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Genetic diversity and genealogical origins of domestic chicken

Published online by Cambridge University Press:  17 December 2010

M. ELTANANY  and
O. DISTL
M. ELTANANY
Affiliation:
Animal Wealth Development Department, Veterinary Medicine Faculty, Benha University, Moshtohor, Toukh, Egypt
O. DISTL*
Affiliation:
Animal Breeding and Genetics Institute, University of Veterinary Medicine Hannover, Bünteweg 17p, 30559, Hannover, Germany
*
Corresponding author: [email protected]
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Abstract

This paper reviews some important features of the chicken genome, genealogical origins and the current status of the genetic diversity of the chicken. The small chicken genome exhibits six times more single nucleotide polymorphisms (>7,000,000 SNPs) than mammalian genomes and considerable microsatellite content (375,000). An obvious debate is still dedicated to whether chicken origin is monophyletic or polyphyletic. Modern genetic analysis conducted across the world's chicken population has determined no restricted phylo-geographical centre of domestication, as has been shown for other livestock species. Wild, unselected native and some fancy and conserved chicken populations showed high microsatellite and SNP diversity. Within-population diversity was higher than between-population diversity in selected or inbred chicken populations, whereas village chickens almost showed no sub-division in clusters. There is a variable degree of mitochondrial-DNA control-region (mtDNA-CR) sequence diversity within native chicken populations. Although commercial broilers exhibited considerable diversity in all marker types, they have lost >50% of SNP alleles found in their ancestors. Moreover, the linkage disequilibrium (LD) within broiler lines extends over shorter distances than in other inbred livestock populations. Domestic chickens are still genetically diverse and further conservation efforts are warranted to maintain the large between-population diversity.

Keywords

chickengenetic diversitymicrosatellitesSNPmtDNA-CR
Type
Review Article
Information
World's Poultry Science Journal , Volume 66 , Issue 4 , December 2010 , pp. 715 - 726
Copyright
Copyright © World's Poultry Science Association 2010

