Comparative Analyses Of Copy Number Variations Betweenbos Taurusandbos Indicus

Background Bos taurusandBos indicusare two main sub-species of cattle. However, the differential copy number variations (CNVs) between them are not yet well studied. Results Based 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 (4Bos taurusand 6Bos indicus), by integrating three detection strategies. While 6990 CNVRs (52.82%) were shared byBos taurusandBos 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 onF(ST), 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,andPLCXD3). Moreover, we obtained 1.74 Mbp indicine-specific sequences, which could only be mapped on theBos indicusreference 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 ofCTHbut was deleted alongBos indicuslineage. Conclusions This study presents a genome wide CNV comparison betweenBos taurusandBos indicus. It supplied essential genome diversity information for understanding of adaptation and phenotype differences between theBos taurusandBos indicuspopulations.