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

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

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

Zhancheng Yang¹(),Hetian Huang¹,Qingxia Yan²,Yachun Wang¹,Ying Yu¹,Shaohu Chen²,Dongxiao Sun¹,Shengli Zhang¹,Yi Zhang¹()

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)

Abstract

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

Zhancheng Yang, Hetian Huang, Qingxia Yan, Yachun Wang, Ying Yu, Shaohu Chen, Dongxiao Sun, Shengli Zhang, Yi Zhang. 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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Estimation of genomic inbreeding coefficients based on high-density SNP markers in Chinese Holstein cattle

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