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References

ANDREESCU, C., AVENDANO, S., BROWN, S.R., HASSEN, A., LAMONT, S.J. and DEKKERS, J.C.M. (2007) Linkage Disequilibrium in Related Breeding Lines of Chickens. Genetics 177: 2161-2169.CrossRefGoogle ScholarPubMed
BAO, W.B., CHEN, G.H., WU, X.S., XU, Q., WU, S.L., SHU, J.T. and WEIGEND, S. (2007) Genetic diversity of red jungle fowl in China (Gallus gallus spadiceus) and red jungle fowl (Gallus gallus gallus) in Thailand. Hereditas (Beijing) 29: 587-92.CrossRefGoogle Scholar
BAO, W.B., CHEN, G.H., LI, B.C., WU, X.S., SHU, J.T., WU, S.L., XU, Q. and WEIGEND, S. (2008) Analysis of genetic diversity and phylogenetic relationships among red jungle fowls and Chinese domestic fowls. Science in China Series C-Life Sciences 51: 560-568.CrossRefGoogle ScholarPubMed
BEN-AVRAHAM, D., BLUM, S., GRANEVITZE, Z., WEIGEND, S., CHENG, H. and HILLEL, J. (2006) W-specific microsatellite loci detected by in silico analysis map to chromosome Z of the chicken genome. Animal Genetics 37: 179-188.CrossRefGoogle Scholar
BERLIN, S. and ELLEGREN, H. (2004) Chicken W: a genetically uniform chromosome in a highly variable genome. Proceedings of National Academy of Sciences USA 101: 15967-15969.CrossRefGoogle Scholar
BERTHOULY, C., BED'HOM, B., TIXIER-BOICHARD, M., CHEN, C.F., LEE, Y.P., LALOE, D., LEGROS, H., VERRIER, E. and ROGNON, X. (2008) Using molecular markers and multivariate methods to study the genetic diversity of local European and Asian chicken breeds. Animal Genetics 39: 121-129.CrossRefGoogle Scholar
BODZSAR, N., EDING, H., REVAY, T., HIDAS, A. and WEIGEND, S. (2009) Genetic diversity of Hungarian indigenous chicken breeds based on microsatellite markers. Animal Genetics 40: 516-523.CrossRefGoogle ScholarPubMed
BRANDSTRÖM, M. and ELLEGREN, H. (2008) Genome-wide analysis of microsatellite polymorphism in chicken circumventing the ascertainment bias. Genome Research 18: 881-887.CrossRefGoogle ScholarPubMed
BURT, D.W. (2006) Chicken genome: Current status and future opportunities. Genome Research 15: 1692-1698.CrossRefGoogle Scholar
CRAWFORD, R.D. (1990) Origin and history of poultry species, in: CRAWFORD, R.D. (Ed.) Poultry Breeding and Genetics, pp. 317-329 (New York, Elsevier).Google Scholar
DOWNING, T., O'FARRELLY, C., BHUIYAN, A.K., SILVA, P., NAQVI, A.N., SANFO, R., SOW, R.-S., PODISI, B., HANOTTE, O. and BRADLEY, D.G. (2010) Variation in chicken populations may affect the enzymatic activity of lysozyme. Animal Genetics 41: 213-217.CrossRefGoogle Scholar
ELLEGREN, H. (2005) The avian genome uncovered. Trends in ecology and evolution 20: 180-186.CrossRefGoogle ScholarPubMed
ERIKSSON, J., LARSON, G., GUNNARSSON, U., BED´HOM, B., TIXIER-BOICHARD, M., STRÖMSTEDT, L., WRIGHT, D., JUNGERIUS, A., VEREIJKEN, A., RANDI, E., JENSEN, P. and ANDERSSON, L. (2008) Identification of the Yellow Skin Gene Reveals a Hybrid Origin of the Domestic Chicken. Public Library of Science Genetics 4: e1000010.Google ScholarPubMed
FANG, L., YE, J., LI, N., ZHANG, Y., LI, S.G., GANE, K-S.W. and WANG, J. (2008) Positive correlation between recombination rate and nucleotide diversity is shown under domestication selection in the chicken genome. Chinese Science Bulletin 53: 746-750.CrossRefGoogle Scholar
FUMIHITO, A., MIYAKE, T., SUMI, S., TAKADA, M., OHNO, S. and KONDO, N. (1994) One subspecies of the red jungle-fowl (G.g. gallus) suffices as the matriarchic ancestor of all domestic breeds. Proceedings of National Academy of Sciences USA 91: 12505-12509.CrossRefGoogle ScholarPubMed
GAO, Y.S., YANG, N., LI, H.F., WANG, K.H. and TONG, H.B. (2004) Analysis of genetic diversity of preserved population of native chicken breeds by microsatellites and file foundation of markers. Hereditas (Beijing) 26: 859-864.Google ScholarPubMed
GONGORA, J., RAWLENCE, N.J., MOBEGI, V.A, JIANLIN, H., ALCALDE, J.A., MATUS, J.T., HANOTTE, O., MORAN, C., AUSTIN, J.J., ULM, S., ANDERSON, A.J., LARSON, G. and COOPER, A. (2008) Indo-European and Asian origins for Chilean and Pacific chickens revealed by mtDNA Indo-European and Asian origins for Chilean and Pacific chickens revealed by mtDNA. Proceedings of National Academy of Sciences USA 105: 10308-10313.CrossRefGoogle Scholar
