Genetic diversity in farm animals - A review

Animal Genetics

Volumn 41, Issue SUPPL. 1, 2010, Pages 6-31

  Groeneveld, L F ^a   Lenstra, J A ^b   Eding, H ^c   Toro, M A ^d   Scherf, B ^e   Pilling, D ^e   Negrini, R ^f   Finlay, E K ^g   Jianlin, H ^h   Groeneveld, E ^a   Weigend, S ^a  

^a FEDERAL RESEARCH INSTITUTE FOR ANIMAL HEALTH   (Germany)

^b UTRECHT UNIVERSITY   (Netherlands)

^c CRV   (Netherlands)

^d UNIVERSIDAD POLITÉCNICA DE MADRID   (Spain)

^e FOOD AND AGRICULTURE ORGANIZATION OF THE UNITED NATIONS   (Italy)

^f UNIVERSITÀ CATTOLICA DEL SACRO CUORE   (Italy)

^g TRINITY COLLEGE DUBLIN   (Ireland)

^h INSTITUTE OF PLANT PROTECTION   (China)

Author keywords

Databases; Domestication; Farm animal genetic resources; Genetic diversity; Livestock; Production environment recording

Indexed keywords

ANIMAL; BIODIVERSITY; BREEDING; CATTLE; DOMESTIC ANIMAL; FEMALE; GENETIC DATABASE; GENETIC VARIABILITY; GENETICS; MALE; POPULATION GENETICS; REVIEW;

ANIMALS; ANIMALS, DOMESTIC; BIODIVERSITY; BREEDING; CATTLE; DATABASES, GENETIC; FEMALE; GENETIC VARIATION; GENETICS, POPULATION; MALE;

ANIMALIA; BOS; BOS GRUNNIENS; BUBALUS; CAMELIDAE; CAPRA HIRCUS; EQUIDAE; GALLUS GALLUS; OVIS ARIES; SUIDAE;

EID: 77951118019     PISSN: 02689146     EISSN: 13652052     Source Type: Journal    
DOI: 10.1111/j.1365-2052.2010.02038.x     Document Type: Review

References (278)

