Comparison of the Transcriptomic studies in indigenous chicken versus IBL-80 broiler chicken
Transcriptomic profiling between chicken strains
110 / 99
Authors
-
JASWINDER KAUR
Department of Bioinformatics, College of Animal Biotechnology, Guru Angad Dev Veterinary and Animal Science University, Ludhiana, Punjab, India.
Author
-
PARAMVIR SINGH
Department of Bioinformatics, College of Animal Biotechnology, Guru Angad Dev Veterinary and Animal Science University, Ludhiana, Punjab, India.
Author
-
YOGESHWAR SINGH SINGH
Department of Bioinformatics, College of Animal Biotechnology, Guru Angad Dev Veterinary and Animal Science University, Ludhiana, Punjab, India.
Author
-
S. K. DASH SINGH
Department of Bioinformatics, College of Animal Biotechnology, Guru Angad Dev Veterinary and Animal Science University, Ludhiana, Punjab, India.
Author
-
C. S. MUKHOPADHYAY SINGH
Department of Bioinformatics, College of Animal Biotechnology, Guru Angad Dev Veterinary and Animal Science University, Ludhiana, Punjab, India.
Author
Keywords:
Aseel, Commercial broiler, Differentially expressed gene, Pathway analysis, Punjab Brown, TranscriptomeAbstract
Indigenous chicken breeds have played a vital role in contributing towards nutritional security and economic assistance to the
rural people in the nation. These birds are well adapted to the local environment and possesses resistance to a number of diseases.
However, they lack performance in terms of growth characteristics for which they are not prefered for raising in commercial broiler
farming. A study was conducted to compare lung and trachea tissue transcriptomic analysis data for three groups of chickens namely
Aseel, Punjab Brown, and IBL80 commercial broiler. RNA-sequencing results provided 5,282 differentially expressed genes (DEGs).
Out of the total DEGs, 1478 from Aseel, were up-regulated and 930 were down-regulated. 1872 DEGs belonged to Punjab Brown in
which 697 were up-regulated and 1175 down-regulated and IBL-80 exhibited 1931 DEGs but 714 were upregulated and 1217
downregulated. Interestingly, all three chicken groups revealed more downregulated DEGs. Gene Ontology (GO) enrichment analysis
led to most of the comparable terms among the chicken groups. The count of genes related to innate immunity were greater in Aseel
compared to Punjab Brown and commercial broiler. The majority of genes were chemokines or chemokine receptors. Aseel exhibited
relatively higher count of chemokines and chemokines receptor-related genes compared to Punjab Brown, and IBL-80 commercial
broiler.
Downloads
References
Ahlawat, S., Arora, R., Sharma, U., Sharma, A., Girdhar, Y., Sharma,
R. and Vijh, R.K. 2021. Comparative gene expression
profiling of milk somatic cells of Sahiwal cattle and Murrah
buffaloes. Gene 764: 145101.
Dalal, D.S., Ratwan, P. and Yadav, A.S. 2022. Genetic evaluation
of growth, production and reproduction traits in Aseel and
Kadaknath chickens in agroclimatic conditions of northern
India. Biological Rhythm Research, 53(1): 40-49.
Georg, I., Díaz-Barreiro, A., Morell, M., Pey, A.L. and AlarcónRiquelme, M.E. 2020. BANK1 interacts with TRAF6 and
MyD88 in innate immune signaling in B cells. Cellular &
Molecular Immunology, 17(9): 954-965.
Halfon, S., Ford, J., Foster, J., Dowling, L., Lucian, L., Sterling,
M. and Zurawski, G. 1998. Leukocystatin, a new class II
cystatin expressed selectively by hematopoietic cells.
Journal of Biological Chemistry, 273(26): 16400-16408.
Haunshi, S. and Prince, L.L.L. (2021). Kadaknath: A popular native
chicken breed of India with unique black colour
characteristics. World’s Poultry Science Journal, 77(2), 427-
440.
Huang, D.W., Sherman, B.T. and Lempicki, R.A. 2009. Systematic
and integrative analysis of large gene lists using DAVID
bioinformatics resources. Nature Protocols, 4(1): 44-57.
Islam, M.T., Meher, M.M., Harun, A.B., and Haider, M.G. 2022.
The common respiratory diseases of poultry in Bangladesh:
present status and future directions. Veterinary Sciences:
Research and Reviews, 8(1): 52-64.
Kanakachari, M., Rahman, H., Chatterjee, R.N., and Bhattacharya,
T.K. 2022. Signature of Indian native chicken breeds: a
perspective. World’s Poultry Science Journal, 78(2): 421-
445.
Liu, Y., Cong, Y., Niu, Y., Yuan, Y., Tan, F., Lai, Q., and Fu, G.
2022. Themis is indispensable for IL-2 and IL-15 signaling
in T cells. Science Signaling, 15(721): eabi9983.
Mortazavi, A., Williams, B.A., McCue, K., Schaeffer, L. and Wold,
B. 2008. Mapping and quantifying mammalian
transcriptomes by RNA-Seq. Nature Methods 5(7): 621-
628.
Niranjan, S.K., Pundir, R.K. and Mishra, B.P. 2022. Breed
registration and the gazette notification: A unique national
framework for protecting native animal germplasm. Indian
Journal of Plant Genetic Resources, 35(03), 279-282.
Padhi, M.K., Chatterjee, R.N. and Rajkumar, U. 2022. Effects of
genotype and age on egg quality traits in crossbred chickens
developed for backyard poultry farming. Indian Journal of
Poultry Science, 57(2):133-138.
Prabhu, M., Malmarugan, S., Sweetline Anne, N., Parthiban, S.,
Balakrishnan, G., and Johnson Rajeswar, J. 2021. Detection
of Mycoplasma gallisepticum infection in Turkey and chicken
farms of Tamilnadu, India. International Journal of Current
Microbiology and Applied Sciences, 10(01), 3151-3158.
Raj, G.D., Rajanathan, T.C., Kumanan, K., and Elankumaran, S.
2009. Expression profile of Toll-like receptor mRNA in an
indigenous Aseel breed of chicken in India. International
Journal of Poultry Science 8(7): 651-655.
Ramasamy, K.T., Reddy, M.R., Raveendranathan, D.N.,
Murugesan, S., Chatterjee, R.N., Ullengala, R., and Haunshi,
S. 2010. Differential expression of Toll-like receptor mRNA
in White Leghorn and indigenous chicken of India. Veterinary
Research Communications 34(7): 633-639.
Saini, J., Dhande, P.L., Ranade, A.S., Avari, P.E. and Desai, D.
2022. Growth performance, meat yields and economics of
broiler chickens fed diets containing selected feed additives.
Indian Poultry Science Association, 57 (2), 145-149.
Sehrawat, R., Sharma, R., Ahlawat, S., Sharma, V., Thakur, M.S.,
Kaur, M. and Tantia, M.S. 2021. First report on better
functional property of black chicken meat from India. Indian
Journal of Animal Research, 55(6), 727-733.
Szklarczyk, D., Morris, J.H., Cook, H., Kuhn, M., Wyder, S.,
Simonovic, M. and Von Mering, C. 2016. The STRING
database in 2017: quality-controlled protein–protein
association networks, made broadly accessible. Nucleic
Acids Research, 45(D1): D362-D368.
Wu, P., Zhang, X., Zhang, G., Chen, F., He, M., Zhang, T. and Dai,
G. 2020. Transcriptome for the breast muscle of Jinghai
Yellow Chicken at early growth stages. Peer J 8: e8950.
