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Linkage disequilibrium in the estimation of genetic and demographic parameters of extensively raised chicken populations

Published online by Cambridge University Press:  04 September 2015

K.S. KHANYILE ,
E.F. DZOMBA  and
F.C. MUCHADEYI
K.S. KHANYILE
Affiliation:
Biotechnology Platform, Agricultural Research Council, Onderstepoort, South Africa Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Pietermaritzburg, South Africa
E.F. DZOMBA
Affiliation:
Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Pietermaritzburg, South Africa
F.C. MUCHADEYI*
Affiliation:
Biotechnology Platform, Agricultural Research Council, Onderstepoort, South Africa
*
Corresponding author: [email protected]
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Abstract

Smallholder farmers in Africa and other developing countries raise village chickens under low input production systems characterised by minimal management and veterinary interventions. However, village chickens have a major contribution to village communities as a source of protein, income and cultural needs. The village chickens are described as nondescript birds that have not been developed as a breed and with uncharacterised genetic attributes. Local chickens are found in the most marginalised farming systems, to which they have adapted and survived the harsh production and environmental conditions. Such survival and adaptive attributes need to be characterised, conserved, and utilised. Several studies on Southern African local chickens have revealed high genetic variation within and among the village chicken populations and indicated that village chickens contribute diversity that is unique and different from that of commercial and specialised chicken populations. The availability of whole genome single nucleotide polymorphism (SNP) data facilitates the use of powerful statistical methods for in depth investigations into the evolutionary history and population demographics of village chickens. Linkage disequilibrium (LD), as a function of effective population size, has been used to estimate rate and level of inbreeding as well as selection pressures in the absence of pedigree information. The extent and distribution of LD in the genome has been exploited to shed light on the origin and domestication of animals and facilitate an understanding of breeds’ relatedness. The Illumina iSelect chicken 60K SNP chip has over 54 000 SNPs that have found application in population and quantitative genetics studies and has revealed demographic history, effective population size and level of genetic erosion in commercial and traditional/village chicken populations. The recent launching of the 600 K Affymetrix® Axiom® HD genotyping array for chickens and the ever decreasing cost of sequencing will see improved estimation of LD and the associated population parameters.

Keywords

Linkage disequilibriumSNPsgenetic diversitydemographic parameterschickens
Type
Reviews
Information
World's Poultry Science Journal , Volume 71 , Issue 3 , September 2015 , pp. 505 - 514
Copyright
Copyright © World's Poultry Science Association 2015 

