Molecular genetic analysis of a cattle population to reconstitute the extinct Algarvia breed

Genetics Selection Evolution

Volumn 42, Issue 1, 2010, Pages

  Ginja, Catarina ^a   Penedo, Maria Ct ^a   Sobral, Maria F ^b   Matos, José ^c   Borges, Carla ^c   Neves, Dina ^d   Rangel Figueiredo, Teresa ^e   Cravador, Alfredo ^d  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b Direcção Geral de Veterinária DSPA ^*  (Portugal)

^c L INIA Pálo do Lumiar Unidade de Investigação em Recursos Genéticos   (Portugal)

^d UNIVERSITY OF ALGARVE   (Portugal)

^e UNIVERSITY OF TRÁS OS MONTES AND ALTO DOURO   (Portugal)

Author keywords

[No Author keywords available]

Indexed keywords

CATTLE; CHROMOSOME; CONSERVATION GENETICS; EXTINCTION; GENETIC ANALYSIS; GENETIC MARKER; GENETIC VARIATION; MITOCHONDRIAL DNA; MOLECULAR ANALYSIS; MORPHOLOGY; RECONSTRUCTION; RELATEDNESS; SPECIES CONSERVATION;

ANIMALIA; BOS;

MICROSATELLITE DNA; MITOCHONDRIAL DNA;

ALLELE; ANIMAL; ARTICLE; BREEDING; CATTLE; CLUSTER ANALYSIS; GENETIC VARIABILITY; GENETICS; GENOTYPE; HAPLOTYPE; INBREEDING;

ALLELES; ANIMALS; BREEDING; CATTLE; CLUSTER ANALYSIS; DNA, MITOCHONDRIAL; GENETIC VARIATION; GENOTYPE; HAPLOTYPES; INBREEDING; MICROSATELLITE REPEATS;

EID: 77956409777     PISSN: 0999193X     EISSN: 12979686     Source Type: Journal    
DOI: 10.1186/1297-9686-42-18     Document Type: Article

References (68)