1. Aberle K.S., Hamann H., Drögemüller C. Distl O. (2004) Genetic diversity in German draught horse breeds compared with a group of primitive, riding and wild horses by means of microsatellite DNA markers. Animal Genetics 35, 270 277.
2. Achilli A., Olivieri A., Pellecchia M. et al. (2008) Mitochondrial genomes of extinct aurochs survive in domestic cattle. Current Biology 18, R157 8.
3. Achilli A., Bonfiglio S., Olivieri A. et al. (2009) The multifaceted origin of taurine cattle reflected by the mitochondrial genome. PLoS ONE 4, e5753.
4. Aishwarya V. Sharma P.C. (2008) UgMicroSatdb: database for mining microsatellites from unigenes. Nucleic Acids Research 36, D53 6.
5. Aishwarya V., Grover A. Sharma P. (2007) EuMicroSatdb: a database for microsatellites in the sequenced genomes of eukaryotes. BMC Genomics 8, 225.
6. Alves E., Ovilo C., Rodríguez M.C. Silió L. (2003) Mitochondrial DNA sequence variation and phylogenetic relationships among Iberian pigs and other domestic and wild pig populations. Animal Genetics 34, 319 324.
7. Amano T., Miyakoshi Y., Takada T., Kikkawa Y. Suzuki H. (1994) Genetic variants of ribosomal DNA and mitochondrial DNA between swamp and river buffaloes. Animal Genetics 25, 29 36.
8. Amaral A.J., Megens H.J., Crooijmans R., Heuven H.C.M. Groenen M.A.M. (2008) Linkage disequilibrium decay and haplotype block structure in the pig. Genetics 179, 569 579.
9. Amills M., Capote J., Tomàs A., Kelly L., Obexer-Ruff G., Angiolillo A. Sanchez A. (2004) Strong phylogeographic relationships among three goat breeds from the Canary Islands. Journal of Dairy Research 71, 257 262.
10. Amills M., Ramírez O., Tomàs A., Badaoui B., Marmi J., Acosta J., Sànchez A. Capote J. (2009) Mitochondrial DNA diversity and origins of South and Central American goats. Animal Genetics 40, 315 322.
11. Andreescu C., Avendano S., Brown S.R., Hassen A., Lamont S.J. Dekkers J.C.M. (2007) Linkage disequilibrium in related breeding lines of chickens. Genetics 177, 2161 2169.
12. Arnason U., Cullberg A. Janke A. (2004) Mitogenomic analysis provide new insights into cetacean origin and evolution. Gene 26, 27 34.
13. Arora R., Lakhchaura B.D., Prasad R.B., Tantia M.S. Vijh R.K. (2004) Genetic diversity analsis of two buffalo populations of northern India using microsatellite markers. Journal of Animal Breeding Genetics 121, 111 118.
14. AVIANDIV (1999) Development of strategy and application of molecular tools to assess biodiversity in chicken genetic resources. Available at: http://aviandiv.tzv.fal.de/.
15. Barker J.S.F. (1999) Conservation of livestock breed diversity. Animal Genetic Resources Information 25, 33 43.
16. Barker J.S., Moore S.S., Hetzel D.J., Evans D., Tan S.G. Byrne K. (1997a) Genetic diversity of Asian water buffalo (Bubalus bubalis): microsatellite variation and a comparison with protein-coding loci. Animal Genetics 28, 103 115.
17. Barker J.S., Tan S.G., Selvaraj O.S. Mukherjee T.K. (1997b) Genetic variation within and relationships among populations of Asian water buffalo (Bubalus bubalis). Animal Genetics 28, 1 13.
18. Barker J.S.F., Tan S.G., Moore S.S., Mukherjee T.K., Matheson J.-L. Selvaraj O.S. (2001) Genetic variation within and relationships among populations of Asian goats (Capra hircus). Journal of Animal Breeding and Genetics 118, 213 233.
19. Beja-Pereira A., Luikart G., England P.R. et al. (2003) Gene-culture coevolution between cattle milk protein genes and human lactase genes. Nature Genetics 35, 311 313.
20. Beja-Pereira A., Caramelli D., Lalueza-Fox C. et al. (2006) The origin of European cattle: evidence from modern and ancient DNA. Proceedings of the National Academy of Sciences of the United States of America 103, 8113 8118.
21. Bennewitz J., Kantanen J., Tapio I. et al. (2006) Estimation of breed contributions to present and future genetic diversity of 44 North Eurasian cattle breeds using core set diversity measures. Genetics Selection Evolution 38, 201 220.
22. Benson D.A., Karsch-Mizrachi I., Lipman D.J., Ostell J. Wheeler D.L. (2008) GenBank. Nucleic Acids Research 36, D25 30.
23. Berthouly C. (2008) Characterisation of the Cattle, Buffalo and Chicken Populations in the Northern Vietnamese Province of Ha Giang. AgroParisTech
24. Berthouly C., Bed'Hom B., Tixier-Boichard M., Chen C.F., Lee Y.P., LaloÎ D., Legros H., Verrier E. 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.
25. Berthouly C., Do Ngoc D., Thévenon S., Bouchel D., Nhu Van T., Danes C., Grosbois V., Hoang Thanh H., Vu Chi C. Maillard J.-C. (2009) How does farmer connectivity influence livestock genetic structure? A case-study in a Vietnamese goat population. Molecular Ecology 18, 3980 3991.
26. Bigi D., Zambonelli P., Perrotta G. Blasi M. (2007) The Ventasso Horse: genetic characterization by microsatellites markers. Italian Journal of Animal Science 6, 50 2.
27. Bjornstad G., Nilsen N.O. Roed K.H. (2003) Genetic relationship between Mongolian and Norwegian horses? Animal Genetics 34, 55 8.
28. Blackburn H.D. (2006) The National Animal Germplasm Program: challenges and opportunities for poultry genetic resources. Poultry Science 85, 210 215.
29. Bollongino R., Elsner J., Vigne J. Burger J. (2008) Y-SNPs do not indicate hybridisation between European aurochs and domestic cattle. PLoS ONE 3, e3418.
30. Bowling A.T., Del Valle A. Bowling M. (2000) A pedigree-based study of mitochondrial D-loop DNA sequence variation among Arabian horses. Animal Genetics 31, 1 7.
31. Bradley D.G., Machugh D.E., Cunningham P. Loftus R.T. (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, 5131 5135.
32. Bradley D.G., Loftus R.T., Cunningham P. Machugh D.E. (1998) Genetics and domestic cattle origins. Evolutionary Anthropology 6, 79 86.
33. Bruford M.W., Bradley D.G. Luikart G. (2003) DNA markers reveal the complexity of livestock domestication. Nature Reviews Genetics 4, 900 910.
34. Buchanan F.C., Adams L.J., Littlejohn R.P., Maddox J.F. Crawford A.M. (1994) Determination of evolutionary relationships among sheep breeds using microsatellites. Genomics 22, 397 403.
35. Bustamante A., Zambelli A., de Lamo D., von Thungen J. Vidal-Rioja L. (2002) Genetic variability of guanaco and llama populations in Argentina. Small Ruminant Research 44, 97 101.
36. Cai X., Chen H., Wang S., Xue K. Lei C. (2006) Polymorphisms of two Y chromosome microsatellites in Chinese cattle. Genetics Selection Evolution 38, 525 534.
37. Cai X., Chen H., Lei C., Wang S., Xue K. Zhang B. (2007) MtDNA Diversity and genetic lineages of eighteen cattle breeds from Bos taurus and Bos indicus in China. Genetica 131, 175 183.
38. Cañón J., Checa M.L., Carleos C., Vega-Pla J.L., Vallejo M. Dunner S. (2000) The genetic structure of Spanish Celtic horse breeds inferred from microsatellite data. Animal Genetics 31, 39 48.
39. Cañón J., García D., García-Atance M.A., Obexer-Ruff G., Lenstra J.A., Ajmone-Marsan P. Dunner S. (2006) Geographical partitioning of goat diversity in Europe and the Middle East. Animal Genetics 37, 327 334.
40. Cañón J., Tupac-Yupanqui I., García-Atance M.A., Cortés O., García D., Fernández J. Dunner S. (2008) Genetic variation within the Lidia bovine breed. Animal Genetics 39, 439 445.
41. Carvajal-Carmona L.G., Bermudez N., Olivera-Angel M., Estrada L., Ossa J., Bedoya G. Ruiz-Linares A. (2003) Abundant mtDNA diversity and ancestral admixture in Colombian criollo cattle (Bos taurus). Genetics 165, 1457 1463.
42. Chen Y.S. Li X.H. (1989) New evidence of the origin and domestication of the Chinese swamp buffalo (Bubalus bubalis). Buffalo Journal 1, 51 5.
43. Chen W. Zu G. (2004) Photograph Album of Chinese Indigenous Farm Animal Breeds. China Agriculture Press
