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Link to original content: https://doi.org/10.1007/s11250-023-03879-8
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Deciphering climate resilience in Indian cattle breeds by selection signature analyses

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Abstract

The signature of selection is a crucial concept in evolutionary biology that refers to the pattern of genetic variation which arises in a population due to natural selection. In the context of climate adaptation, the signature of selection can reveal the genetic basis of adaptive traits that enable organisms to survive and thrive in changing environmental conditions. Breeds living in diverse agroecological zones exhibit genetic “footprints” within their genomes that mirror the influence of climate-induced selective pressures, subsequently impacting phenotypic variance. It is assumed that the genomes of animals residing in these regions have been altered through selection for various climatic adaptations. These regions are known as signatures of selection and can be identified using various summary statistics. We examined genotypic data from eight different cattle breeds (Gir, Hariana, Kankrej, Nelore, Ongole, Red Sindhi, Sahiwal, and Tharparkar) that are adapted to diverse regional climates. To identify selection signature regions in this investigation, we used four intra-population statistics: Tajima’s D, CLR, iHS, and ROH. In this study, we utilized Bovine 50 K chip data and four genome scan techniques to assess the genetic regions of positive selection for high-temperature adaptation. We have also performed a genome-wide investigation of genetic diversity, inbreeding, and effective population size in our target dataset. We identified potential regions for selection that are likely to be caused by adverse climatic conditions. We observed many adaptation genes in several potential selection signature areas. These include genes like HSPB2, HSPB3, HSP20, HSP90AB1, HSF4, HSPA1B, CLPB, GAP43, MITF, and MCHR1 which have been reported in the cattle populations that live in varied climatic regions. The findings demonstrated that genes involved in disease resistance and thermotolerance were subjected to intense selection. The findings have implications for marker-assisted breeding, understanding the genetic landscape of climate-induced adaptation, putting breeding and conservation programs into action.

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Data availability

The WIDDE database and the Dryad repository both contain the genotypic data used for this study (http://widde.toulouse.inra.fr/widde/). The genotypic information for the 72 Tharparkar animals utilized in this work is accessible with the corresponding author, and due to some institutional liabilities, we can disclose this dataset on request.

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Acknowledgements

Support received from the National Agricultural Science Fund (NASF), Indian Council of Agricultural Research, New Delhi, India, for carrying out this work is duly acknowledged. The authors wish to thank the Director and Joint Director (Research), ICAR-Indian Veterinary Research Institute, Bareilly, India, for providing the necessary facilities during this study.

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Authors and Affiliations

  1. Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly, 243122, UP, India

    Sonali Sonejita Nayak, Manjit Panigrahi, Divya Rajawat, Kanika Ghildiyal, Anurodh Sharma, Karan Jain & Bharat Bhushan

  2. Livestock Production and Management Section, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly, 243122, UP, India

    Triveni Dutt

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  1. Sonali Sonejita Nayak
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Contributions

SSN: methodology and writing—original draft. MP: conceptualization, methodology, and writing—review and editing. DR: writing—review and editing. KG: review and editing. AS: writing—review and editing. KJ: writing—review and editing. BB and TD: resources and supervision.

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Correspondence to Manjit Panigrahi.

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Ethical approval

All the procedures performed in this study involving animals were following the ethical standards of the Institutional Animal Ethics Committee (IAEC) of ICAR-IVRI, Izatnagar, Bareilly, India (NO.F.1–53/2018–19/J. D(R)).

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The authors declare no competing interests.

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Nayak, S.S., Panigrahi, M., Rajawat, D. et al. Deciphering climate resilience in Indian cattle breeds by selection signature analyses. Trop Anim Health Prod 56, 46 (2024). https://doi.org/10.1007/s11250-023-03879-8

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