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ARS Home » Northeast Area » Beltsville, Maryland (BARC) » Beltsville Agricultural Research Center » Animal Genomics and Improvement Laboratory » Research » Publications at this Location » Publication #314029
Title: Impact of parental Bos taurus and Bos indicus origins on copy number variation in traditional Chinese cattle breeds

Author
item LIANGZHI, ZHANG - Northwest Agriculture And Forestry University
item SHAN-GANG, JIA - Northwest Agriculture And Forestry University
item MARTIN, PLATH - Northwest Agriculture And Forestry University
item YOUNG-ZHEN, HUANG - Northwest Agriculture And Forestry University
item Li, Congjun - Cj
item CHU-ZHAO, LEI - Northwest Agriculture And Forestry University
item XIN, ZHAO - Northwest Agriculture And Forestry University
item HONG, CHEN - Northwest Agriculture And Forestry University

Submitted to: Scientific Reports
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/28/2015
Publication Date: 8/10/2015
Citation: Liangzhi, Z., Shan-Gang, J., Martin, P., Young-Zhen, H., Li, C., Chu-Zhao, L., Xin, Z., Hong, C. 2015. Impact of parental Bos taurus and Bos indicus origins on copy number variation in traditional Chinese cattle breeds. Scientific Reports. 10;7(8):2352-2361.

Interpretive Summary: Copy number variation (CNV) is an important component of genomic structural variation and plays a role not only in evolutionary diversification but also domestication. However, the patterns of CNV in different breeds of cattle have not been studied, especially the evolution of CNV regions (CNVRs). In this study, we discovered 470 genome-wide CNVRs from 24 Chinese domesticated bulls derived from Bos taurus and Bos indicus. The distribution patterns of CNVRs tended to be lineage-specific, and correlation analysis revealed significant positive or negative co-occurrences of CNVRs across lineages. Our study suggests that CNVs in Chinese cattle partly result from selective breeding during domestication, but also from hybridization and introgression.

Technical Abstract: Copy number variation (CNV) is an important component of genomic structural variation and plays a role not only in evolutionary diversification but also domestication. Chinese cattle were derived from Bos taurus and Bos indicus, and several breeds presumably are of hybrid origin, but the evolution of CNV regions (CNVRs) has not yet been examined in this context. Here we describe the combined analysis of CNVRs, mtDNA D-loop sequence variation, and Y-chromosomal SNPs to assess the impact of maternal and paternal B. taurus and B. indicus origins on the distribution of CNVRs in 24 Chinese domesticated bulls. We discovered 470 genome-wide CNVRs, only 72 of which were shared by all three Y-lineages (B. taurus: Y1, Y2; B. indicus: Y3), while 265 were shared by inferred taurine or indicine paternal lineages, and 228 when considering their maternal taurine or indicine origins. Phylogenetic analysis uncovered eight taurine/indicine hybrids, and principal component analysis on CNVs corroborated genomic exchange during hybridization. The distribution patterns of CNVRs tended to be lineage-specific, and correlation analysis revealed significant positive or negative co-occurrences of CNVRs across lineages. Our study suggests that CNVs in Chinese cattle partly result from selective breeding during domestication, but also from hybridization and introgression.