44. Chen G.H., Bao W.B., Shu J., Ji C.L., Wang M.Q., Eding H., Muchadeyi F. Weigend S. (2008) Assessment of population structure and genetic diversity of 15 Chinese indigenous chicken breeds using microsatellite markers. Asian-Australasian Journal of Animal Sciences 21, 331 339.
45. Chessa B., Pereira F., Arnaud F. et al. (2009) Revealing the history of sheep domestication using retrovirus integrations. Science 324, 532 536.
46. Chikhi L., Goossens B., Treanor A. Bruford M.W. (2004) Population genetic structure of and inbreeding in an insular cattle breed, the Jersey, and its implications for genetic resource management. Heredity 92, 396 401.
47. Cinkulov M., Popovski Z., Porcu K. et al. (2008) Genetic diversity and structure of the West Balkan Pramenka sheep types as revealed by microsatellite and mitochondrial DNA analysis. Journal of Animal Breeding and Genetics 125, 417 426.
48. Cochrane G., Akhtar R., Aldebert P. et al. (2008) Priorities for nucleotide trace, sequence and annotation data capture at the Ensembl Trace Archive and the EMBL Nucleotide Sequence Database. Nucleic Acids Research 36, D5 12.
49. Cockrill W. (1981) The water buffalo: a review. British Veterinary Journal 137, 8 16.
50. Cortés O., Tupac-Yupanqui I., Dunner S., García-Atance M.A., García D., Fernández J. Cañón J. (2008) Ancestral matrilineages and mitochondrial DNA diversity of the Lidia cattle breed. Animal Genetics 39, 649 654.
51. Crawford R.D. (Ed.) (1990) Origin and history of poultry species. In : Poultry Breeding and Genetics, pp. 1 41. Elsevier
52. Cui P., Ji R., Ding F., Qi D., Gao H., Meng H., Yu J., Hu H. Zhang H. (2007) A complete mitochondrial genome sequence of the wild two-humped camel (Camelus bactrianus ferus): an evolutionary history of camelidae. BMC Genomics 8, 241.
53. Cymbron T., Loftus R.T., Malheiro M.I. Bradley D.G. (1999) Mitochondrial sequence variation suggests an African influence in Portuguese cattle. Proceedings of the Royal Society of London, Series B: Biological Sciences 266, 597 603.
54. Cymbron T., Freeman A.R., Malheiro M.I., Vigne J.-D. Bradley D.G. (2005) Microsatellite diversity suggests different histories for Mediterranean and Northern European cattle populations. Proceedings of the Royal Society of London, Series B: Biological Sciences 272, 1837 1843.
55. Darnell D.K., Kaur S., Stanislaw S., Davey S., Konieczka J.H., Yatskievych T.A. Antin P.B. (2007) GEISHA: an in situ hybridization gene expression resource for the chicken embryo. Cytogenetic and Genome Research 117, 30 5.
56. Di Berardino D. Iannuzzi L. (1981) Chromosome banding homologies in Swamp and Murrah buffalo. Journal of Heredity 72, 183 188.
57. Diamond J. (2002) Evolution, consequences and future of plant and animal domestication. Nature 418, 700 707.
58. Edwards C.J., Baird J.F. MacHugh D.E. (2007a) Taurine and zebu admixture in Near Eastern cattle: a comparison of mitochondrial, autosomal and Y-chromosomal data. Animal Genetics 38, 520 524.
59. Edwards C.J., Bollongino R., Scheu A. et al. (2007b) Mitochondrial DNA analysis shows a Near Eastern Neolithic origin for domestic cattle and no indication of domestication of European aurochs. Proceedings of the Royal Society of London, Series B: Biological Sciences 274, 1377 1385.
60. Egito A.A., Paiva S.R., Albuquerque M.D.S.M., Mariante A.S., Almeida L.D., Castro S.R. Grattapaglia D. (2007) Microsatellite based genetic diversity and relationships among ten Creole and commercial cattle breeds raised in Brazil. BMC Genetics 8, 83.
61. Eriksson J., Larson G., Gunnarsson U. et al. (2008) Identification of the Yellow skin gene reveals a hybrid origin of the domestic chicken. PLoS Genetics 4, e1000010.
62. Fabuel E., Barragán C., Silió L., Rodríguez M.C. Toro M.A. (2004) Analysis of genetic diversity and conservation priorities in Iberian pigs based on microsatellite markers. Heredity 93, 104 113.
63. Fang M., Larson G., Soares Ribeiro H. Andersson L. (2009) Contrasting mode of evolution at a coat color locus in wild and domestic pigs. PLoS ONE 5, e1000341.
64. FAO (1992) The management of global animal genetic resources. In : Proceedings of an Expert Consultation, Animal Production and Health Paper No. 104 (Ed. by J. Hodges pp. 1 263. FAO
65. FAO (1998) Production environment descriptors for farm animal genetic resources. In : Report of Working Group.
66. FAO (2007a) Global Plan of Action for Animal Genetic Resources and the Interlaken Declaration. available at http://www.fao.org/docrep/010/a1404e/ a1404e00.HTM.
67. FAO (2007b) The State of the World's Animal Genetic Resources for Food and Agriculture. FAO
68. FAO (2009) Status and trends report on animal genetic resources - 2008. In : Information Document. CGRFA/WG-AnGR-5/09/Inf. 7
69. FAO/WAAP (2008) Production environment descriptors for animal genetic resources. In : Report of FAO/WAAP Expert Meeting (Ed. by D. Pilling, B. Rischkowsky B. Scherf pp. 1 97. FAO/WAAP
70. Felius M. (1995) Cattle Breeds, an Encyclopaedia. Misset
71. Fischer H. Ulbrich F. (1968) Chromosomes of the Murrah buffalo and its crossbreeds with the Asiatic swamp buffalo (Bubalus bubalis). Zeitschrift fur Tierzüchtung und Züchtungsbiologie 84, 110 114.
72. Flicek P., Aken B.L., Beal K. et al. (2008) Ensembl 2008. Nucleic Acids Research 36, D707 14.
73. Foulley J.L., van Schriek M.G.M., Alderson L. et al. (2006) Genetic diversity analysis using lowly polymorphic dominant markers: the example of AFLP in pigs. Journal of Heredity 97, 244 252.
74. Freeman A.R., Meghen C.M., Machugh D.E., Loftus R.T., Achukwi M.D., Bado A., Sauveroche B. Bradley D.G. (2004) Admixture and diversity in West African cattle populations. Molecular Ecology 13, 3477 3487.
75. Freeman A.R., Bradley D.G., Nagda S., Gibson J.P. Hanotte O. (2006a) Combination of multiple microsatellite data sets to investigate genetic diversity and admixture of domestic cattle. Animal Genetics 37, 1 9.
76. Freeman A.R., Hoggart C.J., Hanotte O. Bradley D.G. (2006b) Assessing the relative ages of admixture in the bovine hybrid zones of Africa and the Near East using X chromosome haplotype mosaicism. Genetics 173, 1503 1510.
77. Fumihito A., Miyake T., Takada M., Shingu R., Endo T., Gojobori T., Kondo N. Ohno S. (1996) Monophyletic origin and unique dispersal patterns of domestic fowls. Proceedings of the National Academy of Sciences of the United States of America 93, 6792 6795.
78. Gandini G.C., Ollivier L., Danell B., Distl O., Georgoudis A., Groeneveld E., Martyniuk E., van Arendonk J.A.M. Woolliams J.A. (2004) Criteria to assess the degree of endangerment of livestock breeds in Europe. Livestock Production Science 91, 173 182.
79. Gas S., Eggen A., Samson F., Christophe C., Mungall C., Bessieres P. Leveziel H. (1996) The BOVMAP database: C016. Proceedings of the 25th Isag Conference. Animal Genetics 27, 59.
80. Gautier M., Faraut T., Moazami-Goudarzi K. et al. (2007) Genetic and haplotypic structure in 14 European and African cattle breeds. Genetics 177, 1059 1070.
81. Ginja C., Telo da Gama L. Penedo M. (2009) Y Chromosome haplotype analysis in portuguese cattle breeds using SNPs and STRs. Journal of Heredity 100, 148 157.
82. Ginja C., Melucci L., Quiroz J., Revidatti M.A., Martínez- Martínez A., Delgado J.V., Penedo M.C.T. Gama L.T. (2010) Origin and genetic diversity of New World Creole cattle: inferences from mitochondrial and Y chromosome polymorphisms. Animal Genetics 41, 128 141.
83. Giovambattista G., Ripoli M.V., De Luca J.C., Mirol P.M., Liron J.P. Dulout F.N. (2000) Male-mediated introgression of Bos indicus genes into Argentine and Bolivian Creole cattle breeds. Animal Genetics 31, 302 305.
84. Giuffra E., Kijas J.M.H., Amarger V., Carlborg O., Jeon J.T. Andersson L. (2000) The origin of the domestic pig: independent domestication and subsequent introgression. Genetics 154, 1785 1791.
