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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 #372431

Research Project: Enhancing Genetic Merit of Ruminants Through Improved Genome Assembly, Annotation, and Selection

Location: Animal Genomics and Improvement Laboratory

Title: Comparative analyses of copy number variations between Bos taurus and Bos indicus

item HU, YANG - Huazhong Agricultural University
item XIA, HAN - Huazhong Agricultural University
item LI, MINGXUN - Yangzhou University
item XU, CHANG - Huazhong Agricultural University
item YE, XIAOWEI - Huazhong Agricultural University
item SU, RUIXUE - Huazhong Agricultural University
item ZHANG, MAI - Huazhong Agricultural University
item GUO, AIZHEN - Huazhong Agricultural University
item NASH, OYEKANMI - National Biotechnology Development Agency, Nabda/fmst
item SONSTEGARD, TAD - Recombinetics, Inc
item YANG, LIGUO - Huazhong Agricultural University
item Liu, Ge - George
item ZHOU, YANG - Huazhong Agricultural University

Submitted to: BMC Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 9/23/2020
Publication Date: 10/1/2020
Citation: Hu, Y., Xia, H., Li, M., Xu, C., Ye, X., Su, R., Zhang, M., Guo, A., Nash, O., Sonstegard, T.S., Yang, L., Liu, G., Zhou, Y. 2020. Comparative analyses of copy number variations between Bos taurus and Bos indicus. BMC Genomics. 21(1):682.

Interpretive Summary: Copy number variation (CNV) represents a major source of genomic variation. By performing the genome-wide CNV discovery and comparison between Bos taurus and Bos indicus, we explored indicine-specific CNV events an their potentially functions. These results fill our knowledge gaps and provide the foundation for incorporating CNV into the future goat breeding program. Farmers, scientist, and policy planners who need improve animal health and production based on genome-enable animal selection will benefit from this study.

Technical Abstract: The differential copy number variations (CNVs) between Bos taurus and Bos indicus are not well studied. Here, we detected 13,234 non-redundant CNV regions for 73 animals of 10 cattle breeds (4 Bos taurus and 6 Bos indicus) by combining the advantages of three detection strategies based on the new high quality reference genome (UCD-ARS1.2). The CNVs showed highly diverse among different breeds and successfully divided animals into Bos taurus and Bos indicus groups. We detected 1.74 Mbp sequence in length that only mapped on the Bos indicus reference genome (UOA_Brahman_1) and 16 lineage-differential CNV segments (top 0.1%) showed mostly total deletion in Bos indicus. The genes in the indicine-specific sequences and CNVR were potentially responsible for the heat resistance through gene ontology analyses that were highly enriched in Rho protein signal transduction. The functions of genes overlapped with lineage-differential CNVs ranged from the immune, lipid metabolic process and muscle development. We further analyzed and validated the top significant lineage-differential CNV. This CNV overlapped two genes related to muscle cell differentiation, which might be generated from a retropseudogene of CTH after the speciation of the ruminant but was deleted along Bos indicus lineage. Our results supplied essential genome diversity information between the Bos taurus and Bos indicus populations.