- Volume 31 Issue 12
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Genetic diversity of Saudi native chicken breeds segregating for naked neck and frizzle genes using microsatellite markers
- Fathi, Moataz (Department of Animal Production and Breeding, College of Agriculture and Veterinary Medicine, Qassim University) ;
- El-Zarei, Mohamed (Department of Animal Production and Breeding, College of Agriculture and Veterinary Medicine, Qassim University) ;
- Al-Homidan, Ibrahim (Department of Animal Production and Breeding, College of Agriculture and Veterinary Medicine, Qassim University) ;
- Abou-Emera, Osama (Department of Animal Production and Breeding, College of Agriculture and Veterinary Medicine, Qassim University)
- Received : 2018.01.10
- Accepted : 2018.05.07
- Published : 2018.12.01
Objective: Recently, there has been an increasing interest in conservation of native genetic resources of chicken on a worldwide basis. Most of the native chicken breeds are threatened by extinction or crossing with ecotypes. Methods: Six Saudi native chicken breeds including black naked neck, brown frizzled, black, black barred, brown and gray were used in the current study. The aim of the current study was to evaluate genetic diversity, relationship and population structure of Saudi native chicken breeds based on 20 microsatellite markers. Results: A total of 172 alleles were detected in Saudi native chicken breeds across all 20 microsatellite loci. The mean number of alleles per breed ranged from 4.35 in gray breed to 5.45 in normally feathered black with an average of 8.6 alleles. All breeds were characterized by a high degree of genetic diversity, with the lowest heterozygosity found in the brown breed (72%) and the greatest in the frizzled and black barred populations (78%). Higher estimate of expected heterozygosity (0.68) was found in both black breeds (normal and naked neck) compared to the other chicken populations. All studied breeds showed no inbreeding within breed (negative inbreeding coefficient [
Supported by : Qassim University
- FAO. Molecular genetic characterization of animal genetic resources. FAO Animal Production and Health Guidelines; No. 9. Rome, Italy: FAO; 2011.
- Fulton JE, Delany ME. Poultry genetic resources-operation rescue needed. Science 2003;300:1667-8. https://doi.org/10.1126/science.1085407
- Minga U, Msoffe P, Gwakisa P. Biodiversity in disease resistance and in pathogens within rural chickens. In: Proceedings of the 22nd World's Poultry Congress. June 8-12, Istanbul, Turkey; 2004.
- Fathi MM, Al-Homidan I, Motawei MI, Abou-Emera OK, El-Zarei MF. Evaluation of genetic diversity of Saudi native chicken populations using microsatellite markers. Poult Sci 2017;96:530-6.
- Qu L, Li X, Xu G, et al. Evaluation of genetic diversity in Chinese indigenous chicken breeds using microsatellite markers. Sci China C Life Sci 2006;49:332-41. https://doi.org/10.1007/s11427-006-2001-6
- Fathi MM, Galal A, El-Safty SA, Mahrous M. Naked neck and frizzle genes for improving chickens raised under high ambient temperature: I. Growth performance and egg production. World's Poult Sci J 2013;69:813-32. https://doi.org/10.1017/S0043933913000834
- Zhang X, Leung FC, Chan DKO, Yang G, Wu C. Genetic diversity of Chinese native chicken breeds based on protein polymorphism, randomly amplified polymorphic DNA, and microsatellite polymorphism. Poult Sci 2002;81:1463-72. https://doi.org/10.1093/ps/81.10.1463
- Bodzsar N, Eding H, Revay T, Hidas A, Weigend S. Genetic diversity of Hungarian indigenous chicken breeds based on microsatellite markers. Anim Genet 2009;40:516-23. https://doi.org/10.1111/j.1365-2052.2009.01876.x
- Tadano R, Nagasaka N, Goto N, Rikimaru K, Tsudzuki M. Genetic characterization and conservation priorities of chicken lines. Poult Sci 2013;92:2860-5. https://doi.org/10.3382/ps.2013-03343
- Sartore S, Sacchi P, Soglia D, et al. Genetic variability of two Italian indigenous chicken breeds inferred from microsatellite marker analysis. Br Poult Sci 2016;57:435-43. https://doi.org/10.1080/00071668.2016.1187714
- Hillel J, Granevitze Z, Twito T, et al. Molecular markers for the assessment of chicken biodiversity. World's Poult Sci J 2007;63:33-45. https://doi.org/10.1017/S0043933907001250
- Granevitze Z, Hillel J, Chen GH, et al. Genetic diversity within chicken populations from different continents and management histories. Anim Genet 2007;38:576-83. https://doi.org/10.1111/j.1365-2052.2007.01650.x
- Rajkumar U, Gupta BR, Ahmed N, Venktramaiah A, Reddy AR. Genetic variation and genetic diversity in chicken populations using microsatellite assay. Indian J Anim Sci 2007;77:1194-8.