85. Gizaw S., Van Arendonk J.A.M., Komen H., Windig J.J. Hanotte O. (2007) Population structure, genetic variation and morphological diversity in indigenous sheep of Ethiopia. Animal Genetics 38, 621 628.
86. Glowatzki-Mullis M.-L., Muntwyler J., Bäumle E. Gaillard C. (2008) Genetic diversity measures of Swiss goat breeds as decision-making support for conservation policy. Small Ruminant Research 74, 202 211.
87. Gongora J., Rawlence N.J., Mobegi V.A. et al. (2008) Indo-European and Asian origins for Chilean and Pacific chickens revealed by mtDNA. Proceedings of the National Academy of Sciences of the United States of America 105, 10308 10313.
88. Gonzalez B., Palma R., Zapata B. Marin J. (2006) Taxonomic and biogeographical status of guanaco Lama guanicoe (Artiodactyla, Camelidae). Mammalian Review 36, 157 178.
89. Götherström A., Anderung C., Hellborg L., Elburg R., Smith C., Bradley D.G. Ellegren H. (2005) Cattle domestication in the Near East was followed by hybridization with aurochs bulls in Europe. Proceedings of the Royal Society of London, Series B: Biological Sciences 272, 2345 2350.
90. Granevitze Z., Hillel J., Chen G.H., Cuc N.T.K., Feldman M., Eding H. Weigend S. (2007) Genetic diversity within chicken populations from different continents and management histories. Animal Genetics 38, 576 583.
91. Granevitze Z., Hillel J., Feldman M., Six A., Eding H. Weigend S. (2009) Genetic structure of a wide-spectrum chicken gene pool. Animal Genetics 40, 686 693.
92. Groeneveld E., Duchev Z.I., Imialek M., Soltys L., Wieczorek M., Distl O., Gandini G., Jaszczynska M., Scherf B. Rosati A. (2006) FABISnet - creating national biodiversity websites. In : Book of Abstracts: 8th WCGALP, p. 244. WCGALP
93. Gu Z., Zhao X., Li N. Wu C. (2007) Complete sequence of the yak (Bos grunniens) mitochondrial genome and its evolutionary relationship with other ruminants. Molecular Phylogenetics and Evolution 42, 248 255.
94. Guo S., Savolainen P., Su J., Zhang Q., Qi D., Zhou J., Zhong Y., Zhao X. Liu J. (2006) Origin of mitochondrial DNA diversity of domestic yaks. BMC Evolutionary Biology 6, 73. doi:.
95. Hall S.J.G. Bradley D.G. (1995) Conserving livestock breed diversity. Trends in Ecology and Evolution 10, 267 270.
96. Hanotte O., Tawah C.L., Bradley D.G., Okomo M., Verjee Y., Ochieng J. Rege J.E.O. (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, 387 396.
97. Hanotte O., Bradley D.G., Ochieng J.W., Verjee Y., Hill E.W. Rege J.E.O. (2002) African pastoralism: genetic imprints of origins and migrations. Science 296, 336 339.
98. Harrer S., Begemann F. Roscher S. (2002) Aufbau des Bundesinformationssystems genetische Ressourcen (BIG) über verteilte Datenbanken zu in-situ- und ex-situ-Beständen von Pflanzen. Schriftenreihe des BMVEL "Angewandte Wissenschaft" 494, Biologische Vielfalt mit der Land- und Forstwirtschaft?, 72 7.
99. Hiendleder S., Kaupe B., Wassmuth R. Janke A. (2002) Molecular analysis of wild and domestic sheep questions current nomenclature and provides evidence for domestication from two different subspecies. Proceedings of the Royal Society of London, Series B: Biological Sciences 269, 893 904.
100. Hill E.W., Bradley D.G., Al-Barody M., Ertugrul O., Splan R.K., Zakharov I. Cunningham E.P. (2002) History and integrity of thoroughbred dam lines revealed in equine mtDNA variation. Animal Genetics 33, 287 294.
101. Hillel J., Groenen M.A.M., Tixier-Boichard M. et al. (2003) Biodiversity of 52 chicken populations assessed by microsatellite typing of DNA pools. Genetics Selection Evolution 35, 533 557.
102. Hillel J., Granevitze Z., Twito T., Ben-Avraham D., Blum S., Lavi U., David L., Feldman M.W., Cheng H. Weigend S. (2007) Molecular markers for the assessment of chicken biodiversity. Worlds Poultry Science Journal 63, 33 45.
103. Hoffmann I., Marsan P.A., Barker S.F., Cothran E.G., Hanotte O., Lenstra J.A., Milan D., Weigend S. Simianer H. (2004) New MoDAD marker sets to be used in diversity studies for the major farm animal species: recommendations of a joint ISAG/FAO working group. In : 29th International Conference on Animal Genetics, p. 123 (abstract), Meiji University
104. Hu J., Mungall C., Law A. et al. (2001) The ARKdb: genome databases for farmed and other animals. Nucleic Acids Research 29, 106 110.
105. Hu Z.-L., Fritz E.R. Reecy J.M. (2007) AnimalQTLdb: a livestock QTL database tool set for positional QTL information mining and beyond. Nucleic Acids Research 35, D604 9.
106. Hubbard S.J., Grafham D.V., Beattie K.J. et al. (2005) Transcriptome analysis for the chicken based on 19,626 finished cDNA sequences and 485,337 expressed sequence tags. Genome Research 15, 174 183.
107. Ibeagha-Awemu E.M., Jann O.C., Weimann C. Erhardt G. (2004) Genetic diversity, introgression and relationships among West/Central African cattle breeds. Genetics Selection Evolution 36, 673 690.
108. Jansen T., Forster P., Levine M.A., Oelke H., Hurles M., Renfrew C., Weber J. Olek K. (2002) Mitochondrial DNA and the origins of the domestic horse. Proceedings of the National Academy of Sciences of the United States of America 99, 10905 10910.
109. Ji R., Cui P., Ding F., Geng J., Gao H., Zhang H., Yu J., Hu S. Meng H. (2009) Monophyletic origin of domestic bactrian camel (Camelus bactrianus) and its evolutionary relationship with the extant wild camel (Camelus bactrianus ferus). Animal Genetics 40, 377 382.
110. Jianlin H. (2003) Molecular and cytogenetics in yak - a scientific basis for breeding and evidence for phylogeny. In : The Yak (Ed. by G. Wiener, H. Jianlin L. Ruijun pp. 415 435. Regional Office for Asia and the Pacific of the Food and Agriculture Organization (FAO) of the United Nations
111. Jianlin H. (2005a) Achievement of research in the field of Camelids. In : WAAP Book of the Year - 2005 (Ed. by A. Rosati, A. Tewolde C. Mosconi pp. 177 187. Wageningen Academic Publishers
112. Jianlin H. (2005b) Camelids. In : Encyclopedia of Animal Science (Ed. by W. Pond A. Bell pp. 187 190. Marcel Dekker Inc.
113. Jianlin H., Quan J., Men Z., Zhang Y. Wang W. (1999) Three unique restriction fragment length polymorphisms of EcoR I, Pvu II and Sca I digested mitochondrial DNA of wild Bactrian camel (Camelus bactrianus ferus) in China. Journal of Animal Science 77, 2315 2316.
114. Jianlin H., Ochieng J., Lkhagva B. Hanotte O. (2004) Genetic diversity and relationship of domestic Bactrian camels (Camelus bactrianus) in China and Mongolia. Journal of Camel Practice and Research 12, 97 9.
115. Kadwell M., Fernandez M., Stanley H., Baldi R., Wheeler J., Rosadio R. Bruford M. (2001) Genetic analysis reveals the wild ancestors of the llama and the alpaca. Proceedings of the Royal Society of London, Series B: Biological Sciences 268, 2575 2584.
116. Kakoi H., Tozaki T. Gawahara H. (2007) Molecular analysis using mitochondrial DNA and microsatellites to infer the formation process of Japanese native horse populations. Biochemical Genetics 45, 375 395.
117. Kantanen J., Edwards C.J., Bradley D.G. et al. (2009) Maternal and paternal genealogy of Eurasian taurine cattle (Bos taurus). Heredity 103, 404 415.
118. Kavar T. Dovc P. (2008) Domestication of the horse: genetic relationships between domestic and wild horses. Livestock Science 116, 1 14.
119. Kavar T., Brem G., Habe F., Solkner J. Dovc P. (2002) History of Lipizzan horse maternal lines as revealed by mtDNA analysis. Genetics Selection Evolution 34, 635 648.
120. Keyser-Tracqui C., Blandin-Frappin P., Francfort H.P., Ricaut F.X., Lepetz S., Crubezy E., Samashev Z. Ludes B. (2005) Mitochondrial DNA analysis of horses recovered from a frozen tomb (Berel site, Kazakhstan, 3rd Century BC). Animal Genetics 36, 203 209.
