Selection Signatures in Tropical Cattle Are Enriched for Promoter and Coding Regions and Reveal Missense Mutations in the Damage Response Gene HELB
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BACKGROUND: Distinct domestication events, adaptation to different climatic zones, and divergent selection in productive traits have shaped the genomic differences between taurine and indicine cattle. In this study, we assessed the impact of artificial selection and environmental adaptation by comparing whole-genome sequences from European taurine and Asian indicine breeds and from African cattle. Next, we studied the impact of divergent selection by exploiting predicted and experimental functional annotation of the bovine genome. RESULTS: We identified selective sweeps in beef cattle taurine and indicine populations, including a 430-kb selective sweep on indicine cattle chromosome 5 that is located between 47,670,001 and 48,100,000 bp and spans five genes, i.e. HELB, IRAK3, ENSBTAG00000026993, GRIP1 and part of HMGA2. Regions under selection in indicine cattle display significant enrichment for promoters and coding genes. At the nucleotide level, sites that show a strong divergence in allele frequency between European taurine and Asian indicine are enriched for the same functional categories. We identified nine single nucleotide polymorphisms (SNPs) in coding regions that are fixed for different alleles between subspecies, eight of which were located within the DNA helicase B (HELB) gene. By mining information from the 1000 Bull Genomes Project, we found that HELB carries mutations that are specific to indicine cattle but also found in taurine cattle, which are known to have been subject to indicine introgression from breeds, such as N'Dama, Anatolian Red, Marchigiana, Chianina, and Piedmontese. Based on in-house genome sequences, we proved that mutations in HELB segregate independently of the copy number variation HMGA2-CNV, which is located in the same region. CONCLUSIONS: Major genomic sequence differences between Bos taurus and Bos indicus are enriched for promoter and coding regions. We identified a 430-kb selective sweep in Asian indicine cattle located on chromosome 5, which carries SNPs that are fixed in indicine populations and located in the coding sequences of the HELB gene. HELB is involved in the response to DNA damage including exposure to ultra-violet light and is associated with reproductive traits and yearling weight in tropical cattle. Thus, HELB likely contributed to the adaptation of tropical cattle to their harsh environment.
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Genes involved in heat tolerance have been identified in Indian and African indicine cattle populations, such as heat shock protein genes (HSPA1B, HSPA12A, DNAJC18 and DNAJC8), GRXCR1, FKBP4, HSPA1L, IL6, and HELB.
“Genes involved in heat tolerance have been identified in Indian and African indicine cattle populations, such as heat shock protein genes (HSPA1B, HSPA12A, DNAJC18 and DNAJC8), GRXCR1, FKBP4, HSPA1L, IL6, and HELB [81,100,112,113].”
From The Genomic Landscape of Cattle: Domestication, Dispersal, and Adaptive Evolution (2026) · cites this paper as [112]
The Results section (page unavailable) identifies HELB mutations in Asian indicine cattle and reports their presence in African indicine cattle. It proposes that these mutations could help cattle cope with high temperatures, but does not establish HELB as a heat-tolerance gene. The other genes in the citing sentence are not supported by the passages from this source. (LLM, conf=0.85)
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Signatures of Selection in Nelore Cattle Revealed by Whole-Genome Sequencing Data
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Self-citationWhole Genome Sequencing Reveals Signals of Adaptive Admixture in Creole Cattle
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Genomic Insights into the Population History and Adaptive Traits of Latin American Criollo Cattle
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The Genomic Landscape of Cattle: Domestication, Dispersal, and Adaptive Evolution
Liu, Y., Dao, W., Gao, R., Fan, X., Yang, R., & Miao, Y. (2026) · Animals · doi:10.3390/ani16050776 · Cited by 1 · see citing works
- Authors
- Naval-Sánchez, M., Porto-Neto, L. R., Cardoso, D. F., Hayes, B. J., Daetwyler, H. D., Kijas, J., & Reverter, A.
- Affiliations
- Commonwealth Scientific and Industrial Research Organisation (AU)
- The University of Queensland (AU)
- La Trobe University (AU)
- Corresponding author
- Naval-Sánchez, Marina
- Venue
- Genetics Selection Evolution
- Published
- 2020-05-27
- Volume
- 52
- Issue
- 1
- Pages
- 27-27
- ISSN
- 0999-193X (ISSN-L)
- 1297-9686
- PMC
- PMC7251699
- OpenAlex
- W3030152038
- Cited by
- 43
- References
- 107
- Citations by year
- 2026: 4 · 2025: 7 · 2024: 7 · 2023: 11 · 2022: 5 · 2021: 6 · 2020: 2 · 2018: 1
- FWCI
- 5.72
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Locations
- Genetics Selection Evolution (publishedVersion, cc-by)
- PubMed Central (publishedVersion, cc-by)
- PubMed (publishedVersion)
- HAL (submittedVersion, cc-by)
- DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
- LA Referencia (Red Federada de Repositorios Institucionales de Publicaciones Científicas) (submittedVersion, other-oa)
- Funders
- CSIRO Science Excellence Research Office
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic and phenotypic traits in livestock
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic Mapping and Diversity in Plants and Animals
- Life Sciences › Agricultural and Biological Sciences › Agronomy and Crop Science › Livestock Farming and Management
- Keywords
- tropical cattle, divergent selection, selective sweeps, taurine cattle, Bos indicus, cattle, HELB, missense mutations, introgression, DNA damage response, environmental adaptation, single nucleotide polymorphisms, chromosome 5
- MeSH terms
- Domestication, Whole Genome Sequencing, Alleles, Animals, Base Sequence, Breeding, Cattle, DNA Damage, DNA Helicases, Female, Gene Frequency, Genotype, Male, Phenotype, Promoter Regions, Genetic, Selection, Genetic, Open Reading Frames, Mutation, Missense, Polymorphism, Single Nucleotide, DNA Copy Number Variations
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