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References

ABDELQADER, A., WOLLNY, C.B.A. and GAULY, M. (2007) Characterization of local chicken production systems and their potential under different levels of management practice in Jordan. Tropical Animal Health and Production 39: 155-164.CrossRefGoogle ScholarPubMed
ABUBAKAR, M., AMBALI, A. and TAMJDO, T. (2007) Rural chicken production: Constraints limiting rural chicken production in some areas of Nigeria and Cameroon. Family Poultry 17: 57-62.Google Scholar
ADOMAKO, K., OLYMPIO, O., HAGAN, J. and HAMIDU, J. (2014) Growth performance of crossbred naked neck and normal feathered birds. British Poultry Science 55: 701-708.CrossRefGoogle Scholar
AJAYI, F., AGAVIEZOR, B. and WIHIOKA, S. (2013) Haemoglobin genotypes in the Nigerian indigenous chicken in the Niger Delta region of Nigeria. International Journal of Advanced Biological Research 3: 13-16.Google Scholar
AMARAL, A.J., MEGENS, H.-J., CROOIJMANS, R.P., HEUVEN, H.C. and GROENEN, M.A. (2008) Linkage disequilibrium decay and haplotype block structure in the pig. Genetics 179: 569-579.CrossRefGoogle ScholarPubMed
ANDREESCU, C., AVENDANO, S., BROWN, S.R., HASSEN, A., LAMONT, S.J. and DEKKERS, J.C. (2007) Linkage disequilibrium in related breeding lines of chickens. Genetics 177: 2161-2169.CrossRefGoogle ScholarPubMed
ARDLIE, K.G., KRUGLYAK, L. and SEIELSTAD, M. (2002) Patterns of linkage disequilibrium in the human genome. Nature Reviews Genetics 3: 299-309.CrossRefGoogle ScholarPubMed
BESBES, B. (2009) Genotype evaluation and breeding of poultry for performance under sub-optimal village conditions. World's Poultry Science Journal 65: 260-271.CrossRefGoogle Scholar
CORBIN, L.J., BLOTT, S.C., SWINBURNE, J.E., VAUDIN, M., BISHOP, S.C. and WOOLLIAMS, J.A. (2010) Linkage disequilibrium and historical effective population size in the Thoroughbred horse. Animal Genetics 41: 8-15.CrossRefGoogle ScholarPubMed
CUC, N.T.K., MUCHADEYI, F., BAULAIN, U., EDING, H., WEIGEND, S. and WOLLNY, C. (2006) An assessment of genetic diversity of Vietnamese H`mong chickens. International Journal of Poultry Science 5: 912-920.Google Scholar
EGAHI, J., DIM, N. and MOMOH, O. (2013) Embryonic and post hatch mortality in three genetic groups of the Nigerian local chicken in the Guinea Savanna. Research Journal of Agricultural and Environmental Management 2: 75-77.Google Scholar
EKUE, F.N, PONÉ, K.D., MAFENI, M.J., NFI, A.N. and NJOYA, J. (2002) Survey of the traditional poultry production system in the Bamenda area, Cameroon, In: Characteristics and Parameters of Family Poultry Production in Africa, pp. 15-25 (FAO/IAEA, Vienna).Google Scholar
EKUE, F., PONE, D., NFI, J.M.A. and NJOYA, J. (2006) The effect of vaccination against newcastle disease and feed supplementation on production in village chicken in Bamenda area of Cameroon. Proceedings of the Improving farmyard poultry production in Africa: interventions and their economic assessment: proceedings of a final research coordination meeting, pp. 51-59.Google Scholar
FALCONER, D.S. and MACKAY, T.F.C. (1996) Quantitative Genetics (Harlow, UK).Google Scholar
FAO (1995) Global project for the maintenance of domestic animal genetic diversity (modad), Available at: http://agtr.ilri.cgiar.org/agtrweb/documents/Library/docs/agri34_project.pdf (accessed July 2012).Google Scholar
FAO/IAEA (2002) Characteristics and parameters of family poultry and production in Africa. (IAEA, Austria).Google Scholar
GONDWE, T.N.P. (2004) Characterisation of local chicken in low input–low output production systems: Is there scope for appropriate production and breeding strategies in Malawi? PhD thesis, Georg-August-Universität, Göttingen, Germany.Google Scholar
GRANEVITZE, Z., HILLEL, J., CHEN, G., CUC, N., 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
GROENEN, M., MEGENS, H.-J., ZARE, Y., WARREN, W., HILLIER, L., CROOIJMANS, R., VEREIJKEN, A., OKIMOTO, R., MUIR, W. and CHENG, H. (2011) The development and characterization of a 60K SNP chip for chicken. BMC Genomics 12: 274. Doi:10.1186/1471-2164-12-274.CrossRefGoogle ScholarPubMed
HALL, S.J. and BRADLEY, D.G. (1995) Conserving livestock breed biodiversity. Trends in Ecology and Evolution 10: 267-270.CrossRefGoogle ScholarPubMed
HASSEN, H., NESER, F., DE KOCK, A. and VAN MARLE-KÖSTER, E. (2009) Study on the genetic diversity of native chickens in northwest Ethiopia using microsatellite markers. African Journal of Biotechnology 8: 1347-1353.Google Scholar
HAYES, B. (2013) 1000 bull genome project, Available at: http://www.1000bullgenomes.com/ (Accessed September 2014).Google Scholar
