Assessing the genetic diversity of five Tanzanian chicken ecotypes using molecular tools

The study aimed to evaluate the genetic diversity of Tanzanian chicken populations through phylogenetic relationship, and to trace the history of Tanzanian indigenous chickens. Five ecotypes of Tanzanian local chickens (Ching’wekwe, Kuchi, Morogoro-medium, Pemba and Unguja) from eight regions were studied. Diversity was assessed based on morphological measurements and 29 microsatellite markers recommended by ISAG/FAO advisory group on animal genetic diversity. A principal component analysis (PCA) of morphological measures distinguished individuals most by body sizes and body weight. Morogoro Medium, Pemba and Unguja were grouped together, while Ching'wekwe stood out because of their disproportionate short shanks and ulna bones . Kuchi formed an independent group owing to their comparably long body sizes. Microsatellite analysis revealed three clusters of Tanzanian chicken populations. These clusters encompassed i) Morogoro-medium and Ching’wekwe from Eastern and Central Zones ii) Unguja and Pemba from Zanzibar Islands and iii) Kuchi from Lake Zone regions, which formed an independent cluster. Sequence polymorphism of D-loop region was analysed to disclose the likely maternal origin of Tanzanian chickens. According to reference mtDNA haplotypes, the Tanzanian chickens that were sampled encompass two haplogroups of different genealogical origin. From haplotype network analysis, Tanzanian chickens probably originated on the Indian subcontinent and in Southeast Asia. The majority of Kuchi chickens clustered in a single haplogroup, which was previously found in Shamo game birds sampled from Shikoku Island of Japan in the Kōchi Prefecture. Analysis of phenotypic and molecular data, as well as the linguistic similarity of the breed names, suggests a recent introduction of the Kuchi breed to Tanzania. Keywords: Tanzanian indigenous chickens, genetic diversity, microsatellites, mitochondrial DNA

[1]  G. Brockmann,et al.  Genetic diversity and population structure of five Ethiopian chicken ecotypes. , 2012, Animal genetics.

[2]  K. Dzama,et al.  Erratum to “Diversity and origin of South African chickens” (Poult. Sci. 90(10):2189–2194) , 2012 .

[3]  K. Winker,et al.  Heterogeneity in Genetic Diversity among Non-Coding Loci Fails to Fit Neutral Coalescent Models of Population History , 2012, PloS one.

[4]  O. Distl,et al.  Genetic diversity of ten Egyptian chicken strains using 29 microsatellite markers. , 2011, Animal genetics.

[5]  K. Dzama,et al.  Diversity and origin of South African chickens. , 2011, Poultry science.

[6]  G. Spellman,et al.  Isolation‐driven divergence: speciation in a widespread North American songbird (Aves: Certhiidae) , 2011, Molecular ecology.

[7]  K. Dzama,et al.  Genetic diversity and conservation of South African indigenous chicken populations. , 2011, Journal of animal breeding and genetics = Zeitschrift fur Tierzuchtung und Zuchtungsbiologie.

[8]  O. Hanotte,et al.  Domesticating Animals in Africa: Implications of Genetic and Archaeological Findings , 2011 .

[9]  O. Hanotte,et al.  Mitochondrial DNA reveals multiple introductions of domestic chicken in East Africa. , 2011, Molecular phylogenetics and evolution.

[10]  M. Stephens,et al.  Inferring weak population structure with the assistance of sample group information , 2009, Molecular ecology resources.

[11]  S. Weigend,et al.  Genetic diversity of Hungarian indigenous chicken breeds based on microsatellite markers. , 2009, Animal genetics.

[12]  Pablo Librado,et al.  DnaSP v5: a software for comprehensive analysis of DNA polymorphism data , 2009, Bioinform..

[13]  H. Simianer,et al.  Mitochondrial DNA D-loop sequences suggest a Southeast Asian and Indian origin of Zimbabwean village chickens. , 2008, Animal genetics.

[14]  O. Hanotte,et al.  Mitochondrial DNA Origin of Indigenous Malagasy Chicken , 2008, Annals of the New York Academy of Sciences.

[15]  O. Hanotte,et al.  Indo-European and Asian origins for Chilean and Pacific chickens revealed by mtDNA , 2008, Proceedings of the National Academy of Sciences.

[16]  M. Feldman,et al.  Genetic diversity within chicken populations from different continents and management histories. , 2007, Animal genetics.

[17]  O. Hanotte,et al.  Genetic relationships among Kenyan and other East African indigenous chickens. , 2007, Animal genetics.