1. World watch list for domestic animal diversity. Scherf BD, Book World watch list for domestic animal diversity Rome: Food and Agriculture Organisation of the United Nations 3 2000
2. Measurement of Domestic Animal Diversity-A review of recent diversity studies. FAO, Book Measurement of Domestic Animal Diversity-A review of recent diversity studies Rome: Food and Agriculture Organisation of the United Nations, Commission on Genetic Resources, Working Group on Animal Genetic Resources 1 2004 38
3. Economic evaluation for conservation of farm animal genetic resources. Roosen J, Fadlaoui A, Bertaglia M, J Anim Breed Genet 2005 122 217 228 10.1111/j.1439-0388.2005.00530.x 16060488 (Pubitemid 41039330)
4. Country Report on Farm Animal Genetic Resources. Gama LT, Carolino N, Costa MS, Matos CP, Book Country Report on Farm Animal Genetic Resources Vale de Santarém: Food and Agriculture Organization of the United Nations 2004 68
5. Recursos genéticos animais e sistemas de exploração tradicionais em Portugal. Matos CAP, Arch Zootec 2000 49 363 383
6. Genetic variability and phylogenetic relationships between ten native cattle breeds from Galicia and the north of Portugal. Fernández A, Viana JL, Iglesias A, Sanchez L, Arch Zootec 1998 47 61 71 (Pubitemid 128123976)
7. Genetic characterization of southwestern European bovine breeds: a historical and biogeographical reassessment with a set of 16 microsatellites. Beja-Pereira A, Alexandrino P, Bessa I, Carretero Y, Dunner S, Ferrand N, Jordana J, Laloe D, Moazami-Goudarzi K, Sanchez A, Canon J, J Hered 2003 94 243 250 10.1093/jhered/esg055 12816965 (Pubitemid 36828840)
8. Genetic diversity measures of local European beef cattle breeds for conservation purposes. Cãon J, Alexandrino P, Bessa I, Carleos C, Carretero Y, Dunner S, Ferrand N, Garcia D, Jordana J, Lalo D, Pereira A, Sanchez A, Moazami-Goudarzi K, Genet Sel Evol 2001 33 311 332 10.1186/1297-9686-33-3-311 11403750 (Pubitemid 32591814)
9. Microsatellite diversity suggests different histories for Mediterranean and Northern European cattle populations. Cymbron T, Freeman AR, Isabel Malheiro M, Vigne JD, Bradley DG, Proc Biol Sci 2005 272 1837 1843 10.1098/rspb.2005. 3138 16096097 (Pubitemid 41414665)
10. Identificação de raças bovinas Portuguesas atravès da utilização de marcadores moleculares. Ginja C, Universidade de Trás-os-Montes e Alto Douro 2002
11. Contributions of Portuguese cattle breeds to genetic diversity using marker-estimated kinships. Mateus JC, Eding H, Penedo MC, Rangel-Figueiredo MT, Anim Genet 2004 35 305 313 10.1111/j.1365-2052.2004.01168.x 15265070 (Pubitemid 39040171)
12. Genetic diversity and differentiation in Portuguese cattle breeds using microsatellites. Mateus JC, Penedo MC, Alves VC, Ramos M, Rangel-Figueiredo T, Anim Genet 2004 35 106 113 10.1111/j.1365-2052.2004.01089.x 15025569 (Pubitemid 38458984)
13. Mitochondrial sequence variation suggests an African influence in Portuguese cattle. Cymbron T, Loftus RT, Malheiro MI, Bradley DG, Proc R Soc Lond B Biol Sci 1999 266 597 603 10.1098/rspb.1999.0678 (Pubitemid 29134767)
14. Origins and genetic diversity of New World Creole cattle: inferences from mitochondrial and Y chromosome polymorphisms. Ginja C, Penedo MC, Melucci L, Quiroz J, Martinez Lopez OR, Revidatti MA, Martinez-Martinez A, Delgado JV, Gama LT, Anim Genet 2010 41 128 141 10.1111/j.1365-2052.2009.01976.x 19817725
15. Y chromosome haplotype analysis in Portuguese cattle breeds using SNPs and STRs. Ginja C, Gama LT, Penedo MCT, J Hered 2009 100 148 157 10.1093/jhered/esn080 18832111
16. Mitochondrial genomes of extinct aurochs survive in domestic cattle. Achilli A, Olivieri A, Pellecchia M, Uboldi C, Colli L, Al-Zahery N, Accetturo M, Pala M, Kashani BH, Perego UA, Battaglia V, Fornarino S, Kalamati J, Houshmand M, Negrini R, Semino O, Richards M, Macaulay V, Ferretti L, Bandelt H-J, Ajmone-Marsan P, Torroni A, Curr Biol 2008 18 157 158 10.1016/j.cub.2008. 01.019 (Pubitemid 351258346)
17. Resposta ao Questionário dirigido aos proprietários rurais e lavradores de todos os concelhos do reino. Baganha DA, Book Resposta ao Questionário dirigido aos proprietários rurais e lavradores de todos os concelhos do reino 1868
18. As raças bovinas em Portugal. Sua origem. Cordeiro JP, OMédico Veterinário 1986 29 39
19. Os escritos de Silvestre Bernardo Lima. Bovídeos e Suídeos. Lima BS, Boletim do Ministério da Agricultura 1919 I 1 266