HAYES, B.J., VISSCHER, P.M., MCPARTLAN, H.C. and GODDARD, M.E. (2003) Novel multilocus measure of linkage disequilibrium to estimate past effective population size. Genome Research 13: 635-643.CrossRefGoogle ScholarPubMed
HEDRICK, P.W. (2004) Genetics of Populations (Jones and Bartlett, Canada).Google Scholar
HEIFETZ, E.M., FULTON, J.E., O'SULLIVAN, N., ZHAO, H., DEKKERS, J.C. and SOLLER, M. (2005) Extent and consistency across generations of linkage disequilibrium in commercial layer chicken breeding populations. Genetics 171: 1173-1181.CrossRefGoogle ScholarPubMed
HILLIER, L.W., MILLER, W., BIRNEY, E., WARREN, W., HARDISON, R.C., PONTING, C.P., BORK, P., BURT, D.W., GROENEN, M.A. and DELANY, M.E. (2004) Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature 432: 695-716.Google Scholar
ILLANGO, J., ETOORI, A., OLUPOT, H. and MABONGA, J. (2002) Rural poultry production in two agro-ecological zone of Uganda, in: Characteristics and Parameters of Family Poultry Production in Africa. pp. 117-121 (FAO/IAEA, Vienna).Google Scholar
KELLER, L.F. and WALLER, D.M. (2002) Inbreeding effects in wild populations. Trends in Ecology and Evolution 17: 230-241.CrossRefGoogle Scholar
KHANYILE, K., DZOMBA, E.F. and MUCHADEYI, F.C. (2015) The Extent and Distribution of Linkage Disequilibrium in Extensively Raised Chicken Populations of Southern Africa. Frontiers in Genetics 6: Doi: 10.3389/fgene.2015.00013.CrossRefGoogle Scholar
KRANIS, A., GHEYAS, A.A., BOSCHIERO, C., TURNER, F., YU, L., SMITH, S., TALBOT, R., PIRANI, A., BREW, F. and KAISER, P. (2013) Development of a high density 600K SNP genotyping array for chicken. BMC Genomics 14: 59. Doi:10.1186/1471-2164-14-59.CrossRefGoogle ScholarPubMed
LEE, S., CHO, Y., LIM, D., KIM, H., CHOI, B., PARK, H., KIM, O., KIM, S., KIM, T. and YOON, D. (2011) Linkage disequilibrium and effective population size in Hanwoo Korean cattle. Asian-Australasian Journal of Animal Sciences 24: 1660-1665.CrossRefGoogle Scholar
LI, M.H. and MERILÄ, J. (2009) Extensive linkage disequilibrium in a wild bird population. Heredity 104: 600-610.CrossRefGoogle Scholar
LU, D., SARGOLZAEI, M., KELLY, M., CHANGXI, L., VANDER VOORT, G., WANG, Z., PLASTOW, G., MOORE, S. and MILLER, S.P. (2012) Linkage disequilibrium in Angus, Charolais, and Crossbred beef cattle. Frontiers in Genetics 3: 10. Doi:10.3389/fgene.2012.00152.CrossRefGoogle ScholarPubMed
MAGOTHE, T. and KAHI, A. (2011) Indigenous chicken improvement in Kenya: Past efforts and future prospects, in: MBUKU, S.M. (Ed.) Driving Livestock Enterprenuership Towards Attainment of Food Sufficiency and Kenya Vision 2030, pp. 15-18 (Animal Production Society of Kenya, Nairobi, Kenya).Google Scholar
MAPIYE, C., MWALE, M., MUPANGWA, J., CHIMONYO, M., FOTI, R. and MUTENJE, M. (2008) A research review of village chicken production constraints and opportunities in Zimbabwe. Asian-Australasian Journal of Animal Science 21: 1680-1688.CrossRefGoogle Scholar
MCEVOY, B.P., POWELL, J.E., GODDARD, M.E. and VISSCHER, P.M. (2011) Human population dispersal “Out of Africa” estimated from linkage disequilibrium and allele frequencies of SNPs. Genome Research 21: 821-829.CrossRefGoogle ScholarPubMed
MEADOWS, J.R., CHAN, E.K. and KIJAS, J.W. (2008) Linkage disequilibrium compared between five populations of domestic sheep. BMC Genetics 9: 61. Doi:10.1186/1471-2156-9-61.CrossRefGoogle ScholarPubMed
MOGES, F., MELLESSE, A. and DESSIE, T. (2010) Assessment of village chicken production system and evaluation of the productive and reproductive performance of local chicken ecotype in Bure district, North West Ethiopia. African Journal of Agricultural Research 5: 1739-1748.Google Scholar
MSOFFE, P.L.M., MTAMBO, M.M.A., MINGA, U.M., OLSEN, J.E., JUUL-MADSEN, H.R., GWAKISA, P.S., MUTAYOBA, S.K. and KATULE, A.M. (2004) Productivity and reproductive performance of the free range local domestic fowl ecotypes in Tanzania. Livestock Research for Rural Development 16: Retrieved February 10 2015, from http://www.cipav.org.co/lrrd/lrrd16/9/msof16067.htm.Google Scholar
MTILENI, B., MUCHADEYI, F., MAIWASHE, A., PHITSANE, P., HALIMANI, T., CHIMONYO, M. and DZAMA, K. (2009) Characterisation of production systems for indigenous chicken genetic resources of South Africa. Applied Animal Husbandry and Rural Development 2: 18-22.Google Scholar
MTILENI, B., MUCHADEYI, F., MAIWASHE, A., CHIMONYO, M., GROENEVELD, E., WEIGEND, S. and DZAMA, K. (2011a) Diversity and origin of South African chickens. Poultry science 90: 2189-2194.CrossRefGoogle ScholarPubMed
