A Comparable genetic diversity between chicken ecotypes of different zones using DNA barcoding

Authors

  • Ayman Sabry Biology Department, Faculty of Science, Taif University, Taif, Saudi Arabia; Cell Biology Department, National Research Center, Dokki, Giza, Egypt.
  • Alaa Ahmed Mohamed Biology Department, Faculty of Science, Taif University, Taif, Saudi Arabia; Department of Genetics, Faculty of Agriculture, Minufiya University, Al Minufiyah,Egypt.
  • Mohamed Hassan Biology Department, Faculty of Science, Taif University, Taif, Saudi Arabia; Department of Genetics, Faculty of Agriculture, Minufiya University, Al Minufiyah,Egypt.
  • Salah E. M. Abo-Aba Department of Biological Sciences, Faculty of Science, King Abdul-Aziz University 21589, Jeddah, Saudi Arabia; Princess Doctor Dr. Najla Bint Saud Al Saud Center for Distinguished Research in Biotechnology, Jeddah, Saudi Arabia; Microbial Genetic Department, Genetic Engineering & biotechnology Division, National Research Center, Dokki, Giza, Egypt.

DOI:

https://doi.org/10.22317/jcms.v8i4.1259

Keywords:

DNA barcoding, Haplotype diversity, Chicken ecotypes

Abstract

Objectives: The purpose of the current study was to verify the reliability of COI bar- codes in the assessment of genetic diversity of two ecotypes from different ecozones.

Methods: The DNA sequences of cytochrome oxidase I (COI) barcodes of 50 hens belonging to two ecotypes of Ismalia Egypt (ISM) and Taif Saudi Arabia (TA) were isolated and analyzed.

Results: This study results showed that no noticeable great differences among all barcode’s sequences of both ecotypes. The aver- age length of both ecotypes was 589 bp. ISM ecotypes have a relatively wider length range. The overall mean of GC% content was 48±0.01. Both ecotypes have the same number of sites 548 bp. ISM ecotype has 523 monomorphic sites whereas TA ecotype has slightly fewer monomorphic sites 517. The ISM ecotype has 7 singleton sites and 18 Parsimony informative sites. TA ecotype has little more polymorphic, that is 12 singleton sites and 19 Par- simony informative sites. The number of mutations (η) was larger in ISM (46) compared to 38 mutations for TA ecotype. Both ecotypes had the same number of Haplotypes (25), and haplotypes diversity (1) as well as the variance of haplotype diversity.

Conclusion: These results indicated a comparable level of genetic diversity of both ecotypes, which in turn may refer to a similarity of evolutionary forces that affect both ecotypes. Based on the present results, COI gene can be used in barcoding. The COI provides an objective the foundation for identification of ecotypes and therefore could be used for a rapid establishment of a variety of identifications.

References

Al-Atiyat, R. (2010). Genetic diversity of indigenous chicken ecotypes in Jordan. African Journal of Biotechnology, 9(41), 7014–7019.

Allentoft, M. E., and O’Brien., J. (2010). Global amphibian declines, loss of genetic diversity and fitness: a review. Diversity, 2, 47–71.

Amer, S.A.M., Ahmed, M.M., and Shobrak, S. (2013). Efficient Newly Designed Primers for the Amplification and Sequencing of Bird Mitochondrial Genomes. Bioscience, Biotechnology, and Biochemistry, 77(3). 577-581.

Bekker, EI., Karabanov, DP., Galimov, YR., and Kotov, AA. (2016). DNA Barcoding Reveals High Cryptic Diversity in the North Eurasian Moina Species (Crustacea: Cladocera). PLOS ONE, 11(8), 1-19.

Bondoc, O.L., & Santiago, R.C. (2012). The Use of DNA Barcodes in the Evolutionary Analysis of Domestic Breeds and Strains of Chicken (Gallus gallus domesticus) in the Philippines. Philipp Agric Scientist, 95(4), 358 -369.

Cui, Hi, Ibtisham, F., Xu, C., Huang, H., and Su, Y. (2017). DNA barcoding of Chinese native chicken breeds through COI gene. Thai Journal of Veterinary Medicine, 47, 123–129.

Dave, A.R., Chaudhary, D.F., Mankad, P.M., Koringa, P.G., and Rank, D.N. (2021). Genetic diversity among two native Indian chicken populations using cytochrome c oxidase subunit I and cytochrome b DNA barcodes. Veterinary World, 14(5), 1389–1397.