- Abebe AS, Mikko S, Johansson AM. Genetic diversity of five local Swedish chicken breeds detected by microsatellite markers. PLoS One 2015;10:e0120580. https://doi.org/10.1371/journal.pone.0120580
- Yacoub H, Fathi MM. Phylogenetic analysis using d-loop marker of mtDNA in Saudi native chicken breeds. Mitochondrial DNA 2013;24:538-51. https://doi.org/10.3109/19401736.2013.770494
- Ahmed AS, Alhudaib KA, Soliman AM. Genetic diversity of Hajar1 and Hajar2 local Saudi chicken lines using mitochondrial DNA D-loop markers. S Afr J Anim Sci 2016;46:409-18. https://doi.org/10.4314/sajas.v46i4.9
- Belkhir K, Borsa P, Chikhi L, Raufaste N, Bonhomme F. GENETIX 4.05, logiciel sous Windows TM pour la génétique des populations. Laboratoire Genome, Populations, Interactions, CNRS UMR 5000. Montpellier, France: Universite de Montpellier II; 2004.
- Rousset F. Genepop'007: A complete reimplementation of the Genepop software for Windows and Linux. Mol Ecol Resour 2008;8:103-6. https://doi.org/10.1111/j.1471-8286.2007.01931.x
- Goudet J. FSTAT version 1.2. A computer program to calculate F-statistics. J Hered 1995;86:485-6. https://doi.org/10.1093/oxfordjournals.jhered.a111627
- Nei M. Genetic distance between populations. Am Nat 1972;106:283-92. https://doi.org/10.1086/282771
- Cavalli-Sforza L, Edwards A. Phylogenetic analysis. Models and estimation procedures. Am J Human Genet 1967;19:233-57.
- Takezaki N, Nei M, Tamura K. POPTREE2: software for constructing population trees from allele frequency data and computing other population statistics with Windows interface. Mol Biol Evol 2010;27:747-52. https://doi.org/10.1093/molbev/msp312
- Berthouly C, Bed-Hom B, Tixier-Boichard M, et al. Using molecular markers and multivariate methods to study the genetic diversity of local European and Asian chicken breeds. Anim Genet 2008;39:121-9. https://doi.org/10.1111/j.1365-2052.2008.01703.x
- Pham MH, Berthouly-Salazar C, Tran XH, et al. Genetic diversity of Vietnamese domestic chicken populations as decisionmaking support for conservation strategies. Anim Genet 2013;44:509-21. https://doi.org/10.1111/age.12045
- Shahbazi S, Mirhosseini, SZ, Romanov MN. Genetic diversity in five Iranian native chicken populations estimated by microsatellite markers. Biochem Genet 2007;45:63-75. https://doi.org/10.1007/s10528-006-9058-6
- Kaya M, Yildiz MA. Genetic diversity among Turkish native chickens, Denizli and Gerze, estimated by microsatellite markers. Biochem Genet 2008;46:480-91. https://doi.org/10.1007/s10528-008-9164-8
- Emara MG, Kim H, Zhu J, et al. Genetic diversity at the major histocompatibility complex (B) and microsatellite loci in three commercial broiler pure lines. Poult Sci 2002;81:1609-17. https://doi.org/10.1093/ps/81.11.1609
- Cheng HH, Levin I, Vallejo RL, et al. Development of a genetic map of the chicken with markers of high utility. Poult Sci 1995;74:1855-74. https://doi.org/10.3382/ps.0741855
- Nasiri BMT, Hamidi Z, Tavakoli S. The investigation of genetic variation at microsatellite loci in Mazandaran native chickens. Int J Poult Sci 2007;6:675-8. https://doi.org/10.3923/ijps.2007.675.678
- Nasiri BMT, Shokri F, Khanian SE, Tavakoli S. Study on polymorphism of Island native chicken population using microsatellites markers. Int J Poult Sci 2007;6:835-7. https://doi.org/10.3923/ijps.2007.835.837
- Weir BS, Cockerham CC. Estimating F-statistics forth analysis of populationstructure. Evolution 1984;38:1358-70.