MTILENI, B., MUCHADEYI, F., MAIWASHE, A., GROENEVELD, E., GROENEVELD, L., DZAMA, K. and WEIGEND, S. (2011b) Genetic diversity and conservation of South African indigenous chicken populations. Journal of Animal Breeding and Genetics 128: 209-218.CrossRefGoogle ScholarPubMed
MUCHADEYI, F., EDING, H., WOLLNY, C., GROENEVELD, E., MAKUZA, S., SHAMSELDIN, R., SIMIANER, H. and WEIGEND, S. (2007) Absence of population substructuring in Zimbabwe chicken ecotypes inferred using microsatellite analysis. AnimalGenetics 38: 332-339.Google ScholarPubMed
MUCHADEYI, F., EDING, H., SIMIANER, H., WOLLNY, C., 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
MUCHADEYI, F., WOLLNY, C., EDING, H., WEIGEND, S. and SIMIANER, H. (2009) Choice of breeding stock, preference of production traits and culling criteria of village chickens among Zimbabwe agro-ecological zones. Tropical Animal Health and Production 41: 403-412.CrossRefGoogle ScholarPubMed
MWACHARO, J., BJØRNSTAD, G., MOBEGI, V., NOMURA, K., HANADA, H., AMANO, T., JIANLIN, H. and HANOTTE, O. (2011) Mitochondrial DNA reveals multiple introductions of domestic chicken in East Africa. Molecular Phylogenetics and Evolution 58: 374-382.CrossRefGoogle ScholarPubMed
MWALE, M., BHEBHE, E., CHIMONYO, M. and HALIMANI, T.E. (2005) Use of herbal plants in poultry health management in the Mushagashe small-scale commercial farming area in Zimbabwe. International Journal of Applied Research in Veterinary Medicine 3: 163-170.Google Scholar
OKE, U. (2011) Influence of some major genes on growth traits of local pullets in humid tropical environment. Agricultural Biology Journal of North America 2: 570-576.CrossRefGoogle Scholar
OLWANDE, P.O., OGARA, W.O., OKUTHE, S.O., MUCHEMI, G., OKOTH, E., ODINDO, M.O. and ADHIAMBO, R.F. (2010) Assessing the productivity of indigenous chickens in an extensive management system in southern Nyanza, Kenya. Tropical Animal Health and Production 42: 283-288.CrossRefGoogle Scholar
QANBARI, S., PIMENTEL, E., TETENS, J., THALLER, G., LICHTNER, P., SHARIFI, A. and SIMIANER, H. (2010a) A genome-wide scan for signatures of recent selection in Holstein cattle. Animal Genetics 41: 377-389.CrossRefGoogle ScholarPubMed
QANBARI, S., PIMENTEL, E., TETENS, J., THALLER, G., LICHTNER, P., SHARIFI, A. and SIMIANER, H. (2010b) The pattern of linkage disequilibrium in German Holstein cattle. Animal Genetics 41: 346-356.CrossRefGoogle ScholarPubMed
RAO, Y.S., LIANG, Y., NA XIA, M., SHEN, X., JUN DU, Y., GLONG LUO, C., HUA NIE, Q., ZENG, H. and QUAN ZHANG, X. (2008) Extent of linkage disequilibrium in wild and domestic chicken populations. Hereditas 145: 251-257.CrossRefGoogle ScholarPubMed
SARGOLZAEI, M., SCHENKEL, F., JANSEN, G. and SCHAEFFER, L. (2008) Extent of linkage disequilibrium in Holstein cattle in North America. Journal of Dairy Science 91: 2106-2117.CrossRefGoogle ScholarPubMed
SLATKIN, M. (2008) Linkage disequilibrium—understanding the evolutionary past and mapping the medical future. Nature Reviews Genetics 9: 477-485.CrossRefGoogle ScholarPubMed
TADELLE, D., ALEMU, Y. and PETERS, K.J. (2000) Indigenous chicken in Ethiopia: genetic potential and attempts at improvement. World's Poultry Science Journal 56: 45-54.CrossRefGoogle Scholar
TADELLE, D., MILLION, T., ALEMU, Y. and PETERS, K.J. (2003) . Village chicken production systems in Ethiopia: 1. Flock characteristics and performance. Livestock Research for Rural Development 15: Retrieved February 5, 2013, from http://www.lrrd.org/lrrd15/1/tadea151.htm.Google Scholar
TENESA, A., NAVARRO, P., HAYES, B.J., DUFFY, D.L., CLARKE, G.M., GODDARD, M.E. and VISSCHER, P.M. (2007) Recent human effective population size estimated from linkage disequilibrium. Genome Research 17: 520-526.CrossRefGoogle ScholarPubMed
UIMARI, P. and TAPIO, M. (2011) Extent of linkage disequilibrium and effective population size in Finnish Landrace and Finnish Yorkshire pig breeds. Journal of Animal Science 89: 609-614.CrossRefGoogle ScholarPubMed
WANG, J. (2005) Estimation of effective population sizes from data on genetic markers. Philosophical Transactions of the Royal Society B: Biological Sciences 360: 1395-1409.CrossRefGoogle ScholarPubMed
WAPLES, R.S. (1989) A generalised approach for estimating effective population size from temporal changes in allele frequency. Genetics 121: 379-391.CrossRefGoogle ScholarPubMed
WRAGG, D., MWACHARO, J., ALCALDE, J., HOCKING, P. and HANOTTE, O. (2012) Analysis of genome-wide structure, diversity and fine mapping of Mendelian traits in traditional and village chickens. Heredity 109: 6-18.CrossRefGoogle ScholarPubMed