Abstract
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.
Highlights
Bos taurus and Bos indicus are two main sub-species of cattle
Those copy number variations (CNVs) cluster regions contained 97 genes, but most of them were uncharacterized (64/97). We found those regions were enriched for gene families, such as well-known CNVassociated genes like zinc finger proteins, histones, and defensins (Fig. 1b and Table S2)
When considering the distributions of these CNV regions (CNVRs) in different breeds, we found only 133 CNVRs were shared by all breeds
Summary
Bos taurus and Bos indicus are two main sub-species of cattle. Bos taurus and Bos indicus are two main subspecies that supply beef and milk for human daily life in the whole world. A number of studies have compared their genetic differences in terms of SNP (Single Nucleotide Polymorphism), indel and microsatellite on the genome-wide level [6,7,8]. The two sub-species have their unique alleles and QTLs (Quantitative Trait Loci), as reported by genome-wide association studies. All of these illustrated large differences between Bos taurus and Bos indicus in their genomes, and many variations were probably associated with their specific phenotypes [9]
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