121. Kierstein G., Vallinoto M., Silva A., Schneider M.P., Iannuzzi L. Brenig B. (2004) Analysis of mitochondrial D-loop region casts new light on domestic water buffalo (Bubalus bubalis) phylogeny. Molecular Phylogenetics and Evolution 30, 308 324.
122. Kijas J.W., Townley D., Dalrymple B.P. et al. (2009) A genome wide survey of SNP variation reveals the genetic structure of sheep breeds. PLoS ONE 4, e4668.
123. Kikkawa Y., Takada T., Sutopo, Nomura K., Namikawa T., Yonekawa H. Amano T. (2003) Phylogenies using mtDNA and SRY provide evidence for male-mediated introgression in Asian domestic cattle. Animal Genetics 34, 96 101.
124. Kumar P., Freeman A.R., Loftus R.T., Gaillard C., Fuller D.Q. Bradley D.G. (2003) Admixture analysis of South Asian cattle. Heredity 91, 43 50.
125. Kumar S., Gupta J., Kumar N., Dikshit K., Navani N., Jain P. Nagarajan M. (2006) Genetic variation and relationships among eight Indian riverine buffalo breeds. Molecular Ecology 15, 593 600.
126. Kumar S., Nagarajan M., Sandhu J.S., Kumar N. Behl V. (2007a) Phylogeography and domestication of Indian river buffalo. BMC Evolutionary Biology 7, 186.
127. Kumar S., Nagarajan M., Sandhu J.S., Kumar N., Behl V. Nishanth G. (2007b) Mitochondrial DNA analyses of Indian water buffalo support a distinct genetic origin of river and swamp buffalo. Animal Genetics 38, 227 232.
128. Lai S.-J., Liu Y.-P., Liu Y.-X., Li X.-W. Yao Y.-G. (2006) Genetic diversity and origin of Chinese cattle revealed by mtDNA D-loop sequence variation. Molecular Phylogenetics and Evolution 38, 146 154.
129. Lai S., Chen S., Liu Y. Yao Y. (2007) Mitochondrial DNA sequence diversity and origin of Chinese domestic yak. Animal Genetics 38, 77 80.
130. Larson G., Dobney K., Albarella U. et al. (2005) Worldwide phylogeography of wild boar reveals multiple centers of pig domestication. Science 307, 1618 1621.
131. Larson G., Albarella U., Dobney K. et al. (2007) Ancient DNA, pig domestication, and the spread of the Neolithic into Europe. Proceedings of the National Academy of Sciences of the United States of America 104, 15276 15281.
132. Lau C.H., Drinkwater R.D., Yusoff K., Tan S.G., Hetzel D.J. Barker J.S. (1998) Genetic diversity of Asian water buffalo (Bubalus bubalis): mitochondrial DNA D-loop and cytochrome b sequence variation. Animal Genetics 29, 253 264.
133. Laval G., Iannuccelli N., Legault C. et al. (2000) Genetic diversity of eleven European pig breeds. Genetics Selection Evolution 32, 187 203.
134. Lawson Handley L.-J., Byrne K., Santucci F., Townsend S., Taylor M., Bruford M.W. Hewitt G.M. (2007) Genetic structure of European sheep breeds. Heredity 99, 620 631.
135. Lei C.Z., Zhang W., Chen H. et al. (2007) Independent maternal origin of Chinese swamp buffalo (Bubalus bubalis). Animal Genetics 38, 97 102.
136. Lei C.Z., Su R., Bower M.A. et al. (2009) Multiple maternal origins of native modern and ancient horse populations in China. Animal Genetics 40, 933 944.
137. Lenstra J.A. Bradley D.G. (1999) Systematics and phylogeny of cattle. In : The Genetics of Cattle (Ed. by R. Fries A. Ruvinsky pp. 1 14. CAB International
138. Lenstra J.A., European Cattle Genetic Diversity Consortium (2008) Meta-analysis of microsatellite data allows a Molecular classification of European cattle. In : Proceedings of 31th International Congress on Animal Genetics
139. Lenstra J.A., The Econogene Consortium (2005) Evolutionary and demographic history of sheep and goats suggested by nuclear, mtDNA and Y-chromosomal markers. In : International Workshop on the 'The role of biotechnology for the characterization of crop, forestry, animal and fishery genetic resources'
140. Lenstra J.A. the European Cattle Genetic Diversity Consortium (2006a) Marker-assisted conservation of European cattle breeds: an evaluation. Animal Genetics 37, 475 481.
141. Lenstra J.A., Ajmone Marsan P., European Cattle Genetic Diversity Consortium & Econogene Consortium (2006b) Microsatellites and Y-chromosomal haplotypes of European and Middle-Eastern cattle, sheep and goats. Geographic clines, clusters, male introgression, conflicting views on diversity. In : 30th International Congress on Animal Genetics
142. Li M.H., Tapio I., Vilkki J. et al. (2007) The genetic structure of cattle populations (Bos taurus) in northern Eurasia and the neighbouring Near Eastern regions: implications for breeding strategies and conservation. Molecular Ecology 16, 3839 3853.
143. Lindgren G., Backstrom N., Swinburne J., Hellborg L., Einarsson A., Sandberg K., Cothran G., Vila C., Binns M. Ellegren H. (2004) Limited number of patrilines in horse domestication. Nature Genetics 36, 335 336.
144. Liron J.P., Bravi C.M., Mirol P.M., Peral-García P. Giovambattista G. (2006a) African matrilineages in American Creole cattle: evidence of two independent continental sources. Animal Genetics 37, 379 382.
145. Liron J.P., Peral-Garcia P. Giovambattista G. (2006b) Genetic characterization of Argentine and Bolivian Creole cattle breeds assessed through microsatellites. Journal of Heredity 97, 331 339.
146. Lister A.M. (2001) Tales from the DNA of domestic horses. Science 292, 218.
147. 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. Zhang Y.P. (2006) Multiple maternal origins of chickens: out of the Asian jungles. Molecular Phylogenetics and Evolution 38, 12 9.
148. Loftus R.T., Ertugrul O., Barbar A.H., El-Barody M.A.A., Machugh D.E., Park S.D.E. Bradley D.G. (1999) A microsatellite survey of cattle from a centre of origin: the Near East. Molecular Ecology 8, 2015 2022.
149. Lopes M.S., Mendonca D., Cymbron T., Valera M., da Costa-Ferreira J. Machado A.D. (2005) The Lusitano horse maternal lineage based on mitochondrial D-loop sequence variation. Animal Genetics 36, 196 202.
150. Ludwig A., Pruvost M., Reissmann M. et al. (2009) Coat color variation at the beginning of horse domestication. Science 324, 485.
151. Luikart G., Gielly L., Excoffier L., Vigne J.-D., Bouvet J. Taberlet P. (2001) Multiple maternal origins and weak phylogeographic structure in domestic goats. Proceedings of the National Academy of Sciences of the United States of America 98, 5927 5932.
152. Luis C., Bastos-Silveira C., Cothran E.G. Oom M.D. (2006) Iberian origins of New World horse breeds. Journal of Heredity 97, 107 113.
153. Luis C., Juras R., Oom M.M. Cothran E.G. (2007) Genetic diversity and relationships of Portuguese and other horse breeds based on protein and microsatellite loci variation. Animal Genetics 38, 20 7.
154. MacHugh D.E., Loftus R.T., Cunningham P. Bradley D.G. (1998) Genetic structure of seven European cattle breeds assessed using 20 microsatellite markers. Animal Genetics 29, 333 340.
155. Magee D.A., Meghen C., Harrison S., Troy C.S., Cymbron T., Gaillard C., Morrow A., Maillard J.C. Bradley D.G. (2002) A partial African ancestry for the Creole cattle populations of the Caribbean. Journal of Heredity 93, 429 432.
156. Mannen H., Kohno M., Nagata Y. et al. (2004) Independent mitochondrial origin and historical genetic differentiation in North Eastern Asian cattle. Molecular Phylogenetics and Evolution 32, 539 544.
157. Marín J., Casey C., Kadwell M. et al. (2007) Mitochondrial phylogeography and demographic history of the Vicuna: implications for conservation. Heredity 99, 70 80.
158. Martin-Burriel I., Rodellar C., Lenstra J.A., Sanz A., Cons C., Osta R., Reta M., De Arguello S., Sanz A. Zaragoza P. (2007) Genetic diversity and relationships of endangered Spanish cattle breeds. Journal of Heredity 98, 687 691.
159. Martinez A.M., Delgado J.V., Rodero A. Vega-Pla J.L. (2000) Genetic structure of the Iberian pig breed using microsatellites. Animal Genetics 31, 295 301.
160. Mason I.L. (1984) Evolution of Domesticated Animals. Longman