GRANEVITZE, Z., HILLEL, J., CHEN, G.H., CUC, N.T.K., FELDMAN, M., EDING, H. and WEIGEND, S. (2007) Genetic diversity within chicken populations from different continents and management histories. Animal Genetics 38: 576-583.CrossRefGoogle ScholarPubMed
GRANEVITZE, Z., HILLEL, J., FELDMAN, M., SIX, A., EDING, H. and WEIGEND, S. (2009) Genetic structure of a wide-spectrum chicken gene pool. Animal Genetics 40: 686-693.CrossRefGoogle ScholarPubMed
HILLEL, J., GROENEN, M.A., TIXIER-BIOCHARD, M., KOROLD, B., DAVID, L., KIRZHNER, M.V., BURKE, T., BARRE-DIRIEF, A., CROOIJMANS, M.A., ELO, K., FELDMAN, M.W., FREIDLIN, P.J., MÄKI-TANILA, A., OORTWIJN, M., THOMSON, P., VIGNAL, A., WIMMERS, K. and WEIGEND, S. (2003) Biodiversity of 52 chicken populations assessed by microsatellite typing of DNA pools. Genetics Selection Evolution 35: 533-557.CrossRefGoogle ScholarPubMed
HILLEL, J., GRANEVITZE, Z., TWITO, T., BEN-AVRAHAM, D., BLUM, S., LAVI, U., DAVID, L., FELDMAN, M.W., CHENG, H. and WEIGEND, S. (2007) Molecular markers for the assessment of chicken biodiversity. World's Poultry Science Journal 63: 33-45.CrossRefGoogle Scholar
HOFFMANN, I. (2009) The global plan of action for animal genetic resources and the conservation of poultry genetic resources. World's Poultry Science Journal 65: 286-297.CrossRefGoogle Scholar
INTERNATIONAL CHICKEN GENOME SEQUENCING CONSORTIUM, (2004) Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature 432: 695-716.CrossRefGoogle Scholar
INTERNATIONAL CHICKEN POLYMORPHISM MAP CONSORTIUM, (2004) A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms. Nature 432: 717-722.CrossRefGoogle Scholar
KAYA, M. and YILDIZ, M.A. (2008) Genetic diversity among Turkish native chickens, Denizli and Gerze, estimated by microsatellite markers. Biochemical Genetics 46: 480-491.CrossRefGoogle ScholarPubMed
LIU, Y.P., WU, G.S., YAO, Y.G., MIAO, Y.W., LUIKART, G., BAIG, M., BEJA-PEREIRA, A., DING, Z.L., PALANICHAMY, M.G. and ZHANG, Y.P. (2006a) Multiple maternal origins of chickens: Out of the Asian jungles. Molecular Phylogenettics and Evolution 38: 12-19.CrossRefGoogle ScholarPubMed
LIU, Y.P., ZHU, Q. and YAO, Y.G. (2006b) Genetic relationship of Chinese and Japanese gamecocks revealed by mtDNA sequence variation. Biochemical Genetics 44: 19-29.CrossRefGoogle ScholarPubMed
MARLE-KÖSTER, E., HEFER, C.A., NEL, L.H. and GROENEN, M.A.M. (2008) Genetic diversity and population structure of locally adapted South African chicken lines: Implications for conservation. South African Journal of Animal Science 38: 271-281.Google Scholar
MOISEYEVA, I.G., YUGUO, Z., NIKIFOROV, A.A. and ZAKHAROV, I.A. (1996) Comparative analysis of morphological traits in Mediterranean and Chinese chicken breeds: the problem of the origin of the domestic chicken. Russian Journal of Genetics 32: 1553-1561.Google Scholar
MOISEYEVA, I.G., ROMANOV, M.N., NIKIFOROV, A.A., SEVASTYANOVA, A.A. and SEMYENOVA, S.K. (2003) Evolutionary relationships of red jungle fowl and chicken breeds. Genetics Selection Evolution 35: 403-423.CrossRefGoogle ScholarPubMed
MUCHADEYI, F.C., EDING, H., WOLLNY, C.B.A., GROENEVELD, S.M., SHAMSELDIN, R., SIMIANER, H. and WEIGEND, S. (2007) Absence of population substructuring in Zimbabwe chicken ecotypes inferred using microsatellite analysis. Animal Genetics 38: 332-339.CrossRefGoogle ScholarPubMed
MUCHADEYI, F.C., EDING, H., SIMIANER, H., WOLLNY, C.B., GROENEVELD, E. and WEIGEND, S. (2008) Mitochondrial DNA D-loop sequences suggest a Southeast Asian and Indian origin of Zimbabwean village chickens. Animal Genetics 39: 615-622.CrossRefGoogle ScholarPubMed
MUIR, W.M., WONG, G.K., ZHANG, Y., WANG, J., GROENEN, M.A.M., CROOIJMANS, R.P.M.A., MEGENS, H., ZHANG, H., OKIMOTO, R., VEREIJKEN, A., JUNGERIUS, A., ALBERS, G.A.A., LAWLEY, C.T., DELANY, M.E., MACEACHERN, S. and CHENG, H.H. (2008) Genome-wide assessment of worldwide chicken SNP genetic diversity indicates significant absence of rare alleles in commercial breeds. Proceedings of National Academy of Sciences USA 105: 17312-17317.CrossRefGoogle Scholar
MWACHARO, J.M., NOMURA, K., HANADA, H., JIANLI, H., HANOTTE, O. AND AMANO and T., (2007) Genetic relationships among Kenyan and other East African indigenous chickens. Animal Genetics 38: 485-490.CrossRefGoogle ScholarPubMed
NISHIBORI, M., SHIMOGIRI, T., HAYASHI, T. and YASUE, H. (2005) Molecular evidence for hybridization of species in the genus Gallus except for Gallus varius. Animal Genetics 36: 367-375.CrossRefGoogle ScholarPubMed
