A PRELIMINARY COMPARISON OF MITOCHONDRIAL D-LOOP REGION OF FUNAAB ALPHA AND NIGERIAN INDIGENOUS CHICKENS
Keywords:chickens, diversity, genetic erosion, phylogeny, polymorphism, selection
Nigerian indigenous chickens possess immunity from endemic diseases and have a better survival rate than commercial hybrid strains under local production conditions. FUNAAB Alpha chicken was developed by improving Nigerian indigenous chickens through crossbreeding and selection. This study compared the mitochondrial d-loop of FUNAAB Alpha and Nigerian indigenous chickens to check likely genetic erosion and loss of diversity in development of FUNAAB Alpha breed. Blood samples were collected from Nigerian indigenous (n=23) and FUNAAB Alpha (n=20) chickens sampled from farms and houses in Ogun state, Nigeria. The Hypervariable 1 (HV1) of the mitochondrial d-loop region was amplified and sequenced. Single nucleotide polymorphisms present in HV1 of chickens were identified using Clustal W. Genetic diversity of the region was determined using DnaSp v5 while selective forces acting on the chickens were predicted using HyPhy software implemented inside MEGA 6 software. Phylogenetic relationship among FUNAAB Alpha, Nigerian indigenous and other chicken breeds was determined using MEGA 6 software. Five polymorphisms were identified in FUNAAB Alpha chickens while twelve were identified in Nigerian indigenous chickens. All the polymorphisms identified in FUNAAB Alpha chickens were also observed in Nigerian indigenous chickens while seven polymorphisms were unique to Nigerian indigenous chickens. Higher diversity indices were observed in Nigerian indigenous chickens (number of haplotype: 4; haplotype diversity: 0.743±0.012; nucleotide diversity: 0.014±0.0013 and average number of nucleotide differences: 4.332) compared with FUNAAB Alpha chickens (number of haplotype: 2; haplotype diversity: 0.485±0.001; nucleotide diversity: 0.008±0.0001 and average number of nucleotide differences: 2.424). Positive selective forces were acting on FUNAAB Alpha chickens while negative selective forces were acting on Nigerian indigenous chickens. Phylogenetic analysis revealed that FUNAAB Alpha chickens clustered with Nigerian indigenous and South American chickens. It can be concluded that there was likely genetic erosion and loss of diversity in development of FUNAAB Alpha breed. Breeding programmes aimed at improvement of genetic diversity and reduction of genetic erosion should be applied in subsequent improvement of FUNAAB Alpha chickens.
Adebambo, A.O., Mobegi, V.A., Mwacharo, J.M., Oladejo, B.M., Adewale, R.A, Ilori, L.O., Makanjuola, B.O., Afolayan, O., Bjornstad, G., Jianlin, H., Hanotte, O. 2010. Lack of phylogeographic structure in Nigerian village chickens revealed by mitochondria DNA D-loop sequence analysis. International Journal of Poultry Science 9: 503-507.
Ajibike, A.B., Adeleye, O.O., Ilori, B.M., Osinbowale, D.A., Adeniyi, O.A., Durosaro, S.O., Sanda, A.J., Adebambo, O.A., Adebambo, A.O. 2017. Genetic diversity, phlogeographic structure and effect of selection at the mitochondrial Hypervariable region of Nigerian chicken populations. Journal of Genetics 96(2): 959-968.
Akishinonomiya, F., Miyake, T., Takada, M., Shingu, R., Endo, T., Gojobori, T., Kondo, N., Ohno, S. 1996. Monophyletic origin and uniques dispersal patterns of domestic fowls. Proceedings of the National Academy of Science of United States of America 93: 6792-6795.
Anderson, S., Bankier, A.T., Barell, B.G., Debruijn, M.H., Coulson, A.R., Drouin, J., Young, I.G. 1981. Sequence and organization of the human mitochondrial genome. Nature 290(5806): 457-467
Andolfatto, P. 2005. Adaptive evolution of non-coding DNA in Drosophila. Nature 437: 1149-1152.
Bergstrom, C.T., Pritchard, J. 1998. Germline bottlenecks and the evolutionary maintenance of mitochondrial genome. Genetics 149: 2135-2146.
Crawford, R.D. 1990. Poultry breeding and genetics.1st edition, Elsevier Science Publishers, Amsterdam. Pp 1-42.
Desjardins, P., Conklin, D. 2010. Nanodrop microvolume quantification of nucleic acid. Journal of Visualized Experiments 22(45): 2565.
Elyashiv, E., Sattath, S., Hu, T.T., Strutsovsky, A., McVicker, G. 2016. A genomic map of the effects of linked selection in drosophila. PLoS Genetics 12:e1006130.
Hahn, M.W., Rausher, M.D., Cunningham, C.W. 2002.Distinguishing between selection and population expansion in an experimental lineage of Bacteriophage T7. Genetics 161: 11-20.
Hall, T. A. 1999. BioEdit: A user-friendly biological sequence alignment editor and analysis program for windows 95/98/NT. Nucleic Acids Symposium Series 41: 95–98.