Dawnay, N, Ogden, R., McEwing, R., Carvalho, GR., and Thorpe, RS. (2007). Validation of the barcoding gene COI for use in forensic genetic species identification. Forensic Sci Int., 173, 1–6.

Gaber, A., Hassan, M., Boland, C., Alsuhaibany. A, Bab-bington, J., John Pereira, J., Budd, J., and Shobrak, M. (2020). Molecular identification of Todiramphus chloris subspecies on the Arabian Peninsula using three mitochondrial barcoding genes and ISSR markers. Saudi Journal of Biological Sciences, 480–488.

Gratwicke, B., Mills, J., Dutton, A., Gabriel, G., Long, B. Sei- densticker, J., Wright, B., You, W., and Zhang, L. (2008). Attitudes toward consumption and conservation of tigers in China. PLoS One., 3, e2544.

Habimana, R., Okeno, T.O., Ngeno, K., Mboumba, S., Assami, P., Gbotto, A.A., Keambou, C. T., Nishimwe, K., Mahoro, J. and Mahoro, N. (2020). Genetic diversity and population structure of indigenous chicken in Rwanda using microsatellite markers. PLoS ONE, 15(4). e0225084.

Hebert, P. D. N., Cywinska, A., Shelley, L. B, and deWaard, R.J. (2003). Biological Identifications through DNA Barcodes. Proc Biol Sci, 151, 313–321.

Hebert, P.D.N., Cywinska, A., Ball, S.L., and de-Waard, J. (2002). Biological identifications through DNA barcodes. Proc. R. Soc. Lond. B, 270, 313–321.

Huang, S., Zhang, L., Rehman, M. U., Iqbal, M. K., Lan, Y., Mehmood, K., Zhang, H., Qiu, G., Nabi1, F., Yao, W., Wang, M., & Li, J. (2016a). High altitude hypoxia as a factor that promotes tibial growth plate development in broiler chickens. PLoS ONE, 27(5), 3280.

Huang, X. H., Chen, J.B., D.L., He, Zhang X. Q., and Zhong F. H. (2016b). DNA Barcoding of Indigenous Chickens in China: A Reevaluation. Scientia Agricultura Sinica, 49(13), 2622–2633.

Khan, I.A., Jahan, P., & Hasan, Q. and Rao, P. (2019). Genetic confirmation of T2DM metaanalysis variants studies in gestational diabetes mellitus in an Indian population. Diabetes Metab. Syndr., 13(1), 688–694.

Librado, P., and Rozas, J. (2009). DnaSP v5: a software for comprehensive analysis of DNA polymorphism data. BIOINFORMATICS, 25(11), 1451– 1452.

Mpenda, F. N., Schilling, M. A., Campbell, Z., Mngumi, E. B., and Buza, J. (2019). The genetic diversity of local African chickens: A potential for selection of chickens resistant to viral infections. J. Appl. Poult. Res, 28, 1–12.

Mpenda, F.N., , Schilling, M. A., Campbell, Z., Mngumi, E.B, and Buza, J. (2018). The genetic diversity of local african chickens: A potential for selection of chickens resistant to viral infections. J. Applied Poultry Research, 28, 1–12.

Msoffe, P.L.M., Mtambo, M.M.A., Minga, U.M., Yongolo, M.G.S., Gwakisa, P.S., and Olsen, J.E. (2001). Identification and characteri- sation of the free ranging local chicken eco-types in Tanzania. Pages 81–90 of: G.C. Kifaro, G.C, Kurwujila, R. L., Chenyam- buya, S.W., & Chilewa, R. R. (eds), Proceedings of SUA-MU EN- RECA Project Workshop.

Muchadeyi, F.C., Eding, H., Wollny, C.B., Groeneveld, E., Makuza, S.M., Shamseldin, R., Simianer, H., and Weigend, S. (2007). Absence of population sub-structuring in Zimbabwe chicken ecotypes inferred using microsatellite analysis. Animal Genetics, 38, 332–339.

Mwabvu, T., Lamb, J., Slotow, R., & Hamer, M.and Barra- clough, D. (2015). Do cytochrome c oxidase 1 Gene Sequences Differentiate Species of Spirostreptid Millipedes (Diplopoda: Spirostreptida: Spirostreptidae). African Invertebrates, 3(65), 651–661.

Osaman, S.A.M., Yonezawa, T., and Nishibori, M. (2016). Origin and genetic diversity of Egyptian native chicken based on complete sequence of mitochondrial DNA D-loop region. Poult. Sci, 95, 1248–1256.

