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Study on the muscle transcriptome of two diverse Indian backyard poultry breeds acclimatized to different agro-ecological conditions

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Abstract

Objective

Free-range (FR) poultry production systems are associated with quality products and improved welfare. All the 19 diverse chicken breeds of India have evolved under the FR system and are adapted to different agro-climatic conditions. It is vital to explore indigenous germplasm with modern genomic tools to have insights into genomic characteristics of production traits and adaptation.

Methods

In this study, breast tissue transcriptome profiles were generated and analyzed from four biological replicates of two indigenous backyard poultry breeds of India-Ankaleshwar, a breed of the mainland, and Nicobari, a breed adapted to islands. The read quality of sequences was checked by FASTQC and processed reads were aligned to the reference genome (bGalGal1).

Results

More than 94% mapping to the reference genome was observed for all samples. A total of 12,790 transcripts were common across both groups, while 657 were expressed only in Ankaleshwar and 169 in Nicobari. The highest expressed genes across both groups were associated mainly with muscle structure, contraction, and energy metabolism. The highly expressed genes identified in Ankaleshwar were involved in fatty acid catabolism and oxidative stress mitigation. Functional terms, pathways, and hub genes in Nicobari participated in muscle fiber growth, adipogenesis, and fatty acid anabolism. A key hub gene (RAC1) in Nicobari is a potential candidate affecting the laying rate in chickens. The qRT-PCR results also substantiate the RNA-seq results.

Conclusion

The findings provide a precious molecular resource to advance understanding of the genetic basis of adaptation, meat quality, and egg production in backyard chickens.

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Acknowledgements

This work was financially supported by ICAR-CABin Scheme, New Delhi. We are grateful to the Director, ICAR-National Bureau of Animal Genetic Resources (NBAGR), Karnal, and Indian Council of Agricultural Research (ICAR), New Delhi for providing the necessary facilities.

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Authors and Affiliations

  1. ICAR-National Bureau of Animal Genetic Resources, Karnal, 132001, India

    Rekha Sharma, Reena Arora, Sonika Ahlawat, Pooja Chhabra, Ashish Kumar & Mandeep Kaur

  2. ICAR-Indian Agricultural Statistics Research Institute, New Delhi, 110012, India

    Shashi Bhushan Lal, Dwijesh Chandra Mishra, Md. Samir Farooqi & Sudhir Srivastava

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  1. Rekha Sharma
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Contributions

All authors contributed to the study’s conception and design. Material preparation and data collection were performed by RS, SA, RA, PC, AK, MK, and data curation and analysis were done by SBL, DCM, and MSF. The first draft of the manuscript was written by RS, and all authors commented on and improved the manuscript. All authors read and approved the final manuscript.

Corresponding author

Correspondence to Rekha Sharma.

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Conflict of interest

The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper.

Ethical approval

All protocols were carried out in compliance with Committee for the Purpose of Control and Supervision on Experiments on Animals (CPCSEA) rules. The animals were not experimented upon and the muscle samples were purchased in liaison with the butchers.

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Sharma, R., Arora, R., Ahlawat, S. et al. Study on the muscle transcriptome of two diverse Indian backyard poultry breeds acclimatized to different agro-ecological conditions. Mol Biol Rep 50, 2453–2461 (2023). https://doi.org/10.1007/s11033-022-08223-1

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