161. Maté M., Dirocco F., Zambelli A. Vidal-Rioja L. (2004) Mitochondrial DNA structure and organization of the control region of South American camelids. Molecular Ecology Notes 4, 765 767.
162. Maté M., Bustamante A., Giovambattista G., de Lamo D., von Thungen J., Zambelli A. Vidal-Rioja L. (2005) Genetic diversity and differentiation of guanaco populations from Argentina inferred from microsatellite data. Animal Genetics 36, 316 321.
163. Maté M., Dirocco F., Zambelli A. Vidal-Rioja L. (2007) Mitochondrial heteroplasmy in Control Region DNA of South American camelids. Small Ruminant Research 71, 123 129.
164. Mburu D., Ochieng J., Kuria S., Jianlin H., Kaufmann B., Rege J. Hanotte O. (2003) Genetic diversity and relationships of indigenous Kenyan dromedary (Camelus dromedarius) populations: implications for their classification. Animal Genetics 34, 26 32.
165. McCarthy F., Wang N., Magee G.B. et al. (2006) AgBase: a functional genomics resource for agriculture. BMC Genomics 7, 229.
166. McCarthy F.M., Bridges S.M., Wang N., Magee G.B., Williams W.P., Luthe
167. McGahern A.M., Edwards C.J., Bower M.A., Heffernan A., Park S.D.E., Brophy P.O., Bradley D.G., MacHugh D.E. Hill E.W. (2006) Mitochondrial DNA sequence diversity in extant Irish horse populations and in ancient horses. Animal Genetics 37, 498 502.
168. McKay S., Schnabel R., Murdoch B. et al. (2008) An assessment of population structure in eight breeds of cattle using a whole genome SNP panel. BMC Genetics 9, 3.
169. Meadows J.R.S., Hawken R.J. Kijas J.W. (2004) Nucleotide diversity on the ovine Y chromosome. Animal Genetics 35, 379 385.
170. Meadows J.R.S., Li K., Kantanen J. et al. (2005) Mitochondrial sequence reveals high levels of gene flow between breeds of domestic sheep from Asia and Europe. Journal of Heredity 96, 494 501.
171. Meadows J.R.S., Hanotte O., Drögemüller C., Calvo J., Godfrey R., Coltman D., Maddox J.F., Marzanov N., Kantanen J. Kijas J.W. (2006) Globally dispersed Y chromosomal haplotypes in wild and domestic sheep. Animal Genetics 37, 444 453.
172. Meadows J.R.S., Cemal I., Karaca O., Gootwine E. Kijas J.W. (2007) Five ovine mitochondrial lineages identified from sheep breeds of the Near East. Genetics 175, 1371 1379.
173. Medjugorac I., Kustermann W., Lazar P., Russ I. Pirchner F. (1994) Marker-derived phylogeny of European cattle supports demic expansion of agriculture. Animal Genetics 25 (Suppl. 1 19 27.
174. Medugorac I., Medugorac A., Russ I., Veit-Kensch C.E., Taberlet P., Luntz B., Mix H.M. Förster M. (2009) Genetic diversity of European cattle breeds highlights the conservation value of traditional unselected breeds with high effective population size. Molecular Ecology 18, 3394 3410.
175. Megens H.-J., Crooijmans R.P.M.A., Cristobal M.S., Hui X., Li N. Groenen M.A.M. (2008) Biodiversity of pig breeds from China and Europe estimated from pooled DNA samples: differences in microsatellite variation between two areas of domestication. Genetics Selection Evolution 40, 103 128.
176. Meirelles F.V., Rosa A.J.M., Lôbo R.B., Garcia J.M., Smith L.C. Duarte F.A.M. (1999) Is the American Zebu really Bos indicus? Genetics and Molecular Biology 22, 543 546.
177. Mengoni Goñalons G. Yacobaccio H. (2006) The domestication of South American camelids: a view from the South-Central Andes. In : Documenting Domestication (Ed. by M.A. Zeder, D.G. Bradley, E. Emshwiller B.D. Smith). University of California Press.
178. Minqiang W., Weigend S., Barre-Dirie A., Carnwath J., Zhonglin L. Niemann H. (2003) Analysis of two Chinese yak (Bos grunniens) populations using bovine microsatellite primers. Journal of Animal Breeding and Genetics 120, 237 244.
179. Miretti M.M., Dunner S., Naves M., Contel E.P. Ferro J.A. (2004) Predominant African-derived mtDNA in Caribbean and Brazilian creole cattle is also found in Spanish cattle (Bos taurus). Journal of Heredity 95, 450 453.
180. Mirol P.M., Giovambattista G., Liron J.P. Dulout F.N. (2003) African and European mitochondrial haplotypes in South American Creole cattle. Heredity 91, 248 254.
181. Mohamad K., Olsson M., Van Tol H.T.A. et al. (2009) On the origin of Indonesian cattle. PLoS ONE 4, e5490.
182. Moioli B., Georgoudis A., Napolitano F., Catillo G., Giubilei E., Ligda C. Hassanane M. (2001) Genetic diversity between Italian, Greek and Egyptian buffalo. Livestock Production Science 70, 203 211.
183. Muchadeyi F.C., Eding H., Wollny C.B.A., Groeneveld E., Makuza S.M., Shamseldin R., Simianer H. Weigend S. (2007) Absence of population substructuring in Zimbabwe chicken ecotypes inferred using microsatellite analysis. Animal Genetics 38, 332 339.
184. Muchadeyi F., Eding H., Simianer H., Wollny C.B.A., Groeneveld E. Weigend S. (2008) Mitochondrial DNA D-loop sequences suggest a Southeast-Asian and Indian origin of Zimbabwean village chickens. Animal Genetics 39, 615 622.
185. Muir W.M., Wong G.K.-S., Zhang Y. et al. (2008) Genome-wide assessment of worldwide chicken SNP genetic diversity indicates significant absence of rare alleles in commercial breeds. Proceedings of the National Academy of Sciences of the United States of America 105, 17312 17317.
186. Mwacharo J.M., Nomura K., Hanada H., Jianlin H., Hanotte O. Amano T. (2007) Genetic relationships among Kenyan and other East African indigenous chickens. Animal Genetics 38, 485 490.
187. Naderi S., Rezaei H.-R., Taberlet P. et al. (2007) Large-scale mitochondrial DNA analysis of the domestic goat reveals six haplogroups with high diversity. PLoS ONE 2, e1012.
188. Naderi S., Rezaei H., Pompanon F. et al. (2008) The goat domestication process inferred from large-scale mitochondrial DNA analysis of wild and domestic individuals. Proceedings of the National Academy of Sciences of the United States of America 105, 17659 17664.
189. Negrini R., Nijman I.J., Milanesi E. et al. (2007) Differentiation of European cattle by AFLP fingerprinting. Animal Genetics 38, 60 6.
190. Nguyen T., Genini S., Menetrey F., Malek M., Vogeli P., Goe M. Stranzinger G. (2005) Application of bovine microsatellite markers for genetic diversity analysis of Swiss yak (Poephagus grunniens). Animal Genetics 36, 484 489.
191. Nijman I.J., Bradley D.G., Hanotte O., Otsen M. Lenstra J.A. (1999) Satellite DNA polymorphisms and AFLP correlate with Bos indicus-taurus hybridization. Animal Genetics 30, 265 273.
192. Nijman I.J., Otsen M., Verkaar E.L.C. et al. (2003) Hybridization of banteng (Bos javanicus) and zebu (Bos indicus) revealed by mitochondrial DNA, satellite DNA, AFLP and microsatellites. Heredity 90, 10 6.
193. Nishibori M., Shimogiri T., Hayashi T. Yasue H. (2005) Molecular evidence for hybridization of species in the genus Gallus except for Gallus varius. Animal Genetics 36, 367 375.
194. Nolte M., Kotzé A., van der Bank F. Grobler J. (2005) Microsatellite markers reveal low genetic differentiation among southern African Camelus dromedarius populations. South African Journal of Animal Sciences 35, 152 161.
195. Notter D. (1999) The importance of genetic diversity in livestock populations of the future. Journal of Animal Science 77, 61 9.
196. O'Brien S., Pontius J., Johnson W. Perelman P. (2008) The alpaca enters the genomic era. In : 1st International Workshop on Camelid Gene, pp. 6 9. The Alpaca Research Foundation and The Alpaca Registry Inc.
197. Oddy H., Dalrymple B., McEwan J. et al. (2007) SheepGenomics and the International Sheep Genomics Consortium. Association for the Advancement of Animal Breeding and Genetics. Proceedings 17, 411 417.
198. Ojeda A., Huang L.S., Ren J., Angiolillo A., Cho I.C., Soto H., Lemus-Flores C., Makuza S.M., Folch J.M. Perez-Enciso M. (2008) Selection in the making: a worldwide survey of haplotypic diversity around a causative mutation in porcine IGF2. Genetics 178, 1639 1652.
