Hepatic gene expression reveals functional diversity in indigenous chicken breeds
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Authors
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Meena Bagiyal
Author
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Sonika Ahlawat
ICAR-National Bureau of Animal Genetic Resources, Karnal
Author
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Sunita Khatak
Author
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Pooja Chhabra
Author
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Upasna Sharma
Author
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Reena Arora
Author
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Rekha Sharma
Author
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Ram Parsad
Author
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Ritika Gera
Author
Abstract
Poultry meat ranks among the most widely consumed sources of animal protein across the globe, with chicken breeds varying significantly in their genetic makeup, physiological traits, and adaptability. Indigenous breeds contribute not only to rural livelihoods but also possess valuable traits like disease resistance, stress tolerance, and superior meat quality. The liver, being central to metabolism and lipid regulation, plays a crucial role in determining growth, reproduction, and stress response in poultry. This study employed high-throughput RNA sequencing to compare hepatic transcriptomes of three distinct chicken breeds—Aseel, Kadaknath, and Punjab Brown, to identify gene expression patterns in each. Notably, genes such as APOV1 and VTG2 showed higher expression in Aseel, SPIA3, HMGCS1, and HSP90B1 in Kadaknath and DIO2 and EPAS1 in Punjab Brown. These differences reflect key roles in lipid metabolism, stress response, immunity and reproduction in these breeds, indicating distinct metabolic adaptations among the breeds.
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REFERENCES
1. Aggrey SE, González‐Cerón F, Rekaya R, and Mercier Y. 2018. Gene expression differences in the methionine remethylation and transsulphuration pathways under methionine restriction and recovery with D, L‐methionine or D, L‐HMTBA in meat‐type chickens. Journal of Animal Physiology and Animal Nutrition, 102(1): e468-e475.
2. Ahlawat S, Arora R, Sharma R, Chhabra P, Kumar A, Kaur M, Lal SB, Mishra DC, Farooqi MS and Srivastava S. 2023. Revelation of genes associated with energy generating metabolic pathways in the fighter type Aseel chicken of India through skeletal muscle transcriptome sequencing. Animal Biotechnology, 34(9):4989-5000. doi: 10.1080/10495398.2023.2219718.
3. Ahlawat S, Vasu M, Mir MA, Singh MK, Arora R, Sharma R, Chhabra P and Sharma U. 2024. Molecular insights into Pashmina fiber production: comparative skin transcriptomic analysis of Changthangi goats and sheep. Mammalian Genome, 35(2):160-169. doi: 10.1007/s00335-024-10040-9.
4. Ahn J, Woodfint RM, Lee J, Wu H, Ma J, Suh Y, Hwang S, Cressman M and Lee K. 2019. Comparative identification, nutritional, and physiological regulation of chicken liver-enriched genes. Poultry Science, 98(7):3007-3013. doi: 10.3382/ps/pez057. PMID: 30796787.
5. An J, Li J, Wang Y, Wang J, Li Q, Zhou H, Hu X, Zhao Y and Li N. 2019. A Homeostasis Hypothesis of Avian Influenza Resistance in Chickens. Genes (Basel), 10(7):543. doi: 10.3390/genes10070543.
6. Andrews S. 2010. FastQC: a quality control tool for high throughput sequence data.
7. Arora R, Sharma R, Ahlawat S, Chhabra P, Kumar A, Kaur M, Vijh RK, Lal SB, Mishra DC, Farooqi MS and Srivastava S. 2023. Transcriptomics reveals key genes responsible for functional diversity in pectoralis major muscles of native black Kadaknath and broiler chicken. 3 Biotech, 13(7): 253. https://doi.org/10.1007/s13205-023-03682-0.
8. Arora R, Kumar H, Sharma U, Ahlawat S, Sharma R, Chhabra P, Sankhyan V and Vijh RK. 2024a. Mapping genome-wide diversity and population dynamics in Indian chicken breeds for targeted conservation and breeding. British Poultry Science 10.1080/00071668.2024.2379968.
9. Arora R, Ahlawat S, Sharma R, Chhabra P, Kaur M, Lal SB, Mishra DC, Farooqi MS and Srivastava S. 2024b. Transcriptomics of pectoralis major muscles uncovers a footprint of enriched pathways in five diverse backyard chicken breeds of India. Gene Reports, 36:101949.
