Whole-genome sequencing of copy number variation analysis in Ethiopian cattle reveals adaptations to diverse environments
Open accessAbstract
Background: Genomic structural variations (GSVs), notably copy number variations (CNVs), significantly shape genetic diversity and facilitate adaptation in cattle populations. Despite their importance, the genome-wide characterization of CNVs in indigenous Ethiopian cattle breeds—Abigar, Fellata, and Gojjam-Highland remains largely unexplored. In this study, we applied a read-depth approach to whole genome sequencing (WGS) data to conduct the first comprehensive analysis of CNVs in these populations. Results: We identified 3,893 CNV regions (CNVRs) covering 19.15 Mb (0.71% of the cattle genome). These CNVRs ranged from 1.60 kb to 488.0 kb, with an average size of 4.92 kb. These CNVRs included deletions (1713), duplications (1929), and mixed events (251) showing notable differences in distribution among the breeds. Four out of five randomly selected CNVRs were successfully validated using real time polymerase chain reaction (qPCR). Further analyses identified candidate genes associated with high-altitude adaptation ( GBE1 and SOD1 ), heat stress adaptation ( HSPA13 , DNAJC18 , and DNAJC8 ) and resistance to tick infestations ( BoLA and KRT33A ). In addition, variance stabilizing transformation ( V ST ) statistics highlighted population-specific CNVRs, emphasizing the unique genetic signatures of high-altitude adaptation in the Gojjam-Highland cattle breed. Among the detected CNVRs, 4.93% (192 out of 3,893) overlapped with 520 quantitative traits loci (QTLs) associated with six economically important trait categories suggesting that these CNVRs may significantly contribute to the genetic variation underlying these traits. Conclusions: Our comprehensive analysis reveals significant CNVRs associated with key adaptive traits in Ethiopian cattle breeds highlighting their genetic diversity and resilience. These findings offer valuable insights into the genetic basis of adaptability and can inform sustainable breeding practices and conservation efforts. Future research should prioritize the functional validation of these CNVRs and their integration into breeding programs to enhance traits such as disease resistance and environmental adaptability.
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In Ethiopian highland breed Gojjam, genes involved in HIF-1 signaling (GBE1, NEK7) and oxidative stress resistance (SOD1) exhibited strong signatures of selection.
“In the Ethiopian highland breed Gojjam, which resides at altitudes above 4000 m, genes involved in the hypoxia-inducible factor-1 signaling pathway (GBE1, NEK7) and oxidative stress resistance (SOD1) exhibited strong signatures of selection [99].”
From The Genomic Landscape of Cattle: Domestication, Dispersal, and Adaptive Evolution (2026) · cites this paper as [99]
The Discussion identifies GBE1 and SOD1 as candidate genes associated with high-altitude hypoxia and oxidative-stress protection, while the Results report significant highland–lowland differentiation for a CNVR containing NEK7. It does not establish strong selection signatures for all three genes or identify NEK7 itself as a HIF-1 signaling gene. Materials and methods places the sampled Gojjam cattle at 4,000 m, not above 4,000 m; page numbers are unavailable in our copy. (LLM, conf=0.88)
Experimental — accuracy not yet measuredIn African cattle, genomic selection signatures have been identified in genes involved in antigen response, keratin formation, light coat color, and sebum secretion.
“In African cattle, genomic selection signatures have been identified in genes involved in antigen response (BoLA, SLC25A48), keratin formation (KRT33A, KRT222, KRT24, KRT25, KRT26, KRT27, TGM1, TGM3), light coat color (MLPH), and sebum secretion (MC5R) [81,82,99,103].”
From The Genomic Landscape of Cattle: Domestication, Dispersal, and Adaptive Evolution (2026) · cites this paper as [99]
The Results (Functional annotations and enrichment analysis; page unavailable) identify BoLA and SLC25A48 in copy-number-variation regions associated with tick resistance. The Discussion (CNVR functional enrichment; page unavailable) links BoLA to antigen presentation and identifies KRT33A as a keratin-family gene. Our copy does not identify the other listed keratin genes, MLPH, or MC5R, or report light coat color or sebum secretion; it also describes CNVRs rather than establishing selection signatures for the full list. (LLM, conf=0.86)
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References 78 · Cited by 15
Research works printed but not linked: 4
- [20]Alberro M, Haile-Mariam S. The indigenous cattle of Ethiopia Part I. FAO World Anim Rev. 1982;41:2–10.
- [25]Kebede FG, Ayalew W. On-farm phenotypic characterization of indigenous cattle populations of Awi, East and West Gojjam Zones of Amhara region, Ethiopia. Res J Agric Environ Manage. 2014;3(4):227–37.
- [53]Alkan C, Coe BP, Eichler EE. Genome structural variation discovery and genotyping. Nat Rev Genet. 2011;12(5):363–76. 21358748 PMC4108431 · DOI · Paper page
- [55]Taye M, Lee W, Caetano-Anolles K, Dessie T, Cho S, Jong Oh S, Lee HK, Kim H. Exploring the genomes of East African Indicine cattle breeds reveals signature of selection for tropical environmental adaptation traits. Volume 4. Cogent Food & Agriculture; 2018. p. 1552552.
- Authors
- Ayalew, W., Xiaoyun, W., Tarekegn, G. M., Tessema, T. S., Chu, M., Liang, C., Naboulsi, R., Van Damme, R., Bongcam-Rudloff, E., & Ping, Y.
- Affiliations
- South China Agricultural University (CN)
- Roslin Institute (GB)
- Addis Ababa University (ET)
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences (CN)
- Karolinska Institutet (SE)
- Corresponding author
- Tarekegn, Getinet Mekuriaw
- ORCID
- Venue
- BMC Genomics
- Published
- 2024-11-15
- Volume
- 25
- Issue
- 1
- Pages
- 1088-1088
- ISSN
- 1471-2164 (ISSN-L)
- PMC
- PMC11566455
- OpenAlex
- W4404388799
- Cited by
- 15
- References
- 78
- Citations by year
- 2026: 9 · 2025: 6
- FWCI
- 3.97
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- BMC Genomics (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- Funders
- Sveriges Lantbruksuniversitet
- Addis Ababa University
- Agricultural Science and Technology Innovation Program (TCYC-TP2023, 25‐LZIHPS‐01, TZRC-2023)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic and phenotypic traits in livestock
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genomic variations and chromosomal abnormalities
- Life Sciences › Agricultural and Biological Sciences › Agronomy and Crop Science › Livestock Farming and Management
- Keywords
- copy number variation, high-altitude adaptation, heat stress adaptation, tick resistance, bovine leukocyte antigen, GBE1, SOD1, quantitative trait loci, structural variants, cattle genetic diversity, indigenous cattle breeds
- MeSH terms
- Whole Genome Sequencing, Adaptation, Physiological, Animals, Cattle, Ethiopia, Genome, DNA Copy Number Variations
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