Horst, P. 1989. Native fowl as reservoir for genomes and major genes with direct and indirect effects on the adaptability and their potential for tropically oriented breeding plans. Archiv fur Geflugelkunde 53(3): 93-101.
Ilori, B.M., Oyeniyi-Dada, Q.A., Ayankeye, T.R., Hamzat, F., Durosaro, S.O., Wheto, M., Adebambo, A.O., Adebambo, O.A. 2017. Effect of crossbreeding and selection for meat on Nigerian indigenous chickens. Bulletin of Animal Health and Production in Africa 65: 277-287.
Joshi, J., Salar, R.K., Banerjee, P., Upasna, S., Tantia, M.S., Vijh, R.K. 2013. Genetic variation and phylogenetic relationships of Indian buffaloes of Uttar Pradesh. Asian Australian Journal of Animal Science 26(9): 1229-1236.
Librado, P., Rozas, J. 2009. DnaSP v5: A software for comprehensive analysis of DNA polymorphism data. Bioinformatics 25(11): 1451-1452.
Liu, Y., Wu, G., Yao, Y., Miao, Y., Luikart, G., Baig, m., Beja-Pereira, A., Ding, Z., Palanichamy, M.G., Zhang, Y. 2006. Multiple maternal origin of chickens: Out of the Asian jungles. Molecular Phylogenetics and Evolution 38: 12-19.
Mannen, H., Kohno, M., Nagata, Y., Tsuji, S., Bradley, D.G., Yeo, J.S., Amanof, T. 2004. Independent mitochondrial origin historical genetic differentiation in North Eastern Asian cattle. Molecular Phylogenetics and Evolution 32(2): 539-544.
Marinate, A.S., Egito, A.A. 2002. Animal genetic resources in Brazil: Results of five centuries of natural selection. Theriogenology 57(1): 223-235.
Minga, U.M., Msoffe, P.L., Gwasika, P.S. 2004. Biodiversity (variation) in disease resistance and in pathogens within rural chickens. Proceedings of XXII World’s Poultry Congress, Istanbul, Turkey
Momoh, O.M., Ehiobu, N.O., Nwosu, C.C. 2007. Egg production of two Nigerian local chicken ecotypes under improved management. Proceedings of the 32nd Annual Conference of Nigerian Society for Animal Production, 18-21 March, 2007. University of Calabar 278-281.
Mtileni, B.J., Muchadeyi, F.C., Maiwashe, A., Groeneveld, E., Groeneveld, L.F., Dzama, K., Weigend, S. 2011. Genetic diversity and conservation of South African indigenous chicken populations. Journal of Animal Breeding and Genetics 128:209-218.
Omondi, S.O. 2018. Economic analysis of small scale poultry production in Kenyan medium-sized cities of Kisumu and Thika. Proceedings of the 10th International Conference of Agricultural Economists, Vancouver. Pp 1-35.
Osman, S.A.M., Yonezawa, T., Nishibori, M. 2016. Origin and genetic diversity of Egyptian native chickens based on complete sequence of mitochondrial DNA D-loop region. Poultry Science 95:1248-1256.
Savolainen, P., Zhang, Y.P., Luo, J., Lundeberg, J., Leitner, T. 2002. Genetic evidence for an East Asian origin of domestic dogs. Science 298(5598): 1610-1613
Simonsen K.L., Churchill, G.A., Aquadro, C.F. 1995.Properties of statistical tests of neutrality for DNA polymorphism data. Genetics 141(1): 413-429.
Sonaiya, E.B., Olori, V.E. 1990. Family poultry production in south western Nigeria. Proceedings of International Workshop held in November 13-16, 1989 at Obafemi Awolowo University, Ile Ife Nigeria. Pp 243-247.
Taberlet, P., Coissac, E., Pansu, J., Pompanon, F. 2011. Conservation genetics of cattle, sheep and goats. Cell Research Biology 334: 247-254.
Tamura, K., Stecher, G., Peterson, D., Filipski, A., Kumar, S. 2013. MEGA6: Molecular Evolutionary Genetics Analysis version 6.0. Molecular Biology Evolution 30: 2725–2729.
Teinlek, P., Siripattarapravat, K., Tirawattanawanich, C. 2018. Genetic diversity analysis of Thai indigenous chickens based on complete sequences of mitochondrial DNA D-loop region. Asian-Australasian Journal of Animal Science 31(6): 804-811.
Thompson, J.D., Higgins, D.G., Gibson, T.J. 1994. CLUSTAL W: Improving the sensitivity of progressive multiple sequence alignment through sequence weighing, position-specific gap penalties and weight matrix choice. Nucleic Acids Research 22: 4673-4680.
Wani, C.E., Yousif, I.A., Ibrahim, M.E., Musa, H.H. 2014. Molecular characterization of Sudanese and Southern Sudanese chicken breeds using mtDNA D-loop. Genetics Research International 928420: 1-8.
Wolf, C., Reutsch, J., Hubner, P. 1999. PCR-RFLP analysis of mitochondrial DNA: a reliable method for species identification. Journal of Agricultural and Food Chemistry 47(4):