- Hillel J, Groenen MA, Tixier-Boichard M, et al. Biodiversity of 52 chicken populations assessed by microsatellite typing of DNA pools. Genet Sel Evol 2003;35:533-57. https://doi.org/10.1186/1297-9686-35-6-533
- Wei L, Chen B, Li X, Liu S, Wang J. Genetic diversity of four protected indigenous chicken breeds in China using microsatellite markers. S Afr J Anim Sci 2013;43:464-72.
- Ramadan S, Kayang BB, Inoue E, et al. Evaluation of genetic diversity and conservation priorities for Egyptian chickens. Open J Anim Sci 2012;2:183-90. https://doi.org/10.4236/ojas.2012.23025
- Muchadeyi FC, Eding H, Wollny CB, et al. Absence of population substructuring in Zimbabwe chicken ecotypes inferred using microsatellite analysis. Anim Genet 2007;38:332-9. https://doi.org/10.1111/j.1365-2052.2007.01606.x
- Tadano R, Nishibori M, Nagasaka N, Tsudzuki M. Assessing genetic diversity and population structure for commercial chicken lines based on forty microsatellite analyses. Poult Sci 2007;86:2301-8. https://doi.org/10.3382/ps.2007-00233
- Ding FX, Zhang GX, Wang JY, et al. Genetic diversity of a Chinese native chicken breed, Bian chicken, based on twenty-nine microsatellite markers. Asian-Australas J Anim Sci 2010;23:154-61.
- Msoffe PL, Minga UM, Olsen JE, et al. Phenotypes including immunocompetence in scavenging local chicken ecotypes in Tanzania. Trop Anim Health Prod 2001;33:341-54. https://doi.org/10.1023/A:1010544221028
- Mwacharo JM, Nomura K, Hanada H, et al. Genetic relationships among Kenyan and other East African indigenous chickens. Anim Genet 2007;38:485-90. https://doi.org/10.1111/j.1365-2052.2007.01641.x
- Chen G, Bao W, Shu J, et al. Assessment of population structure and genetic diversity of 15 chinese indigenous chicken breeds using microsatellite markers. Asian-Australas J Anim Sci 2008;21:331-9. https://doi.org/10.5713/ajas.2008.70125
- Rajkumar U, Gupta BR, Reddy AR. Genomic heterogeneity of chicken populations of India. Asian-Australas J Anim Sci 2008;21:1710-20. https://doi.org/10.5713/ajas.2008.80299
- Cuc N, Simianer H, Eding H, et al. Assessing genetic diversity of Vietnamese local chicken breeds using microsatellites. Anim Genet 2010;41:545-7. https://doi.org/10.1111/j.1365-2052.2010.02039.x
- Dana N, Dessie T, van der Waaij LH, van Arendonk JAM. Morphological features of indigenous chicken populations of Ethiopia. Anim Genet Resour 2010;46:11-23. https://doi.org/10.1017/S2078633610000652
- Mtileni BJ, Muchadeyi FC, Maiwashe A, et al. Genetic diversity and conservation of South African indigenouschicken populations. J Anim Breed Genet 2011;128:209-18. https://doi.org/10.1111/j.1439-0388.2010.00891.x
- Leroy G, Kayang BB, Youssao IAK, et al. Gene diversity, agroecological structure and introgression patterns among village chicken populations across North, West and Central Africa. BMC Genet 2012;13:34.
- Lyimo CM, Weigend A, JanBen-Tapken U, et al. Assessing the genetic diversity of five Tanzanian chicken ecotypes using molecular tools. S Afr J Anim Sci 2013;43:499-510.
- Bao W, Chen G, Li B, et al. Analysis of genetic diversity and phylogenetic relationships among red jungle fowls and Chinese domestic fowls. Sci China Ser C Life Sci 2008;51:560-8. https://doi.org/10.1007/s11427-008-0076-y
- El-Tanany M, Distl O. Genetic diversity and genealogical origins of domestic chicken. World's Poult Sci J 2010;66:715-26. https://doi.org/10.1017/S0043933910000681
- Osman SAM, Sekino M, Nishihata A, et al. The genetic variability and relationships of Japanese and Foreign chickens assessed by microsatellite DNA profiling. Asian-Australas J Anim Sci 2006;19:1369-78. https://doi.org/10.5713/ajas.2006.1369