10. Chen J, Fang Z, Luo Q, Wang X, Warda M, Das A, Oldoni F and Luo F. 2024. Unlocking the mysteries of VLDL: exploring its production, intracellular trafficking, and metabolism as therapeutic targets. Lipids in health and disease, 23(1):14. doi: 10.1186/s12944-023-01993-y.
11. Du X, Lai S, Zhao W, Xu X, Xu W, Zeng T, Tian Y and Lu L. 2022. Single-cell RNA sequencing revealed the liver heterogeneity between egg-laying duck and ceased-laying duck. BMC Genomics, 23:857. https://doi.org/10.1186/s12864-022-09089-0.
12. Fatima S, Sur S, Tiwari J, Rani S and Malik S. 2025. Endogenous regulation of behavior and reproductive physiology in a resident passerine songbird. Biology of Reproduction, 113(1):154-168. doi: 10.1093/biolre/ioaf073.
13. Ge XK, Wang AA, Ying ZX, Zhang LG, Su WP, Cheng K, Feng CC, Zhou YM, Zhang LL and Wang T. 2019. Effects of diets with different energy and bile acids levels on growth performance and lipid metabolism in broilers. Poultry Science, 98(2):887-895. doi: 10.3382/ps/pey434.
14. Gunawan A, Listyarini K, Furqon A, Sumantri C, Akter SH and Uddin MJ. 2019. RNA deep sequencing reveals novel transcripts and pathways involved in the unsaturated fatty acid metabolism in chicken. Gene Reports, 15: 100370.
15. He J, Huang D, Di R, Wang J, Chu M, Liu Q, Hu W, Wang X and Pan Z. 2016. Polymorphism of exon 2 of DIO2 gene and its association with seasonal reproduction in sheep. Turkish Journal of Veterinary & Animal Sciences, 40(2):142-9.
16. Heberle H, Meirelles GV, da Silva FR, Telles GP and Minghim R. 2015. InteractiVenn: a web-based tool for the analysis of sets through Venn diagrams. BMC Bioinformatics, 16: 1-7.
17. Katarzyńska-Banasik D, Kowalik K and Sechman A. 2024. Influence of silver nanoparticles on mRNA expression of thyroid hormone-related genes in the thyroid gland and liver of laying hens. Domestic Animal Endocrinology, 86, 106820.
18. Li H, Ma Z, Jia L, Li Y, Xu C, Wang T, Han R, Jiang R, Li Z, Sun G, Kang X and Liu X. 2016. Systematic analysis of the regulatory functions of microRNAs in chicken hepatic lipid metabolism. Scientific Reports, 6:31766. doi: 10.1038/srep31766.
19. Li H, Wang T, Xu C, Wang D, Ren J, Li Y, Tian Y, Wang Y, Jiao Y, Kang X and Liu X. 2015. Transcriptome profile of liver at different physiological stages reveals potential mode for lipid metabolism in laying hens. BMC Genomics, 16:763. doi: 10.1186/s12864-015-1943-0.
20. Li Y, Sun X, Bai Y, Ji Y, Ren H, Yu X, Yan Y, He X, Dong Y, Zhang L, Luo X, Wang H. 2021. Vitellogenin 2 promotes muscle development and stimulates the browning of white fat. Aging (Albany NY), 13(19):22985-23003. doi: 10.18632/aging.203590.
21. Lim HA, Lee EK, Kim JM, Park MH, Kim DH, Choi YJ, Ha YM, Yoon JH, Choi JS, Yu BP and Chung HY. 2012. PPARγ activation by baicalin suppresses NF-κB-mediated inflammation in aged rat kidney. Biogerontology, 13(2):133-45. doi: 10.1007/s10522-011-9361-4.
22. Luo L, Wang Q and Ma F. 2021. RNA-Seq transcriptome analysis of ileum in Taiping chicken supplemented with the dietary probiotic. Tropical Animal Health and Production, 53:131. https://doi.org/10.1007/s11250-021-02566-w
23. Nawaz AH and Zhang L. 2021. Oxidative stress in broiler chicken and its consequences on meat quality. International Journal of Life Science Research Archive, 1(1): 045-054.
