164 836个亲缘关系对,依据个体间的亲缘系数,判定出134个全同胞关系,912个半同胞关系,136个疑似亲子关系或全同胞关系,520个疑似半同胞关系或叔侄关系,205个疑似半同胞关系或叔侄关系或祖孙关系。结合群体进化树和亲缘关系分析,将保种群划分为12个家系(G1~G12)。家系遗传多样性分析结果表明,12个家系的观测杂合度(observed heterozygosity,Ho)为0.288 9~0.305 5,期望杂合度(expected heterozygosity,He)为0.307 4~0.307 6,平均Ho低于平均He,表明12个家系均存在一定程度的近交,G8的Ho最小,为0.288 9,其F_IS最大,为0.060 7。本研究利用GBS技术获得的SNP判定了麦洼牦牛保种群的亲属关系,并将保种群划分为12个家系,初步完善了保种群的系谱,为后续保种选育方案的实施奠定了基础。

关键词: 麦洼牦牛, GBS技术, 亲缘关系, 分子系谱

Abstract: The study aimed to construct the pedigree of three preserved populations of the Maiwa yaks (Black hair, Pink lips and Fulo) in Longri breeding farm, Sichuan Province using genotyping-by-sequencing(GBS) technique,and to lay a solid foundation for the breeding and selection of the Maiwa Yak. A total of 406 Maiwa yaks (211 from the Black hair group, 140 from the Pink lips group and 55 from the Fulo group) were selected from the conserved populations, blood was collected and sequenced by GBS, and the high-quality SNPs obtained were used to study the coefficient of kinship for the entire population and construct its pedigree. The results are as follows:126 122 high-quality SNPs were obtained after GBS sequencing and quality control. Principal component analysis(PCA) showed that both the Pink lips group and the Black hair group showed a clear trend of genetic differentiation, and some individuals from Fulo group clustered closely with the Black hair group and the Pink lips group. A total of 164 836 genetic relationship pairs were calculated in this study. Based on the coefficients of kinship between individuals, 134 full siblings, 912 half-siblings, 136 suspected parent-child relationships or full siblings, 520 suspected half-siblings or uncle-nephew relationships, 205 supposed half-siblings or uncle-nephew relationships or grandchild relationships were identified. Combining population evolutionary tree and kinship analysis, the entire population could be divided into 12 lineages (G1-G12). The genetic diversity analysis of them showed that the observed heterozygosity (Ho) was 0.288 9-0.305 5 and the expected heterozygosity (He) was 0.307 4-0.307 6, with the average Ho lower than the average He, indicating a certain degree of inbreeding within families, with G8 having the smallest Ho at 0.288 9 and its F_IS the largest at 0.060 7. In this study, SNPs obtained by GBS technology were used to determine the kinship of the preserved population, and the entire population was divided into 12 families, which initially improved the pedigree of the preserved population and laid a solid foundation for implementation of the subsequent breeding selection program.

Key words: Maiwa yak, GBS technology, kinship, molecular pedigree

中图分类号:

S823.85

李在文, 李响, 李小伟, 李飙, 江明锋. 基于GBS简化基因组测序数据重建麦洼牦牛保种群系谱[J]. 畜牧兽医学报, 2023, 54(9): 3710-3721.

LI Zaiwen, LI Xiang, LI Xiaowei, LI Biao, JIANG Mingfeng. The Pedigree Reconstruction of the Maiwa Yak Preserved Population Based on GBS Technology[J]. Acta Veterinaria et Zootechnica Sinica, 2023, 54(9): 3710-3721.

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