Comparative analyses of copy number variations between Bos taurus and Bos indicus
Yan Hu1, Han Xia1, Mingxun Li2,3
1Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education & College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China.
BMC Genomics
|October 2, 2020
Summary
Copy number variations (CNVs) reveal significant genetic differences between Bos taurus and Bos indicus cattle. These CNVs offer insights into subspecies adaptation and distinct traits, aiding cattle breeding and research.
Area of Science:
- Genomics
- Comparative genomics
- Animal genetics
Background:
- Bos taurus and Bos indicus are the two primary cattle subspecies.
- Differential copy number variations (CNVs) between these subspecies are not well-studied.
Purpose of the Study:
- To identify and compare copy number variation regions (CNVRs) between Bos taurus and Bos indicus.
- To understand the genomic diversity and genetic basis for phenotypic differences.
Main Methods:
- Utilized the ARS-UCD1.2 cattle reference genome.
- Integrated three CNV detection strategies across 73 animals from 10 breeds.
- Analyzed copy number variation regions (CNVRs) and their overlap with genes.
Main Results:
- Identified 13,234 non-redundant CNVRs, with 52.82% shared between subspecies.
- Discovered significant CNV differences enabling subspecies separation.
- Found 2212 and 538 genes uniquely overlapping with indicine-specific and taurine-specific CNVRs, respectively.
- Detected 16 candidate lineage-differential CNV segments under selection, including genes related to heat resistance and metabolism.
Conclusions:
- Presents a genome-wide CNV comparison between Bos taurus and Bos indicus.
- Provides crucial genomic diversity data for understanding adaptation and phenotypic variations.
- Highlights the role of CNVs in differentiating cattle subspecies and their traits.
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