199. Oka T., Ino Y., Nomura K. et al. (2007) Analysis of mtDNA sequences shows Japanese native chickens have multiple origins. Animal Genetics 38, 287 293.
200. Ollivier L., Alderson L., Gandini G.C. et al. (2005) An assessment of European pig diversity using molecular markers: partitioning of diversity among breeds. Conservation Genetics 6, 729 741.
201. Palma R., Marín J., Spotorno A. Galaz J. (2002) Phylogenetic relationships among South American subspecies of camelids based on sequences of cytochrome b mitochondrial gene. In : Progress in South American Camelids Research. Proceedings of the 3rd European Symposium and SUPREME European Seminar, Goettingen, Germany, 27-29 May 1999 (Ed. by M. Gerken C. Renieri pp. 44 52. Wageningen Academic Publishers
202. Pellecchia M., Negrini R., Colli L. et al. (2007) The mystery of Etruscan origins: novel clues from Bos taurus mitochondrial DNA. Proceedings of the Royal Society of London, Series B: Biological Sciences 274, 1175 1179.
203. Pereira F., Queirós S., Gusmão L., Nijman I.J., Cuppen E., Lenstra J.A., The Econogene Consortium, Davis S.J.M., Nejmeddine F. Amorim A. (2009) Tracing the history of goat pastoralism in North Africa: new clues from mitochondrial and Y chromosome DNA. Molecular Biology and Evolution 26, 2765 2773.
204. Peter C., Bruford M., Perez T., Dalamitra S., Hewitt G. Erhardt G. (2007) Genetic diversity and subdivision of 57 European and Middle-Eastern sheep breeds. Animal Genetics 38, 37 44.
205. Peters J. (1997) The dromedary: ancestry, history of domestication and medical treatment in early historic times. Tierarztl Prax Ausg G Grosstiere Nutztiere 25, 559 565.
206. Peters J. von den Driesch A. (1997) The two-humped camel (Camelus bactrianus): new light on its distribution, management and medical treatment in the past. Journal of Zoology, London 242, 651 679.
207. Potts D.T. (2004) Camel hybridization and the role of Camelus bactrianus in the ancient Near East. Journal of the Economic and Social History of the Orient 47, 143 165.
208. Pritchard J.K., Stephens M. Donnely P. (2000) Inference of population structure using multilocus genotype data. Genetics 155, 945 959.
209. Qi X., Jianlin H., Blench R., Rege J. Hanotte O. (2008) Understanding the yak pastoralism in Central Asian Highlands: genetic evidence for origin, domestication and dispersion of domestic yak. In : Past Human Migrations in East Asia: Matching Archaeology, Linguistics and Genetics (Ed. by A. Sanchez-Mazas, R. Blench, M. Ross, I. Peiros M. Lin pp. 427 442. Routledge, Taylor & Francis Group
210. Ramirez O., Ojeda A., Tomas A. et al. (2009) Integrating Y-chromosome, mitochondrial, and autosomal data to analyze the origin of pig breeds. Molecular Biology and Evolution 26, 2061 2072.
211. Reed K. Chaves L. (2008) Simple sequence repeats for genetic studies of alpaca. Animal Biotechnology 19, 243 309.
212. Rieder S., Bärlocher H., Jörg H., Hagger C. Stranzinger G. (2000) Characterization of Swiss new world camelid breeds using microsatellite markers. Schweizer Archiv für Tierheilkunde 142, 120 125.
213. Rodrigáñez J., Barragán C., Alves E., Gortázar C., Toro M.A. Silió L. (2008) Genetic diversity and allelic richness in Spanish wild and domestic pig population estimated from microsatellite markers. Spanish Journal of Agricultural Research 6, 107 115.
214. Rosenberg N.A., Burke T., Elo K. et al. (2001) Empirical evaluation of genetic clustering methods using multilocus genotypes from 20 chicken breeds. Genetics 159, 699 713.
215. Rosenberg N.A., Pritchard J.K., Weber J.L., Cann H.M., Kidd K.K., Zhivotovsky L.A. Feldman M.W. (2002) Genetic structure of human populations. Science 298, 2381 2385.
216. Rout P., Joshi M., Mandal A., Laloe D., Singh L. Thangaraj K. (2008) Microsatellite-based phylogeny of Indian domestic goats. BMC Genetics 9, 11.
217. Ruan J., Guo Y., Li H., Hu Y., Song F., Huang X., Kristiensen K., Bolund L. Wang J. (2007) PigGIS: pig genomic informatics system. Nucleic Acids Research 35, D654 7.
218. Ruane J. (2000) A framework for prioritizing domestic animal breeds for conservation purposes at the national level: a Norwegian case study. Conservation Biology 14, 1385 1393.
219. Russell G.A., Archibald A.L., Haley C.S. Law A.S. (2003) The pig genetic diversity database and the WWW. Archivos de Zootecnia 52, 165 172.
220. SanCristobal M., Chevalet C., Haley C.S. et al. (2006a) Genetic diversity within and between European pig breeds using microsatellite markers. Animal Genetics 37, 189 198.
221. SanCristobal M., Chevalet C., Peleman J. et al. (2006b) Genetic diversity in European pigs utilizing amplified fragment length polymorphism markers. Animal Genetics 37, 232 238.
222. Santos-Silva F., Ivo R.S., Sousa M.C.O., Carolino M.I., Ginja C. Gama L.T. (2008) Assessing genetic diversity and differentiation in Portuguese coarse-wool sheep breeds with microsatellite markers. Small Ruminant Research 78, 32 40.
223. Sarno R., Franklin W., O'Brien S. Johnson W. (2001) Patterns of mtDNA and microsatellite variation in an island and mainland population of guanacos in southern Chile. Animal Conservation 4, 93 101.
224. Sarno R., Villalba L., Bonacic C., Gonzalez B., Zapata B., MacDonald D., O'Brien S. Johnson W. (2004) Phylogeography and subspecies assessment of vicuñas in Chile and Bolivia utilizing mtDNA and microsatellite markers: implications for vicuña conservation and management. Conservation Genetics 5, 89 102.
225. Scherf B.D. (2000) World Watch List for Domestic Animal Diversity. Food and Agriculture Organization of the United Nations
226. Schmid M., Nanda I., Hoehn H. et al. (2005) Second report on chicken genes and chromosomes 2005. Cytogenetic and Genome Research 109, 415 479.
227. Schmidt C.J., Romanov M., Ryder O., Magrini V., Hickenbotham M., Glasscock J., McGrath S., Mardis E. Stein L.D. (2008) Gallus GBrowse: a unified genomic database for the chicken. Nucleic Acids Research 36, D719 23.
228. Sethi R.K. (2001) Buffalo breeding in India. In : All India Dairy Business Directory: Dairy Yearbook, pp. 264 270. Sadana Publishers and Distributers
229. Simianer H. (2005) Decision making in livestock conservation. Ecological Economics 53, 559 572.
230. Simon D.L. (1990) The global animal genetic data bank. In : FAO Animal production and Health Paper 80, pp. 153 166. FAO
231. Skidmore J., Billah M., Binns M., Short R. Allen W. (1999) Hybridizing Old and New World camelids: Camelus dromedaries × Lama guanicoe. Proceedings of the Royal Society of London, Series B: Biological Sciences 266, 649 656.
232. Stanley H., Kadwell M. Wheeler J. (1994) Molecular evolution of the family Camelidae: a mitochondrial study. Proceedings of the Royal Society of London, Series B: Biological Sciences 256, 1 6.
233. Stock F., Edwards C., Bollongino R., Finlay E., Burger J. Bradley D. (2009) Cytochrome b sequences of ancient cattle and wild ox support phylogenetic complexity in the ancient and modern bovine populations. Animal Genetics 40, 694 700.
234. Sugawara H., Ogasawara O., Okubo K., Gojobori T. Tateno Y. (2008) DDBJ with new system and face. Nucleic Acids Research 36, D22 4.
235. Svensson E. Götherström A. (2008) Temporal fluctuations of Y-chromosomal variation in Bos taurus. Biology Letters 4, 752 754.
236. Svensson E., Anderung C., Baubliene J., Persson P., Malmström H., Smith C., Vretemark M., Daugnora L. Götherström A. (2007) Tracing genetic change over time using nuclear SNPs in ancient and modern cattle. Animal Genetics 38, 378 383.
237. Tadano R., Sekino M., Nishibori M. Tsudzuki M. (2007) Microsatellite marker analysis for the genetic relationships among Japanese long-tailed chicken breeds. Poultry Science 86, 460 469.