Peng, W., Yang, H., Cai, K., Zhou, L., Tan, Z, and Wu, K. (2019). Molecular identification of the Danzhou chicken breed in China using DNA barcoding. Mitochondrial DNA Part B, 4(2), 2459–2463. PMID: 33365583.

Pius, L.O., Strausz, P., and Kusza, S. (2021). Overview of Poultry Management as a Key Factor for Solving Food and Nutritional Security with a Special Focus on Chicken Breeding in East African Countries. Biology, 10, 810–830.

Reed, D. H., and Frankham, R. (2003). Correlation between fitness and genetic diversity. Conserv. Biol, 17, 230–237.

Reeves, J.T., and Weil, J.V. (2001). Adv. Exp. Med. Biol., 502: 419–437. 2001. Chronic mountain sickness. A view from the crow’s nest. Adv. Exp. Med. Biol., 502, 419–437.

Roe, A. D., and Sperling, F.A.H. (2007). 44(1):325-45. 2007. Patterns of Evolution of Mitochondrial Cytochrome c Oxidase I and II DNA and Implications for DNA Barcoding. Mol Phylogenet Evol, 44, 325–345.

Rudresh, B. H., Murthy, H.N.N., Jayashankar, M. R., Nagaraj, C. S., Kotresh, A. M., and Byregowda, S. M. (2015). Microsatellite-based genetic diversity study in indigenous chicken ecotypes of Karnataka. Veterinary World, 8, 970–976.

Sabry, A., Hassan, M.M., Mohamed, A.A., & Allam, H. H.and Gaber, A. (2017). Quantitative assessment of genetic diversity among local chicken breeds detected by microsatellite markers. Biosci. Res, 14, 900–907.

Sabry, A., Ramadan, S., Hassan, M.M., Mohamed, A.A., A., Mohammedein, A.,,and Inoue-Murayma, M. (2021). Assessment of genetic diversity among Egyptian and Saudi chicken ecotypes and local Egyptian chicken breeds using microsatellite markers. Journal of Environmental Bi- ology, 42, 33–39.

Salo, S., Tadesse, G., and Hilemeskel, D. (2016). Village Chicken Pro- duction System and Constraints in Lemo District, Hadiya Zone, Ethiopia. Poult Fish Wildl Sci, 4(2), 158–162.

Shapiro, B. (2017). Pathways to de-extinction: how close can we get to resurrection of an extinct species? Funct. Ecol, 996–1002.

Tadelle, D., Kijora, C., and Peters, K.J. (2003). Indigenous Chicken Ecotypes in Ethiopia: Growth and Feed Utilization Potentials. Interna- tional Journal of Poultry Science, 2(2), 144–152.

Vingron, M., Brazma, A., Coulson, R., VAN Helden, J., Manke, T., Palin, K., Sand, O., and Ukkonen, E. (2009). Integrating sequence, evolution and functional genomics in regulatory genomics. Genome Biol- ogy, 10, 202–209.

Wimmers, K., Ponsuksili, S., Hardge, T., Valle-Zarate, A., Mathur, P.K., and Horst, P. (2000). Genetic distinctness of African, Asian and South American chickens. Animal Genetics, 31, 159–165.

Wu, H., Wan, Q-H., Fang, H-G., and Zhang. S. (2005). Application of Mitochondrial DNA Sequence Analysis in the Forensic Identification of Chinese Sika Deer Subspecies. Forensic science international, 148(2–3), 101–105.

Xun-he, H., Jie-bo, G., Dan-lin, H., Xi-quan, Z, and Fu-sheng, Z. (2016). DNA Barcoding of Indigenous Chickens in China: A Reevaluation HUANG. Scientia Agriculra Sinca, 49(13), 2622–2633.

Yu-Shi, G., Tu, Y-J., Tang, X-J., Lu, J-Xi., and Zhan, X-Y. (2011). Studies on the DNA barcoding of two newly discovered chicken breeds by mtDNA COI gene. Journal of Animal and Veterinary Advances, 10(13), 1711–1713.

Published

2022-08-26

How to Cite

Sabry, A. ., Ahmed Mohamed, A. . ., Hassan, M. ., & E. M. Abo-Aba, S. . (2022). A Comparable genetic diversity between chicken ecotypes of different zones using DNA barcoding. Journal of Contemporary Medical Sciences, 8(4). https://doi.org/10.22317/jcms.v8i4.1259