24. Ning C, Ma T, Hu S, Xu Z, Zhang P, Zhao X, Wang Y, Yin H, Hu Y, Fan X, Zeng B, Yang M, Yang D, Ni Q, Li Y, Zhang M, Xu H, Yao Y, Zhu Q and Li D. 2020. Long Non-coding RNA and mRNA Profile of Liver Tissue During Four Developmental Stages in the Chicken. Frontier in Genetics, 11:574. doi: 10.3389/fgene.2020.00574.
25. Pan W, Liu C, Zhang J, Gao X, Yu S, Tan H, Yu J, Qian D, Li J, Bian S, Yang J, Zhang C, Huang L, Jin J. 2019. Association Between Single Nucleotide Polymorphisms in PPARA and EPAS1 Genes and High-Altitude Appetite Loss in Chinese Young Men. Frontiers in Physiology, 10:59. doi: 10.3389/fphys.2019.00059.
26. Rathi P, Dalal DS, Patil CS. 2024. Least square means and heritability estimates of egg quality traits in Aseel and Kadaknath chicken. Journal of Livestock Biodiversity, 13(1):44-50.
27. Ren J, Tian W, Jiang K, Wang Z, Wang D, Li Z, Yan F, Wang Y, Tian Y, Ou K, Wang H, Kang X, Li H and Liu X. 2021. Global investigation of estrogen-responsive genes regulating lipid metabolism in the liver of laying hens. BMC Genomics, 22(1):428. doi: 10.1186/s12864-021-07679-y.
28. Sharma R, Arora R, Ahlawat S, Chhabra P, Kumar A, Kaur M, Lal SB, Mishra DC, Farooqi MS and Srivastava S. 2023. Study on the muscle transcriptome of two diverse Indian backyard poultry breeds acclimatized to different agro-ecological conditions. Molecular Biology Reports, 50(3):2453-2461. doi: 10.1007/s11033-022-08223-1.
29. Shi X, Sun X, Xu P, Zhang C, Zhang M, Yuan X, Jiang J, Jin K, Chen C, Zuo Q and Zhang Y. 2021. HMGCS1 Promotes male differentiation of chicken embryos by regulating the generate of cholesterol. All Life, 14(1):577-87.
30. Soman A and Nair SA. 2022. Unfolding the cascade of SERPINA3: Inflammation to cancer. Biochimica et Biophysica Acta (BBA)-Reviews on Cancer, 1877(5):188760.
31. Wan Y, Ma C, Wei P, Fang Q, Guo X, Zhou B and Jiang R. 2017. Dynamic expression of HSP90B1 mRNA in the hypothalamus of two Chinese chicken breeds under heat stress and association analysis with a SNP in Huainan chickens. Czech Journal of Animal Science, 62(2): 82-87.
32. Xu E, Zhang L, Yang H, Shen L, Feng Y, Ren M and Xiao Y. 2019. Transcriptome profiling of the liver among the prenatal and postnatal stages in chickens. Poultry Science, 98(12): 7030-7040.
33. Yadav R, Kumar R, Pandey G, Tiwari A, Bisht R, Kumar A, Mishra A, Bhatt P. 2022. Comparative adaptive immune response in Indian and exotic breeds of domestic chicken. The Indian Journal of Animal Sciences, 92(2):183-6.
34. Zhang J, Zhuang H, Cao J, Geng A, Wang H, Chu Q, Yan Z, Zhang X, Zhang Y and Liu H. 2022. Breast Meat Fatty Acid Profiling and Proteomic Analysis of Beijing-You Chicken During the Laying Period. Frontiers in Veterinary Science, 9:908862. doi: 10.3389/fvets.2022.908862.
35. Zhou B, Chen J, Li Z, Liu H, Xu J, Xu H and Ruan Y. 2025. Genetic polymorphisms in HMGCS1 gene and its association with slaughter characteristics, meat quality, and organ coefficients in Guizhou white goats. Animal Bioscience, 38(5), 910–928. https://doi.org/10.5713/ab.24.0499
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