利用高密度SNP标记分析中国荷斯坦牛基因组近交

doi:10.16288/j.yczz.16-283

遗传 ›› 2017, Vol. 39 ›› Issue (1): 16-23.doi: 10.16288/j.yczz.16-283

利用高密度SNP标记分析中国荷斯坦牛基因组近交

杨湛澄¹(),黄河天¹,闫青霞²,王雅春¹,俞英¹,陈绍祜²,孙东晓¹,张胜利¹,张毅¹()

1. 中国农业大学动物科技学院,北京 100193
2. 中国奶业协会奶牛数据中心,北京 100192

收稿日期:2016-08-19 修回日期:2016-11-16 出版日期:2017-01-20 发布日期:2017-12-24
作者简介:杨湛澄,硕士研究生,专业方向：动物遗传育种。E-mail: 729284396@qq.com|张毅，博士，副教授，研究方向：动物遗传育种。E-mail: yizhang@cau.edu.cn
基金资助:
现代农业(奶牛)产业技术体系建设专项资金项目(CARS-37);北京市奶牛产业创新团队项目(BAIC06-2016);教育部“分子育种技术”创新团队基金项目(IRT1191);国家科技支撑计划项目(2011BAD28B02)

Estimation of genomic inbreeding coefficients based on high-density SNP markers in Chinese Holstein cattle

Yang Zhancheng¹(),Huang Hetian¹,Yan Qingxia²,Wang Yachun¹,Yu Ying¹,Chen Shaohu²,Sun Dongxiao¹,Zhang Shengli¹,Zhang Yi¹()

1. College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
2. Dairy Data Center of China , Beijing 100192, China

Received:2016-08-19 Revised:2016-11-16 Online:2017-01-20 Published:2017-12-24
Supported by:
Modern Agriculture Industrial Technology System Construction Special Funds(CARS-37);Beijing Innovation Team of Technology System in Dairy Industry(BAIC06-2016);the Ministry of Education Innovation Team Funds for "Molecular Breeding Technology"(IRT1191);the National Science and Technology Support Plan(2011BAD28B02)

摘要/Abstract

摘要：

畜禽育种中传统上利用系谱信息评估群体近交程度?近年来随着高通量单核苷酸多态(single nucleotide polymorphism, SNP)检测成本降低,使利用基因组信息分析真实的基因组近交程度成为可能?本研究利用牛54 K SNP 芯片数据统计了北京地区2107头荷斯坦牛基因组上的长纯合片段(runs of homozygosity, ROH)的频率和分布,计算了2种基因组近交系数,即染色体上ROH的长度占基因组总长度的比例(Froh)及个体所有标记基因型中纯合子所占比例,即基因组纯合度(Fhom),进而分析了两种基因组近交系数之间的相关性以及基因组近交与系谱近交系数之间的相关性?结果表明,共检测到44 676个ROH片段,其长度主要分布在1~10 Mb之间?不同长度的ROH散布于个体基因组内,短ROH较长ROH更为常见?ROH在染色体上并非均匀分布,ROH频率最高的区域为10号染色体中部?两种基因组近交系数之间相关性很高(91%以上),但基因组近交与系谱近交之间的相关性较低(低于50%)?系谱完整性是影响基因组近交与系谱近交结果一致的重要因素,基因组近交系数能够反映个体真实的近交,本研究为评估群体近交水平提供了有力工具?

关键词: 近交系数, 基因组纯合度, 系谱, ROH, 中国荷斯坦牛

Abstract:

In livestock, inbreeding coefficient based on pedigree information is usually used to evaluate the level of inbreeding. Recently, with cost reduction of high-density SNP genotyping, it’s possible to analyze real genomic inbreeding degree using genomic information. In this study, utilizing high-density SNP chip data, we analyzed the frequency and distribution of runs of homozygosity (ROH) in 2107 Chinese Holstein cattle in Beijing area, and calculated 2 genomic inbreeding coefficients, i.e., 1) the proportion of ROH length in the total length of autosomal genome (Froh), and 2) the percentage of homozygous SNPs (Fhom). Then we analyzed the correlation between 2 genomic inbreeding coefficients and the correlation between genomic and pedigree inbreeding coefficients. We totally detected 44 676 ROHs that mainly ranged from 1 to 10 Mb. Various lengths of ROHs existed in the genome. There were more short ROHs than long ROHs. ROHs aren’t evenly distributed in chromosomes. The area with most ROHs is in the middle part of chromosome 10. Strong correlation (r > 0.90) existed between 2 kinds of genomic inbreeding coefficients, but the correlation between pedigree and genomic inbreeding coefficients were much lower (r < 0.50). Our finding suggests that pedigree completeness influences the correlation between genomic and pedigree inbreeding. Genomic inbreeding measures may reflect individuals’ real inbreeding, which could be a useful tool to evaluate population inbreeding.

Key words: inbreeding coefficient, genomic homozygosity, pedigree, ROH, Chinese Holstein cattle

杨湛澄, 黄河天, 闫青霞, 王雅春, 俞英, 陈绍祜, 孙东晓, 张胜利, 张毅. 利用高密度SNP标记分析中国荷斯坦牛基因组近交[J]. 遗传, 2017, 39(1): 16-23.

Yang Zhancheng, Huang Hetian, Yan Qingxia, Wang Yachun, Yu Ying, Chen Shaohu, Sun Dongxiao, Zhang Shengli, Zhang Yi. Estimation of genomic inbreeding coefficients based on high-density SNP markers in Chinese Holstein cattle[J]. Hereditas(Beijing), 2017, 39(1): 16-23.

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利用高密度SNP标记分析中国荷斯坦牛基因组近交

Estimation of genomic inbreeding coefficients based on high-density SNP markers in Chinese Holstein cattle

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