article · BMC Genomics
Comparative genomic analysis of whole genome sequences from Ethiopian cattle, sheep, and goats identifies seven shared genes linked to adaptation across high- and low-altitude environments. The gene CSMD3 appears in genomic regions under selection in both high- and low-altitude populations, with sheep displaying duplications on chromosomes 9 and 10 linked to neuronal and membrane functions. At low altitudes, all three species share selection signatures overlapping MAN1C1 and multiple HOXC cluster genes, which associate with skeletal morphogenesis and embryonic development in sheep and goats. In contrast, high-altitude animals share candidate selection in PLEKHA1, pointing to convergent adaptation to hypoxia and oxidative stress. Differences in MAN1C1 function highlight evolutionary divergence between cattle and small ruminants. These findings outline genomic mechanisms of environmental adaptation that could support cross-species livestock improvement.
Livestock in Africa must thrive across contrasting eco-climates, from lowlands to high-altitude regions. Pinpointing the genetic mechanisms behind how cattle, sheep, and goats adapt to stress, reduced oxygen, and altitude deepens understanding of evolutionary biology. These insights help explain how diverse species develop similar biological solutions to environmental pressures, providing a foundation for breeding animals that can better withstand extreme climates.
This early-stage discovery research identifies candidate genes that could inform marker-assisted breeding programmes for climate-resilient livestock. Livestock breeders, agricultural biotechnology companies, and veterinary geneticists could eventually use these genomic targets to select animals suited to low-oxygen or high-stress environments. However, real-world breeding applications remain distant because experimental validation is still required to confirm the functional roles and practical effects of the identified genetic loci in livestock populations.
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African livestock have co-existed and co-adapted to Africa’s diverse eco-climates which have likely impacted their genomes. Such impacts however remain poorly investigated across multiple livestock species. Using whole genome sequences of African cattle, sheep, and goats in Ethiopia, we conducted a cross and within-species comparative genomic analysis and identified seven common genes associated with high- and low-altitude adaptation. One gene CSMD3 was found in a genomic region under selection in low- and high-altitude individuals suggesting a potential role for convergent selection. CSMD3 was duplicated on chromosomes 9 and 10 in sheep and was enriched for Gene Ontology (GO) terms linked to cellular component organization, neuron projection development, and membrane dynamics. Shared selection signatures overlapping HOXC4 , HOXC5 , HOXC6 , HOXC9 , and MAN1C1 , were found in low-altitude individuals of the three species. The HOXC gene cluster was functionally enriched in sheep and goats for skeletal morphogenesis, embryonic development, and transcriptional regulation. MAN1C1 also showed species-specific roles including hydrolase activity and stress response in cattle, and ion binding and protein metabolism in sheep and goats, suggesting convergence within Caprinae and their divergence from Bovinae. PLEKHA1 was found in a candidate region in high-altitude individuals indicating possible convergent adaptation to hypoxia, and oxidative stress. These results provide insights into the genomic architecture of genomic convergence/divergence in African livestock and likely highlight possible mechanisms of adaptive evolution that could inform cross-species climate-resilient livestock breeding. Experimental validation will however be necessary to confirm the precise functional roles of the putative loci.
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DOI: 10.1186/s12864-026-13247-z
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