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Genome-wide genetic diversity, population structure and admixture analysis in African and Asian cattle breeds

  • Z. Edea (a1) (a2), M. S. A. Bhuiyan (a3), T. Dessie (a2), M. F. Rothschild (a4), H. Dadi (a5) and K. S. Kim (a1)...

Abstract

Knowledge about genetic diversity and population structure is useful for designing effective strategies to improve the production, management and conservation of farm animal genetic resources. Here, we present a comprehensive genome-wide analysis of genetic diversity, population structure and admixture based on 244 animals sampled from 10 cattle populations in Asia and Africa and genotyped for 69 903 autosomal single-nucleotide polymorphisms (SNPs) mainly derived from the indicine breed. Principal component analysis, STRUCTURE and distance analysis from high-density SNP data clearly revealed that the largest genetic difference occurred between the two domestic lineages (taurine and indicine), whereas Ethiopian cattle populations represent a mosaic of the humped zebu and taurine. Estimation of the genetic influence of zebu and taurine revealed that Ethiopian cattle were characterized by considerable levels of introgression from South Asian zebu, whereas Bangladeshi populations shared very low taurine ancestry. The relationships among Ethiopian cattle populations reflect their history of origin and admixture rather than phenotype-based distinctions. The high within-individual genetic variability observed in Ethiopian cattle represents an untapped opportunity for adaptation to changing environments and for implementation of within-breed genetic improvement schemes. Our results provide a basis for future applications of genome-wide SNP data to exploit the unique genetic makeup of indigenous cattle breeds and to facilitate their improvement and conservation.

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Bhuiyan, MS, Bhuiyan, AK, Yoon, DH, Jeon, JT, Park, CS and Lee, JH 2007. Mitochondrial DNA diversity and origin of Red Chittagong cattle. Asian-Australasian Journal of Animal Sciences 20, 14781484.
Bradley, DG, MacHugh, DE, Cunningham, P and Loftus, RT 1996. Mitochondrial diversity and the origins of African and European cattle. Proceedings of the National Academy of Sciences of the United States of America 93, 51315135.
Brumfield, RT, Beerli, P, Nickerson, DA and Edwards, SV 2003. The utility of single nucleotide polymorphisms in inferences of population history. Trend in Ecology & Evolution 18, 249256.
Chen, S, Lin, BZ, Baig, M, Mitra, B, Lopes, RJ, Santos, AM, Magee, DA, Azevedo, M, Tarroso, P, Sasazaki, S, Ostrowski, S, Mahgoub, O, Chaudhuri, TK, Zhang, Y, Costa, V, Royo, LJ, Goyache, F, Luikart, G, Boivin, N, Fulle, DQ, Mannen, H, Bradley, DG and Beja-Pereira, A 2010. Zebu cattle are an exclusive legacy of the South Asia neolithic. Molecular Biology and Evolution 27, 16.
Dadi, H, Tibbo, M, Takahashi, Y, Nomura, K, Hanada, H and Amano, T 2008. Microsatellite analysis reveals high genetic diversity but low genetic structure in Ethiopian indigenous cattle populations. Animal Genetics 39, 425431.
Dadi, H, Tibbo, M, Takahashi, Y, Nomura, K, Hanada, H and Amano, T 2009. Variation in mitochondrial DNA and maternal genetic ancestry of Ethiopian cattle populations. Animal Genetics 40, 556559.
DAGRIS 2007. Domestic Animal Genetic Resources Information System (DAGRIS) (ed. S Kemp, Y Mamo, B Asrat and T Dessie). International Livestock Research Institute, Addis Ababa, Ethiopia. http://dagris.ilri.cgiar.org
Decker, JE, McKay, SD, Rolf, MM, Kim, JW, Alcalá, AM, Sonstegard, TS, Hanotte, O, Götherström, A, Seabury, CM, Praharani, L, Babar, ME, Regitano, LC, Yildiz, MA, Heaton, PM, Liu, WS, Lei, CZ, Reecy, JM, Saif-Ur-Rehman, M, Schnabel, RD and Taylor, JF 2014. Worldwide patterns of ancestry, divergence, and admixture in domesticated cattle. PLoS Genetics 10, e1004254.
Edea, Z, Dadi, H, Kim, SW, Park, JH, Shin, GH, Dessie, T and Kim, KS 2014. Linkage disequilibrium and genomic scan to detect selective loci in cattle populations adapted to different ecological conditions in Ethiopia. Journal of Animal Breeding and Genetics 131 (5), 358366.