[18]  H. Simianer,et al.  Absence of population substructuring in Zimbabwe chicken ecotypes inferred using microsatellite analysis. , 2007, Animal genetics.

[19]  M. Stephens,et al.  Inference of population structure using multilocus genotype data: dominant markers and null alleles , 2007, Molecular ecology notes.

[20]  N. Takahata,et al.  Analysis of mtDNA sequences shows Japanese native chickens have multiple origins. , 2007, Animal genetics.

[21]  J. L. Bouzat,et al.  Effects of recent population bottlenecks on reconstructing the demographic history of prairie‐chickens , 2007, Molecular ecology.

[22]  J. E. Olsen,et al.  Differences in resistance to Salmonella enterica serovar Gallinarum infection among indigenous local chicken ecotypes in Tanzania , 2006, Avian pathology : journal of the W.V.P.A.

[23]  D. Huson,et al.  Application of phylogenetic networks in evolutionary studies. , 2006, Molecular biology and evolution.

[24]  G. Evanno,et al.  Detecting the number of clusters of individuals using the software structure: a simulation study , 2005, Molecular ecology.

[25]  N. Rosenberg.  distruct: a program for the graphical display of population structure , 2003 .

[26]  P. Dunn,et al.  Contrasting patterns of mitochondrial and microsatellite population structure in fragmented populations of greater prairie‐chickens , 2003, Molecular ecology.

[27]  T. Gojobori,et al.  Where is the origin of the Japanese gamecocks? , 2003, Gene.

[28]  M. Feldman,et al.  Genetic Structure of Human Populations , 2002, Science.

[29]  J. E. Olsen,et al.  Phenotypes Including Immunocompetence in Scavenging Local Chicken Ecotypes in Tanzania , 2001, Tropical Animal Health and Production.

[30]  P. Donnelly,et al.  Inference of population structure using multilocus genotype data. , 2000, Genetics.

[31]  L. Excoffier,et al.  The impact of population expansion and mutation rate heterogeneity on DNA sequence polymorphism. , 1996, Molecular biology and evolution.

[32]  H. Bandelt,et al.  Mitochondrial portraits of human populations using median networks. , 1995, Genetics.

[33]  L. Excoffier,et al.  Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. , 1992, Genetics.

[34]  K. Macdonald.  The domestic chicken (Gallus gallus) in sub-Saharan Africa: A background to its introduction and its osteological differentiation from indigenous fowls (Numidinae and Francolinus sp.) , 1992 .

[35]  F. Tajima.  Statistical method for testing the neutral mutation hypothesis by DNA polymorphism. , 1989, Genetics.

[36]  N. Saitou,et al.  The neighbor-joining method: a new method for reconstructing phylogenetic trees. , 1987, Molecular biology and evolution.

[37]  B. Weir,et al.  ESTIMATING F‐STATISTICS FOR THE ANALYSIS OF POPULATION STRUCTURE , 1984, Evolution; international journal of organic evolution.

[38]  B S Weir,et al.  Estimation of the coancestry coefficient: basis for a short-term genetic distance. , 1983, Genetics.

[39]  S WRIGHT,et al.  Genetical Structure of Populations , 1950, British medical journal.

[40]  J. E. Olsen,et al.  The effect of supplementation on the performance of free range local chickens in Tanzania , 2012 .

[41]  M. Tixier-Boichard,et al.  Assessment of the genetic diversity of Cameroon indigenous chickens by the use of microsatellites , 2010 .

[42]  Thomas Vernet.  Slave trade and slavery on the Swahili coast (1500-1750) , 2009 .

[43]  M. Groenen,et al.  Genetic diversity and population structure of locally adapted South African chicken lines: Implications for conservation , 2008 .

[44]  G. Luikart,et al.  Multiple maternal origins of chickens: out of the Asian jungles. , 2006, Molecular phylogenetics and evolution.

[45]  P. Msoffe,et al.  Genetic structure among the local chicken ecotypes of Tanzania based on microsatellite DNA typing , 2005 .

[46]  J. E. Olsen,et al.  Productivity and reproductive performance of the free range local domestic fowl ecotypes in Tanzania , 2004 .

[47]  Stephen D. E. Park.  Trypanotolerace in West African cattle and the population genetic effects of selection , 2002 .

[48]  J. Goudet.  FSTAT, a program to estimate and test gene diversities and fixation indices (version 2.9.3). Updated from Goudet (1995) , 2001 .

[49]  N. Saito.  The neighbor-joining method : A new method for reconstructing phylogenetic trees , 1987 .

[50]  J. Crow.  Basic concepts in population, quantitative, and evolutionary genetics , 1986 .