Genome-wide analysis reveals genetic diversity, linkage disequilibrium, and selection for milk production traits in Chinese buffalo breeds
文献类型： 外文期刊
作者： Lu, X. R. 1 ; Duan, A. Q. 1 ; Li, W. Q. 2 ; Abdel-Shafy, H. 3 ; Rushdi, H. E. 3 ; Liang, S. S. 1 ; Ma, X. Y. 1 ; Liang, X 1 ;
作者机构： 1.Chinese Acad Agr Sci, Buffalo Res Inst, Key Lab Buffalo Genet Breeding & Reprod Technol, Nanning 530001, Peoples R China
2.BGI Shenzhen, BGI Genom, Shenzhen 518083, Peoples R China
3.Cairo Univ, Fac Agr, Dept Anim Prod, Giza 12613, Egypt
关键词： buffalo; linkage disequilibrium; population analysis; selection signature
期刊名称：JOURNAL OF DAIRY SCIENCE （ 影响因子：4.034； 五年影响因子：4.354 ）
ISSN： 0022-0302
年卷期： 2020 年 103 卷 5 期
页码：
收录情况： SCI
摘要： The water buffalo is an important dual-purpose livestock that is widespread throughout central and southern China. However, there has been no characterization of the population genetics of Chinese buffalo. Using an Axiom buffalo genotyping array (Thermo Fisher Scientific, Wilmington, DE), we analyzed the genetic diversity, linkage disequilibrium pattern, and signature of selection in 176 Chinese buffaloes from 13 breeds. A total of 35,547 SNP passed quality control and were used for further analyses. Population genetic analysis revealed a clear separation between swamp and river types. Ten Chinese indigenous breeds were clustered into the swamp group, the Murrah and Nili-Ravi breeds were clustered into the river group, and the crossbred breed was closer to the river group. Genetic diversity analysis showed that the swamp group had a lower average expected heterozygosity. Linkage disequilibrium decay distance was much shorter in the swamp group compared with the river group, with an average square of correlation coefficient value of 0.2 of approximately 50 kb. Analysis of runs of homozygosity indicated extensive remote and recent inbreeding within swamp and river groups, respectively. Moreover, one genomic region under selection was detected between the river and swamp groups. Our findings contribute to our understanding of the characterization of population genetics in Chinese buffaloes, which in turn may be used in buffalo breeding programs.
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