Edea, Z, Dadi, H, Kim, SW, Dessie, T, Lee, T, Kim, H, Kim, JJ and Kim, KS 2013. Genetic diversity, population structure and relationships in indigenous cattle populations of Ethiopia and Korean Hanwoo breeds using SNP markers. Frontiers in Genetics 4, 35.
Epstein, H 1957. The sanga cattle of East Africa. East African Agricultural Journal 22, 149164.
Epstein, H 1971. The origin of the domestic animals of Africa. 1. Cattle. Africana Publishing Corporation, New York, USA. 573pp.
Excoffier, L, Laval, G and Schneider, S 2005. Arlequin (version 3.0): an integrated software package for population genetics data analysis. Evolutionary Bioinformatics online 1, 4750.
Freeman, AR, Meghen, CM, MacHugh, DE, Loftus, RT, Achukwi, MD, Bado, A, Sauveroche, B and Bradley, DG 2004. Admixture and diversity in West African cattle populations. Molecular Ecology 13, 34773487.
Gautier, M, Laloe, D and Moazami-Goudarzi, K 2010. Insights into the genetic history of French cattle from dense SNP data on 47 worldwide breeds. PLoS One 5, e13038.
Gautier, M, Faraut, T, Moazami-Goudarzi, K, Navratil, V, Foglio, M, Grohs, C, Boland, A, Garnie, JG, Boichard, D, Lathrop, GM, Gut, IG and Eggen, A 2007. Genetic and haplotypic structure in 14 European and African cattle breeds. Genetics 177, 10591070.
Gifford-Gonzalez, D and Hanotte, O 2011. Domesticating animals in Africa: implications of genetic and archaeological findings. Journal of World Prehistory 24, 123.
Golden Helix and Variation Suite Version 7. Retrieved August 20, 2014, from http://www. goldenhelix.com
Grigson, C 1991. An African origin for African cattle? some archaeological evidence. African Archaeological Review 9, 119144.
Groeneveld, LF, Lenstra, JA, Eding, H, Toro, MA, Scherf, B, Pilling, D, Negrini, R, Finlay, EK, Jianlin, H, Groeneveld, E and Weigend, S, The GLOBALDIV Consortium 2010. Genetic diversity in farm animals – a review. Animal Genetics 41, 631.
Hanotte, O, Dessie, T and Kemp, S 2010. Time to tap Africa’s livestock genomics. Science 328, 16401641.
Hanotte, O, Bradley, DG, Ochieng, JW, Verjee, Y, Hill, EW and Rege, JE 2002. African pastoralism: genetic imprints of origins and migrations. Science 296, 336339.
Hanotte, O, Tawah, CL, Bradley, DG, Okomo, M, Verjee, Y, Ochieng, J and Rege, JEO 2000. Geographic distribution and frequency of a taurine Bos taurus and an indicine Bos indicus Y specific allele amongst sub-Saharan African cattle breeds. Molecular Ecology 9, 387396.
Herráez, DL, Bauchet, M, Tang, K, Theunert, C, Pugach, I, Li, J, Nandineni, MR, Gross, A, Scholz, M and Stoneking, M 2009. Genetic variation and recent positive selection in worldwide human populations: evidence from nearly 1 million SNPs. PLoS One 4, e7888.
Ibeagha-Awemu, EM and Erhardt, G 2005. Genetic structure and differentiation of 12 African Bos indicus and Bos taurus cattle breeds, inferred from protein and microsatellite polymorphisms. Journal of Animal Breeding and Genetics 122, 1220.
Kijas, JW, Lenstra, JA, Hayes, B, Boitard, S, Porto Neto, LR, Cristobal, MS, Servin, B, McCulloch, R, Whan, V, Gietzen, K, Paiva, S, Barendse, W, Ciani, E, Raadsma, H, McEwan, J and Dalrymple, B, International Sheep Genomics Consortium 2012. Genome-wide analysis of the world’s sheep breeds reveals high levels of historic mixture and strong recent selection. PLoS Biology 10, e1001258.
Lachance, J and Tishkoff, SA 2013. SNP ascertainment bias in population genetic analyses: Why it is important, and how to correct it. Bioessays 35, 780786.
Lawson, DJ, Hellenthal, G, Myers, S and Falush, D 2012. Inference of population sructure using dense haplotype data. PLoS Genetics 8, e1002453.
Li, MH, Zerabruk, M, Vangen, O, Olsaker, I and Kantanen, J 2007. Reduced genetic structure of north Ethiopian cattle revealed by Y-chromosome analysis. Heredity 98, 214221.
