Signatures of Selection in Nelore Cattle Revealed by Whole-Genome Sequencing Data
Open accessAbstract
Nelore cattle breed was farmed worldwide due to its economic importance in the beef market and adaptation to the tropics. In Brazil, purebred Nelore animals (PO) receive a certificate from the breeders' association based on the animal's genealogy and morphological characterization. The top 20 to 30% of the superior animals are eligible to receive the Special Certificate of Identification and Production (CEIP), meaning animals from this category were selected and evaluated in a breeding program to improve economically important traits. We used whole-genome sequencing and approaches based on haplotype differentiation and allelic differentiation to detect regions of selection signatures in Nelore cattle by comparing animals from PO and CEIP categories. From a total of 150 animals, a hierarchical clustering analysis was performed to choose the more unrelated animals from each category (16 PO and 40 CEIP). The hapFLK statistic was performed, and extensions of hapFLK values were investigated considering continuous regions with significant q-values. The Weir and Cockerham's Fst estimator (wcFst) was computed using the GPAT++ software library. The total of 82,326 SNPs with hapFLK values passed the FDR control (q-value<0.05), and 718 segments were target as signatures of selection. A total of 1713 highly differentiated genomic regions were identified based on the segmentFst approach. The signatures of selection were spread across the genome. Annotation of overlapping selection signature regions between the two methods revealed 118 genes in common. A variant located within the 3' region of the BOLA-DRB3 gene was found as a promising candidate polymorphism. Within genomic regions that deserves attention, we found genes previously associated with adaptation to tropical environments (HELB), growth and navel size (HMGA2), fat deposition and domestication (IRAK3), and feed efficiency and postmortem carcass traits (GABRG3). The genes BOLA-DQA2, BOLA-DQB, BOLA-DQA5, BOLA-DQA1, BOLA-DRB3, ENSBTAG00000038397 on chromosome 23 are part of the Bovine Major Histocompatibility Complex (MHC) Class II gene family, representing good candidates for immune response and adaptation to tropical conditions. The BoLA family genes and the interaction of ROBO1 with SLIT genes appeared in the enrichment results. Genomic regions located in intronic regions were also identified and might play a regulatory role in traits under selection in PO and CEIP subpopulations. The regions here identified contribute to our knowledge regarding genes and variants that have an important role in complex traits selected in this breed.
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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 [113]
Section 3.5 identifies HELB in a selection region in Nelore cattle and reports a proposed role for it in adaptation to high temperatures in Asian indicine tropical cattle. The passages do not substantiate the other listed genes or findings in African indicine populations. (LLM, conf=0.88)
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de Castilhos, A. M., Branco, R. H., Razook, A. G., et al. (2011) · Revista Brasileira de Zootecnia · doi:10.1590/s1516-35982011000200010 · Cited by 17 · see citing works
A whole genomic scan to detect selection signatures between Berkshire and Korean native pig breeds
Edea, Z., & Kim, K. (2014) · Journal of Animal Science and Technology · doi:10.1186/2055-0391-56-23 · Cited by 16 · see citing works
SRGAP2 and the gradual evolution of the modern human language faculty
Martins, P. T., Marí, M., & Boeckx, C. A. (2018) · Journal of Language Evolution · doi:10.1093/jole/lzx020 · Cited by 16 · see citing works
Genome-wide association study for mammary structure in Canadian Angus cows
Devani, K., Plastow, G. S., Orsel, K., et al. (2020) · PLoS ONE · doi:10.1371/journal.pone.0237818 · Cited by 16 · see citing works
Ferraz, J. B. S., Eler, J. P., & de Rezende, F. M. (2012) · Animal Reproduction · Cited by 11 · see citing works
Selection signatures in candidate genes and QTL for reproductive traits in Nellore heifers
Montes-Vergara, D. E., Braz, C. U., Ribeiro, A. M. F., Cavani, L., Barbero, M. M. D., de Albuquerque, L. G., Curi, R. A., & de Oliveira, H. N. (2019) · Animal Reproduction Science · doi:10.1016/j.anireprosci.2019.06.004 · Cited by 9 · see citing works
Flagged first, then by citations
Research works printed but not linked: 1
- A.N. Rosa, R.B. Lôbo, I.F. Leite, F.P. Lima, C.U. Magnabosco, F.A.M. Duarte, Proposta de mudanças no regulamento do registro genealógico das raças zebuínas vol. 17, EMBRAPA-CNPGC, Campo Grande, 1997 (EMBRAPA-CNPGC. Documentos, 67).
Cited by
Sorted by citations
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
- Maiorano, A. M., Cardoso, D. F., Carvalheiro, R., Júnior, G. A. F., de Albuquerque, L. G., & de Oliveira, H. N.
- Affiliations
- Universidade Federal de Uberlândia (BR)
- University of Guelph (CA)
- Universidade Estadual Paulista (Unesp) (BR)
- Corresponding author
- Maiorano, Amanda Marchi
- ORCID
- Venue
- Genomics
- Publisher
- Elsevier BV
- Published
- 2022-03
- Volume
- 114
- Issue
- 2
- Pages
- 110304
- ISSN
- 0888-7543 (ISSN-L)
- OpenAlex
- W4213365622
- Cited by
- 33
- References
- 86
- Citations by year
- 2026: 6 · 2025: 4 · 2024: 12 · 2023: 9 · 2022: 2
- FWCI
- 4.54
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- Locations
- Genomics (publishedVersion, cc-by)
- PubMed (publishedVersion)
- LA Referencia (Red Federada de Repositorios Institucionales de Publicaciones Científicas) (submittedVersion, other-oa)
- Funders
- Fundação de Amparo à Pesquisa do Estado de São Paulo (2009/16118-5, 2017/10630-2, 2019/15397-0)
- 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
- Nelore cattle, selection signatures, hapFLK, haplotype differentiation, BoLA-DRB3, tropical adaptation, beef cattle breeding, ROBO1, HMGA2, GABRG3, IRAK3
- MeSH terms
- Whole Genome Sequencing, Alleles, Animals, Cattle, Haplotypes, Nerve Tissue Proteins, Receptors, Immunologic, Polymorphism, Single Nucleotide
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
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