基于简化基因组测序的黄色波尔山羊公羊亲缘关系及近交系数分析

doi:10.16431/j.cnki.1671-7236.2021.08.020

中国畜牧兽医 ›› 2021, Vol. 48 ›› Issue (8): 2878-2888.doi: 10.16431/j.cnki.1671-7236.2021.08.020

基于简化基因组测序的黄色波尔山羊公羊亲缘关系及近交系数分析

兰蓉, 朱兰, 江炎庭, 欧阳依娜, 邵庆勇

云南省畜牧兽医科学院, 昆明 650224

收稿日期:2021-03-03 出版日期:2021-08-20 发布日期:2021-08-19
通讯作者: 邵庆勇 E-mail:shaoqingyong@163.com
作者简介:兰蓉(1969-),女,云南昆明人,研究员,研究方向:家畜分子遗传育种,E-mail:rtlankitty@163.com
基金资助:
云南省重点研发计划（2018BB002）；国家现代肉羊产业技术体系建设项目（CARS-38）；云南省高层次人才培养支持计划"产业技术领军人才"专项

Analysis on Genetic Relationship and Inbreeding Coefficient of Yellow Boer Rams by Genotyping-by-Sequencing

LAN Rong, ZHU Lan, JIANG Yanting, OUYANG Yina, SHAO Qingyong

Yunnan Institute of Animal Science and Veterinary, Kunming 650224, China

Received:2021-03-03 Online:2021-08-20 Published:2021-08-19

摘要/Abstract

摘要： 为提高云南黄山羊新品种培育的育种效率和遗传进展，准确度量育种素材波尔山羊黄色群体的近交程度及亲缘关系是一个有效途径。本研究采用简化基因组测序（GBS）技术对来自云南省种羊推广中心的37只黄色波尔山羊公羊进行测序，通过质控获取高质量高密度SNP变异信息，并使用Gmatrix v2、Plink v1.90、MegaX v10.0等软件进行主成分分析（PCA）、状态同源距离计算（identity by state，IBS）、基因型亲缘关系G矩阵构建、亲缘系数计算、NJ聚类分析和基因组近交系数计算。结果显示，在37只黄色公羊中检测出位于29条常染色体上的高质量SNPs位点88 393个，共检测出长纯合片段（ROH）1 537条，大小在1 000.582~18 400.12 kb之间，平均每条ROH长2 576.34 kb，平均含有93.15个SNPs；37只黄色公羊被分为11个家系，其中3个家系仅各有1只黄色公羊，家系A与K亲缘关系最远；基于ROH的群体平均基因组近交系数为0.043，其中3只黄色公羊的基因组近交系数>0.125，存在较多的近交积累。本研究结果为波尔山羊黄色群体在云南黄山羊新品种培育中的合理利用提供了科学依据，也为评估山羊个体近交水平、防止近交衰退、优化选种选配方案提供了有力的技术手段。

关键词: 黄色波尔山羊公羊; 简化基因组测序; 长纯合片段; 基因组近交系数; 亲缘系数

Abstract: Accurate measuring of the inbreeding degree and genetic relationship on yellow Boer goat was an effective way to improve breeding efficiency and genetic progress of Yunnan Yellow goat breeding.The genotyping-by-sequencing (GBS) was used to sequence 37 yellow Boer rams from Yunnan breeding promotion center.High quality and high density SNP variation information was obtained through quality control.Principal component analysis (PCA), calculation of identity by state (IBS), construction of G matrix, calculation of genetic coefficient, NJ cluster analysis and calculation of inbreeding coefficient were carried out by Gmatrix v2, Plink v1.90 and MegaX v10.0 software.The results showed that 88 393 high-quality SNPs were detected on 29 autosomes in 37 yellow Boer rams, and 1 537 long homozygous fragments (ROH) ranging in length from 1 000.582 to 18 400.12 kb with an average length of 2 576.34 kb and 93.15 SNPs were detected.37 yellow Boer rams were divided into 11 families and 3 families had only one ram each.The genetic relationship between family A and family K was the farthest.The average genomic inbreeding coefficient (F_ROH) based on ROH was 0.043 and the F_ROH of 3 yellow Boer rams was more than 0.125 which meant more inbreeding accumulation existing.This study provided a scientific basis for the rational use of yellow Boer goat in the breeding of Yunnan Yellow goat, and also provided a powerful technical means for evaluating the inbreeding level of goats, preventing inbreeding decline, and optimizing the breeding and matching scheme.

Key words: yellow Boer rams; GBS; ROH; F_ROH; kinship coefficient

中图分类号:

S813.3

兰蓉, 朱兰, 江炎庭, 欧阳依娜, 邵庆勇. 基于简化基因组测序的黄色波尔山羊公羊亲缘关系及近交系数分析[J]. 中国畜牧兽医, 2021, 48(8): 2878-2888.

LAN Rong, ZHU Lan, JIANG Yanting, OUYANG Yina, SHAO Qingyong. Analysis on Genetic Relationship and Inbreeding Coefficient of Yellow Boer Rams by Genotyping-by-Sequencing[J]. China Animal Husbandry and Veterinary Medicine, 2021, 48(8): 2878-2888.

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基于简化基因组测序的黄色波尔山羊公羊亲缘关系及近交系数分析

Analysis on Genetic Relationship and Inbreeding Coefficient of Yellow Boer Rams by Genotyping-by-Sequencing

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