Liu, K and Muse, SV 2005. PowerMarker: integrated analysis environment for genetic marker data. Bioinformatics 21, 21282129.
Loftus, RT, MacHugh, DE, Bradley, DG, Sharp, PM and Cunningham, P 1994. Evidence for two independent domestications of cattle. Proceedings of the National Academy of Sciences of the United States of America 91, 27572761.
Loftus, RT, Ertugrul, O, Harba, AH, El-Barodys, MA, Machugh, DE, Park, SD and Bradley, DG 1999. A microsatellite survey of cattle from a centre of origin: the Near East. Molecular Ecology 8, 20152022.
Mannen, H, Kohno, M, Nagata, Y, Tsuji, S, Bradley, DG, Yeo, JS, Nyamsamba, D, Zagdsuren, Y, Yokohama, M, Nomura, K and Amano, T 2004. Independent mitochondrial origin and historical genetic differentiation in North Eastern Asian cattle. Molecular Phylogenetics and Evolution 32, 539544.
Mbole-Kariuki, MN, Sonstegard, T, Orth, A, Thumbi, SM, Bronsvoort, BM de C, Kiara, H, Toye, P, Conradie, I, Jennings, A, Coetzer, K, Woolhouse, MEJ, Hanotte, O and Tapio, M 2014. Genome-wide analysis reveals the ancient and recent admixture history of East African Shorthorn Zebu from Western Kenya. Heredity 113 (4), 297305.
McVean, G 2009. A genealogical interpretation of principal components analysis. PLoS Genetics 5, e1000686.
Metta, M, Kanginakudru, S, Gudiseva, N and Nagaraju, J 2004. Genetic characterization of the Indian cattle breeds, Ongole and Deoni (Bos indicus), using microsatellite markers – a preliminary study. BMC Genetics 5, 16.
Neuditschko, M, Khatkar, MS and Raadsma, HW 2012. NETVIEW: a high-definition network-visualization approach to detect fine-scale population structures from genome-wide patterns of variation. PLoS One 7, e48375.
Nielsen, R 2004. Population genetic analysis of ascertained SNP data. Human Genomics 1, 218224.
Patterson, N, Price, A and Reich, D 2006. Population structure and Eigen analysis. PLOS Genetics 2, e190.
Pritchard, JK, Stephens, M and Donnelly, P 2000. Inference of population structure using multilocus genotype data. Genetics 155, 945959.
R Development Core Team 2009. R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria.
Rege, JE 1999. The state of African cattle genetic resources I. Classification framework and identification of threatened and extinct breeds. Animal Genetic Resources Information 25, 125.
Reist-Marti, SB, Simianer, H, Gibson, JP, Hanotte, O and Rege, JE 2004. Measures of diversity as inputs for decisions in conservation of livestock genetic resources. Conservation Biology 17, 12991311.
Reynolds, J, Weir, BS and Cockerham, CC 1983. Estimation of the coancestry coefficient: basic for a short-term genetic distance. Genetics 105, 767779.
Shah, TM, Patel, JS, Bhong, CD, Doiphode, A, Umrikar, UD, Parmar, SS, Rank, DN, Solanki, JV and Joshi, CG 2012. Evaluation of genetic diversity and population structure of west-central Indian cattle breeds. Animal Genetics 44, 442445.
Stein, J, Ayalew, W, Rege, E, Mulatu, EW, Lemecha, H, Tadesse, Y, Tekle, T and Philipsson, J 2011. Trypanosomosis and phenotypic features of four indigenous cattle breeds in an Ethiopian field study. Veterinary Parasitology 178, 4047.
Tamura, K, Dudley, J, Nei, M and Kumar, S 2007. MEGA4. Molecular evolutionary genetics analysis (MEGA) software version 4.0. Molecular biology and Evolution 24, 15961599.
Vali, U, Einarsson, A, Waits, L and Ellegren, H 2008. To what extent do microsatellite markers reflect genome-wide genetic diversity in natural populations? Molecular Ecology 17, 38083817.
Weir, BS 1996. Genetic data analysis II. Sinauer Associates, Sunderland, MA, USA.
Wright, S 1978. Evolution and the genetics of populations. Variability within and among natural populations, vol. 4, University of Chicago Press, Chicago.
Zerabruk, M, Li, MH, Kantanen, J, Olsaker, I, Ibeagha-Awemu, EM, Erhardt, G and Vangen, O 2011. Genetic diversity and admixture of indigenous cattle from North Ethiopia: implications of historical introgressions in the gateway region to Africa. Animal Genetics 43, 257266.
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