NIU, D., FU, Y., LUO, J., RUAN, H., YU, X.P., CHEN, G. and ZHANG, Y.P. (2002) The Origin and Genetic Diversity of Chinese Native Chicken Breeds. Biochemical Genetics 40: 163-174.CrossRefGoogle ScholarPubMed
OKA, T., INO, Y., NOMURA, K., KAWASHIMA, S., KUWAYAMA, T., HANADA, H., AMANO, T., TAKADA, M., TAKAHATA, N., HAYASHI, Y. and AKISHINONOMIYA, F. (2007) Analysis of mtDNA sequences shows Japanese native chickens have multiple origins. Animal Genetics 38: 287-293.CrossRefGoogle ScholarPubMed
PIRANY, N., ROMANOV, M.N., GANPULE, S.P., DEWAGOWDA, G. and PRASAD, D.T. (2007) Microsatellite analysis of genetic diversity in Indian chicken populations. Journal of Poultry Science 44: 19-28.CrossRefGoogle Scholar
PONSUKSILI, S., WIMMERS, K. and HORST, P. (1996) Genetic variability in chickens using polymorphic microsatellite makers. Thailand Journal of Agricultural Science 29: 571-580.Google Scholar
PRIMMER, C.R., RAUDSEPP, T., CHOWDHARY, B.P., MØLLER, A.P. and ELLEGREN, H. (1997) Low frequency of microsatellites in the avian genome. Genome Research 7: 471-482.CrossRefGoogle ScholarPubMed
ROSENBERG, N.A., BURKE, T., ELO, K., FELDMAN, M.W., FREIDLIN, P.J. and GROENEN, M.A.M. (2001) Empirical evaluation of genetic clustering methods using multilocus genotypes from 20 chicken breeds. Genetics 159: 699-713.CrossRefGoogle ScholarPubMed
RUBIN, C., ZODY, M.C., ERIKSSON, J., MEADOWS, J.R.S., SHERWOOD, E., WEBSTER, M.T., JIANG, L., INGMAN, M., SHARPE, , T, , KA, S., HALLBÖÖK, F., BESNIER, F., CARLBORG, , Ö., , BED`HOM, B., TIXIER-BOICHARD, M., JENSEN, P., SIEGEL, , P, KERSTIN LINDBLAD-TOH and K. AND ANDERSSON, L. (2010) Whole-genome resequencing reveals loci under selection during chicken domestication. Nature 464: 587-591.CrossRefGoogle ScholarPubMed
SHAHBAZI, S., MIRHOSSEINI, S.Z. and ROMANOV, M.N. (2007) Genetic diversity in five Iranian chicken populations estimated by microsatellite markers. Biochemical Genetics 45: 63-75.CrossRefGoogle ScholarPubMed
SILVA, P., GUAN, X., HO-SHING, O., JONES, J., XU, J., HUI, D., NOTTER, D. and SMITH, E. (2009) Mitochondrial DNA-based analysis of genetic variation and relatedness among Sri Lankan indigenous chickens and the Ceylon junglefowl (Gallus lafayetti). Animal Genetics 40: 1-9.CrossRefGoogle ScholarPubMed
SUNDSTRÖM, H., WEBSTER, M.T. and ELLEGREN, H. (2004) Reduced variation on chicken Z chromosome. Genetics 167: 377-385.CrossRefGoogle ScholarPubMed
TADANO, R., NISHIBORI, M., NAGASAKA, N. and TSUDZUKI, M. (2007a) Assessing Genetic Diversity and Population Structure for Commercial Chicken Lines Based on Forty Microsatellite Analyses. Poultry Science 86: 2301-2308.CrossRefGoogle ScholarPubMed
TADANO, R., SEKINO, M., NISHIBORI, M. and TSUDZUKI, M. (2007b) Microsatellite marker analysis for the genetic relationships among Japanese long-tailed chicken breeds. Poultry Science 86: 460-469.CrossRefGoogle ScholarPubMed
TADANO, R., NISHIBORI, M., IMAMURA, Y., MATSUZAKI, M., KINOSHITA, K., MIZUTANI, M., NAMIKAWA, T. and TSUDZUKI, M. (2008) High genetic divergence in miniature breeds of Japanese native chickens compared to Red Jungle fowl, as revealed by microsatellite analysis. Animal Genetics 39: 71-78.CrossRefGoogle ScholarPubMed
TWITO, T., WEIGEND, S., BLUM, S., GRANEVITZE, Z., FELDMAN, M.W., PERL-TREVES, R., LAVI, U. and HILLEL, J. (2007) Biodiversity of 20 chicken breeds assessed by SNPs located in gene regions. Cytogenetic and Genome Research 117: 319-326.CrossRefGoogle ScholarPubMed
VANHALA, T., TUISKULA-HAAVISTO, M., ELO, K., VILKKI, J. and MAKI-TANILA, A. (1998) Evaluation of genetic variability and genetic distances between eight chicken lines using microsatellite markers. Poultry Science 77: 783-790.CrossRefGoogle ScholarPubMed
WALTARI, E. and EDWARDS, S.V. (2002) Evolutionary dynamics of intron size, genome size, and physiological correlates in archosaurs. The American Naturalist 160: 539-552.CrossRefGoogle ScholarPubMed
WEST, B. and ZHOU, B-X. (1989) Did chickens go north? New evidence for domestication. World's Poultry Science Journal 45: 205-218.CrossRefGoogle Scholar
WIMMERS, K., PONSUKSILI, S., HARDGE, T., VALLE-ZARATE, A., MATHUR, P.K. and HORST, P. (2000) Genetic distinctness of African, Asian and South American local Chickens. Animal Genetics 31: 159-165.CrossRefGoogle ScholarPubMed