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

BMC Genomics

Tad S. Sonstegard¹  George E. Liu²  Mingxun Li³  Oyekanmi Nash⁴  Ruixue Su⁵  Yang Zhou⁵  Chang Xu⁵  Han Xia⁵  Liguo Yang⁵  Xiaowei Ye⁵  Mai Zhang⁵  Yan Hu⁵ 

[1] Acceligen, 3388 Mike Collins Drive, 55121, Eagan, MN, USA;Animal Genomics and Improvement Laboratory, BARC, USDA-ARS, Building 306, Room 111, BARC-East, 20705, Beltsville, MD, USA;Animal Genomics and Improvement Laboratory, BARC, USDA-ARS, Building 306, Room 111, BARC-East, 20705, Beltsville, MD, USA;College of Animal Science and Technology, Yangzhou University, 225009, Yangzhou, China;Centre for Genomics Research and Innovation, National Biotechnology Development Agency, Abuja, Nigeria;Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & College of Animal Science and Technology, Huazhong Agricultural University, 430070, Wuhan, China;

关键词: Copy number variation (CNV);    Indicine;    Taurine;    Lineage-differential;    CNV boundaries;   

DOI  :  10.1186/s12864-020-07097-6

来源: Springer

【 摘 要 】

BackgroundBos taurus and Bos indicus are two main sub-species of cattle. However, the differential copy number variations (CNVs) between them are not yet well studied.ResultsBased on the new high-quality cattle reference genome ARS-UCD1.2, we identified 13,234 non-redundant CNV regions (CNVRs) from 73 animals of 10 cattle breeds (4 Bos taurus and 6 Bos indicus), by integrating three detection strategies. While 6990 CNVRs (52.82%) were shared by Bos taurus and Bos indicus, large CNV differences were discovered between them and these differences could be used to successfully separate animals into two subspecies. We found that 2212 and 538 genes uniquely overlapped with either indicine-specific CNVRs and or taurine-specific CNVRs, respectively. Based on FST, we detected 16 candidate lineage-differential CNV segments (top 0.1%) under selection, which overlapped with eight genes (CTNNA1, ENSBTAG00000004415, PKN2, BMPER, PDE1C, DNAJC18, MUSK, and PLCXD3). Moreover, we obtained 1.74 Mbp indicine-specific sequences, which could only be mapped on the Bos indicus reference genome UOA_Brahman_1. We found these sequences and their associated genes were related to heat resistance, lipid and ATP metabolic process, and muscle development under selection. We further analyzed and validated the top significant lineage-differential CNV. This CNV overlapped genes related to muscle cell differentiation, which might be generated from a retropseudogene of CTH but was deleted along Bos indicus lineage.ConclusionsThis study presents a genome wide CNV comparison between Bos taurus and Bos indicus. It supplied essential genome diversity information for understanding of adaptation and phenotype differences between the Bos taurus and Bos indicus populations.

【 授权许可】

CC BY