238. Tadano R., Nishibori M., Imamura Y., Matsuzaki M., Kinoshita K., Mizutani M., Namikawa T. Tsudzuki M. (2008) High genetic divergence in miniature breeds of Japanese native chickens compared to Red Junglefowl, as revealed by microsatellite analysis. Animal Genetics 39, 71 8.
239. Tanaka K., Yamagata T., Masangkay J., Faruque M., Vu-Binh D., Salundik, Mansjoer S., Kawamoto Y. Namikawa T. (1995) Nucleotide diversity of mitochondrial DNAs between the swamp and the river types of domestic water buffaloes, Bubalus bubalis, based on restriction endonuclease cleavage patterns. Biochemical Genetics 33, 137 148.
240. Tanaka K., Solis C.D., Masangkay J.S., Maeda K., Kawamoto Y. Namikawa T. (1996) Phylogenetic relationship among all living species of the genus Bubalus based on DNA sequences of the cytochrome b gene. Biochemical Genetics 34, 443 452.
241. Tapio I., Tapio M., Grislis Z., Holm L.-E., Jeppsson S., Kantanen J., Miceikiene I., Olsaker I., Viinalass H. Eythorsdottir E. (2005a) Unfolding of population structure in Baltic sheep breeds using microsatellite analysis. Heredity 94, 448 456.
242. Tapio M., Tapio I., Grislis Z., Holm L.E., Jeppsson S., Kantanen J., Miceikiene I., Olsaker I., Viinalass H. Eythorsdottir E. (2005b) Native breeds demonstrate high contributions to the molecular variation in northern European sheep. Molecular Ecology 14, 3951 3963.
243. Tapio I., Värv S., Bennewitz J. et al. (2006a) Prioritization for conservation of northern European cattle breeds based on analysis of microsatellite data. Conservation Biology 20, 1768 1779.
244. Tapio M., Marzanov N., Ozerov M., Cinkulov M., Gonzarenko G., Kiselyova T., Murawski M., Viinalass H. Kantanen J. (2006b) Sheep mitochondrial DNA variation in European, Caucasian, and Central Asian areas. Molecular Biology and Evolution 23, 1776 1783.
245. The Bovine HapMap Consortium, Gibbs R.A., Taylor J.F. et al. (2009) Genome-wide survey of SNP variation uncovers the genetic structure of cattle breeds. Science 324, 528 532.
246. Toro M. Caballero A. (2005) Characterization and conservation of genetic diversity in subdivided populations. Philosophical Transactions of the Royal Society of London, Series B: Biological Sciences 360, 1367 1378.
247. Toro M., Fernández J. Caballero A. (2009) Molecular characterization of breeds and its use in conservation. Livestock Science 120, 174 195.
248. Traoré A., Álvarez I., Tambourá H.H. et al. (2009) Genetic characterisation of Burkina Faso goats using microsatellite polymorphism. Livestock Science 123, 322 328.
249. Troy C.S., MacHugh D.E., Bailey J.F., Magee D.A., Loftus R.T., Cunningham P., Chamberlain A.T., Sykes B.C. Bradley D.G. (2001) Genetic evidence for Near-Eastern origins of European cattle. Nature 410, 1088 1091.
250. Uenishi H., Eguchi-Ogawa T., Shinkai H., Okumura N., Suzuki K., Toki D., Hamasima N. Awata T. (2007) PEDE (Pig EST Data Explorer) has been expanded into Pig Expression Data Explorer, including 10 147 porcine full-length cDNA sequences. Nucleic Acids Research 35, D650 3.
251. Ulbrich F. Fischer H. (1967) The chromosomes of the Asiatic buffalo (Bubalus bubalis) and the African buffalo (Syncerus caffer). Zeitschrift für Tierzüchtung und Züchtungsbiologie 83, 219 223.
252. Ursing B., Slack K. Arnason U. (2000) Subordinal artiodactyl relationships in the light of phylogenetic analysis of 12 mitochondrial protein-coding genes. Zoologica Scripta 29, 83 8.
253. Vijh R., Tantia M., Mishra B. Kumar S. (2007) Genetic diversity and differentiation of dromedarian camel of India. Animal Biotechnology 18, 81 90. (Pubitemid 46571236)
254. Vijh R.K., Tantia M.S., Mishra B. Bharani Kumar S.T. (2008) Genetic relationship and diversity analysis of Indian water buffalo (Bubalus bubalis). Journal of Animal Science 86, 1495 1502.
255. Vila C., Leonard J.A., Götherström A., Marklund S., Sandberg K., Liden K., Wayne R.K. Ellegren H. (2001) Widespread origins of domestic horse lineages. Science 291, 474 477.
256. Visscher P.M., Smith D., Hall S.J.G. Williams J.L. (2001) A viable herd of genetically uniform cattle. Nature 409, 303.
257. Wang J., He X., Ruan J. et al. (2005) ChickVD: a sequence variation database for the chicken genome. Nucleic Acids Research 33, D438 41.
258. Wang Y., Wang Z., Li J., Wang Y. Leung F.C.C. (2007) Database for chicken full-length cDNAs. Physiological Genomics 28, 141 145.
259. Weitzman M.L. (1993) What to preserve? An application of diversity theory to crane conservation. Quarterly Journal of Economy 108, 157 183.
260. West B. Zhou B.-X. (1988) Did chickens go North? New evidence for domestication. Journal of Archaeological Science 15, 515 533.
261. Wheeler D.L., Barrett T., Benson D.A. et al. (2005) Database resources of the National Center for Biotechnology Information. Nucleic Acids Research 33, D39 45.
262. Wheeler J., Chikhi L. Bruford M. (2006) Genetic analysis of the origins of domestic South American camelids. In : Archaeology and Animal Domestication: New Genetic and Archaeological Paradigms (Ed. by M. Zeder pp. 329 341. University of California Press
263. Wiener G. Jianlin H. (2005) The yak. In : Encyclopedia of Animal Science (Ed. by W. Pond A. Bell pp. 898 900. Marcel Dekker, Inc
264. Wiener G., Jianlin H. Ruijun L. (2003) The Yak. Regional Office for Asia and the Pacific of the Food and Agriculture Organization (FAO) of the United Nations
265. Williams J. (2002) CaDBase: genetic diversity in cattle. Available at: http://www.projects.roslin.ac.uk/cdiv/.
266. Wimmers K., Ponsuksili S., Hardge T., Valle-Zarate A., Mathur P.K. Horst P. (2000) Genetic distinctness of African, Asian and South American local chickens. Animal Genetics 31, 159 165.
267. Wong G.K.S., Liu B., Wang J. et al. (2004) A genetic variation map for chicken with 2.8 million single-nucleotide polymorphisms. Nature 432, 717 722.
268. Wood R. Orel V. (2001) Genetic Prehistory in Selective Breeding. Oxford University Press
269. Wu G.-S., Yao Y.-G., Qu K.-X., Ding Z.-L., Li H., Palanichamy M., Duan Z.-Y., Li N., Chen Y.-S. Zhang Y.-P. (2007) Population phylogenomic analysis of mitochondrial DNA in wild boars and domestic pigs revealed multiple domestication events in East Asia. Genome Biology 8, R245.
270. Xuebin Q., Jianlin H., Rege J. Hanotte O. (2002) Y-chromosome specific microsatellite polymorphism in Chinese yak. In : 7th World Congress on Genetics Applied to Livestock Production, pp. 509 512. INRA (Institut National de la Recherche Agronomique)
271. Xuebin Q., Jianlin H., Lkhagva B., Chekarova I., Badamdorj D., Rege J. Hanotte O. (2005) Genetic diversity and differentiation of Mongolian and Russian yak populations. Journal of Animal Breeding and Genetics 122, 117 126.
272. Yang Y.H., Kim K.I., Cothran E.G. Flannery A.R. (2002) Genetic diversity of cheju horses (Equus caballus) determined by using mitochondrial DNA D-loop polymorphism. Biochemical Genetics 40, 175 186.
273. Yang D.Y., Liu L., Chen X. Speller C.F. (2008) Wild or domesticated: DNA analysis of ancient water buffalo remains from north China. Journal of Archaeological Science 35, 2778 2785.
274. Zanetti E., Dalvit C., Marchi M.d., Zotto R.d. Cassandro M. (2007) Genetic characterisation of Italian chicken breeds using a panel of twenty microsatellite markers. Poljoprivreda 13, 197 200.
275. Zeder M.A., Bradely D.G., Emshwiller E. Smith B.D. (2006) Documenting Domestication: New Genetic and Archaeological Paradigms. University of California Press
276. Zeuner F.E. (1963) A History of Domesticate Animals. Hutchinson
277. Zhang G.X., Wang Z.G., Chen W.S. et al. (2007a) Genetic diversity and population structure of indigenous yellow cattle breeds of China using 30 microsatellite markers. Animal Genetics 38, 550 559.
278. Zhang Y., Sun D., Yu Y. Zhang Y. (2007b) Genetic diversity and differentiation of Chinese domestic buffalo based on 30 microsatellite markers. Animal Genetics 38, 569 575.