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Modeling genotype-by-environment interactions across climatic conditions reveals environment-specific genomic regions and candidate genes underlying feed efficiency traits in tropical beef cattle

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Abstract

Heat stress represents a major limitation for livestock production systems, negatively affecting feed efficiency, animal health and welfare, and overall performance. In this context, the objective of this study was to identify genomic regions, candidate genes, biological pathways, and functional networks associated with dry matter intake (DMI) and residual feed intake (RFI) in Nellore cattle exposed to varying levels of thermal stress. The dataset comprised records from 22,838 animals, with genotypes available for 18,567 individuals. The data were collected during 296 feed efficiency trials between 2011 and 2023 across 21 Brazilian farms. Genome-wide association studies (GWAS) were performed using the single-step GBLUP (ssGBLUP) approach to account for genotype-by-environment (G×E) interactions in Nellore cattle. Environmental variation was modeled using the temperature-humidity index (THI) as the environmental gradient, with analyses stratified across three environmental gradients (EG): low (THI = 66), medium (THI = 74), and high (THI = 81). Fifty-one SNPs were significantly associated with RFI, including 27 shared across all three EGs, 10 exclusive to the low EG, one to the high EG, and 13 shared between the moderate and high EGs. These associations were mapped to 44 candidate genes, with 19 genes commonly identified across all EGs, including key candidates such as PIPOX, GTF2F2, KCTD4, MYO18A, and NFIA. For DMI, 136 significant SNPs were identified: 12 and 39 exclusive to the low and moderate EGs, respectively; 28 shared across all EGs; and 57 shared between the moderate and high EGs. These variants were linked to 58 candidate genes, of which 19 were common to all EGs, including NCAPG, LCORL, FAM13A, HERC3, CCND1, and FGF19. Gene network analyses revealed a clear reconfiguration of interaction structures across thermal gradients, particularly for RFI, where gene connectivity declined with increasing THI levels. For DMI, gene networks remained highly integrated, especially in the lowest THI level. Functional annotation highlighted both conserved and environment-specific regulatory architectures, involving key biological processes such as growth regulation, lipid and protein metabolism, intracellular signaling, stress response, and neuroendocrine control. These findings uncover the environmental sensitivity of RFI and DMI, highlight the complex and dynamic genomic basis of these traits under varying climatic conditions, and support the identification of candidate genes for genomic selection programs aiming to enhance climatic resilience in tropical beef cattle.

Data availability

The data analyzed in this study were obtained from the National Association of Breeders and Researchers (ANCP). The phenotypic and genotypic information was provided to the authors for academic research purposes only. The following restrictions apply: the dataset is not publicly available and its use requires formal authorization. Requests to access these datasets should be directed to Dr. João Carlos G. Giffoni Filho, President of ANCP (email: [email protected]).

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Acknowledgements

The authors thank the National Association of Breeders and Researchers (ANCP, Ribeirão Preto, SP, Brazil) for providing the datasets for the research.

Funding

The authors thank the São Paulo Research Foundation (FAPESP, Brazil) for financial support through a PhD scholarship in Brazil and an international research internship (BEPE), both granted to the first author (Grant Numbers #2022/15385-4 and #2023/13417-9). This study was also partially financed by the Coordination for the Improvement of Higher Education Personnel (CAPES, Brazil)—Finance Code 001.

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Authors and Affiliations

  1. Department of Animal Science, School of Agricultural and Veterinarian Sciences (FCAV), São Paulo State University (UNESP), Jaboticabal, SP, 14884-900, Brazil

    João B. Silva Neto, Lucio F. M. Mota & Gustavo R. D. Rodrigues

  2. Department of Animal Sciences, Purdue University, West Lafayette, IN, 47907, USA

    João B. Silva Neto, Luiz F. Brito & Gustavo R. D. Rodrigues

  3. Department of Animal Science, Faculty of Animal Science and Food Engineering, University of São Paulo, Pirassununga, SP, 13635-900, Brazil

    Fernando Baldi

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  1. João B. Silva Neto
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Contributions

J.B. Silva Neto: Conceptualization, formal analysis, investigation, methodology, validation, writing—original draft and editing; L.F. Brito: Conceptualization, formal analysis, supervision, validation, writing—original draft and review; L.F.M. Mota: Conceptualization, Formal analysis, writing—review; G.R.D. Rodrigues: Visualization, writing—original draft and review; F. Baldi: Conceptualization, Data curation, formal analysis, project administration, supervision, validation, writing—original draft and review.

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João B. Silva Neto.

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The collection of the phenotypes was restricted to routine on-farm procedures that did not cause any inconvenience or stress to the animals. Therefore, no specific ethical approval was required. In accordance with national legislation and institutional guidelines, ethical review was not necessary for this study, as all data were obtained from an existing database and no additional animal procedures were conducted.

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Neto, J.B.S., Brito, L.F., Mota, L.F.M. et al. Modeling genotype-by-environment interactions across climatic conditions reveals environment-specific genomic regions and candidate genes underlying feed efficiency traits in tropical beef cattle.
Sci Rep (2026). https://doi.org/10.1038/s41598-025-33952-1

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Keywords

  • Climate resilience
  • Dry matter intake
  • Functional enrichment
  • Nellore cattle
  • Residual feed intake
  • Temperature-humidity index
  • Tropical environments

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