Genomic Scans for Selection Signatures Revealed Candidate Genes for Adaptation and Production Traits in a Variety of Cattle Breeds
Open accessAbstract
Domestication and selection are the major driving forces responsible for the determinative genetic variability in livestock. These selection patterns create unique genetic signatures within the genome. BovineSNP50 chip data from 236 animals (seven indicine and five taurine cattle breeds) were analyzed in the present study. We implemented three complementary approaches viz. iHS (Integrated haplotype score), ROH (Runs of homozygosity), and F ST, to detect selection signatures. A total of 179, 56, and 231 regions revealed 518, 277, and 267 candidate genes identified by iHS, ROH, and F ST methods, respectively. We found several candidate genes (e.g., NCR3, ARID5A, HIST1H2BN, DEFB4, DEFB7, HSPA1L, HSPA1B, and DNAJB4) related to production traits and the adaptation of indigenous breeds to local environmental constraints such as heat stress and disease susceptibility. However, further studies are warranted to refine the findings using a larger sample size, whole-genome sequencing, and/or high density genotyping.
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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 [100]
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References 67 · Cited by 98
- Authors
- Saravanan, K. A., Panigrahi, M., Kumar, H., Parida, S., Bhushan, B., Gaur, G. K., Dutt, T., Mishra, B. P., & Singh, R. K.
- Affiliations
- Indian Veterinary Research Institute (IN)
- Corresponding author
- Panigrahi, Manjit
- ORCID
- Venue
- Genomics
- Publisher
- Elsevier BV
- Published
- 2021-05
- Volume
- 113
- Issue
- 3
- Pages
- 955-963
- ISSN
- 0888-7543 (ISSN-L)
- OpenAlex
- W3129922466
- Cited by
- 98
- References
- 67
- Citations by year
- 2026: 14 · 2025: 19 · 2024: 24 · 2023: 21 · 2022: 16 · 2021: 4
- FWCI
- 10.45
- Type
- journal article
- Language
- en
- Open access
- bronze
- doi.org
- Licence
- www.elsevier.com/tdm/userlicense/1.0/ (tdm)
- www.elsevier.com/legal/tdmrep-license (tdm)
- www.elsevier.com/open-access/userlicense/1.0/ (vor, 549 d)
- doi.org/10.15223/policy-017 (stm-asf)
- doi.org/10.15223/policy-037 (stm-asf)
- doi.org/10.15223/policy-012 (stm-asf)
- doi.org/10.15223/policy-029 (stm-asf)
- doi.org/10.15223/policy-004 (stm-asf)
- Locations
- Genomics (publishedVersion)
- PubMed (publishedVersion)
- 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 › Biochemistry, Genetics and Molecular Biology › Genetics › Genetic diversity and population structure
- Keywords
- cattle breeds, selection signatures, genome scan, candidate genes, adaptation, production traits, Bos indicus, taurine cattle, heat stress, disease susceptibility, integrated haplotype score, runs of homozygosity, FST, domestication, NCR3, Arid5a, human beta-defensin 2, HSPA1L, HSPA1B
- MeSH terms
- Animals, Cattle, Haplotypes, Phenotype, Selection, Genetic, Polymorphism, Single Nucleotide, Genomics
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