20. Recenseamento Geral de Gados no Continente do Reino de Portugal em 1870. Lima S, Lisboa: Imprensa Nacional 1 1873
21. Les animaux agricoles. Nogueira JVP, Le Portugal au Point de Vue Agricole Lisbonne: Imprimerie Nationale 1900 310
22. A raça bovina Algarvia. Pereira MT, Boletim Pecuário da Direcção Geral dos Serviços Pecuários 1960 1 137 189
23. Bovinos. Vale JM, Gado Bissulco:suinos bovinos, arietinos caprinos Lisboa: Livraria Sá da Costa 1949 81 168
24. Genus Bos: Cattle breeds of the world. Felius M, New Jersey: Merck & Co. Inc 1 1985
25. Raça bovina Algarvia. Inquérito para a sua caracterização e seu sistema de exploração. Rosado J, Almeida JM, Gouveia JM, Sobral M, Lobo JMS, Bovinos em Portugal Lisboa: Direcção Geral dos Serviços Veterinários, Rodrigues A, 1981 217 222
26. Classificação e caracterização morfolágica de raças bovinas autáctones nacionais utilizando a taxonomia numérica. Sobral MF, Cravador A, Navas D, Roberto C, C R, Lima MB, Rev Port Zootec 2001 2 123 137
27. Identification of descendants of an extinct bovine population from the Algarve region of Portugal using numerical taxonomy analysis of morphological traits. Sobral MF, Roberto C, Navas D, Palmilha I, Lima MB, Cravador A, J Anim Breed Genet 2009 126 319 326 10.1111/j.1439-0388.2008.00787.x 19630883
28. STRand Nucleic Acids Analysis Software. Hughes SS, 1.2.90 2000 11052354
29. Contributions of Portuguese cattle breeds to genetic diversity using marker-estimated kinships. Mateus JC, Eding H, Penedo MC, Rangel-Figueiredo MT, Anim Genet 2004 35 305 313 10.1111/j.1365-2052.2004.01168.x 15265070 (Pubitemid 39040171)
30. Genalex 6: genetic analysis in Excel. Population genetic software for teaching and research. Peakall R, Smouse PE, Mol Ecol Notes 2006 6 288 295 10.1111/j.1471-8286.2005.01155.x (Pubitemid 43373825)
31. GENEPOP: population genetics software for exact tests and ecumenicism. Raymond M, Rousset F, J Hered 1995 86 248 249
32. GENETIX: logiciel sous Windows TM pour la génétique des populations. Belkhir K, Borsa P, Chikhi L, Raufaste N, Bonhomme F, Laboratoire Genome Populations,Interactions CNRS, Université de Montpellier II 4.02 1996 2004
33. Analysis of gene diversity in subdivided populations. Nei M, Proc Natl Acad Sci USA 1973 70 3321 3323 10.1073/pnas.70.12.3321 4519626
34. Estimating F-statistics for the analysis of population structure. Weir BS, Cockerham CC, Evolution 1984 38 1358 1370 10.2307/2408641 (Pubitemid 16277759)
35. FSTAT a program to estimate and test gene diversities and fixation indices. Goudet J, Updated from Goudet 1995 2.9.3 2001
36. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Saitou N, Nei M, Mol Biol Evol 1987 4 406 425 3447015
37. Accuracy of estimated phylogenetic trees from molecular data. Nei M, Tajima F, Tateno Y, J Mol Evol 1983 19 153 170 10.1007/BF02300753 6571220 (Pubitemid 13042712)
38. POPULATIONS 1.2.28. Langella O, CNRS UPR9034 1999
39. TREEVIEW: an application to display phylogenetic trees on personal computers. Page RD, Comput Appl Biosci 1996 12 357 358 8902363
40. STRUCTURE software. Users Manual. Pritchard JK, Wen W, 2 2004
41. Inference of population structure using multilocus genotype data: linked loci and correlated allele frequencies. Falush D, Stephens M, Pritchard JK, Genetics 2003 164 1567 1587 12930761 (Pubitemid 37102217)
42. Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Evanno G, Regnaut S, Goudet J, Mol Ecol 2005 14 2611 2620 10.1111/j.1365-294X.2005.02553.x 15969739 (Pubitemid 40886055)
43. GENECLASS2: a software for genetic assignment and first-generation migrant detection. Piry S, Alapetite A, Cornuet JM, Paetkau D, Baudouin L, Estoup A, J Hered 2004 95 536 539 10.1093/jhered/esh074 15475402 (Pubitemid 39383165)
44. Detecting immigration by using multilocus genotypes. Rannala B, Mountain JL, Proc Natl Acad Sci USA 1997 94 9197 9201 10.1073/pnas.94.17.9197 9256459 (Pubitemid 27357806)
45. Genetic assignment methods for the direct real-time estimation of migration rate: a simulation-based exploration of accuracy and power. Paetkau D, Slade R, Burden M, Estoup A, Mol Ecol 2004 13 55 65 10.1046/j.1365-294X.2004. 02008.x 14653788 (Pubitemid 38106473)
46. New methods employing multilocus genotypes to select or exclude populations as origins of individuals. Cornuet JM, Piry S, Luikart G, Estoup A, Solignac M, Genetics 1999 153 1989 2000 10581301
47. Aggregate diversity: new approach combining within- and between-breed genetic diversity. Ollivier L, Foulley JL, Livest Prod Sci 2005 95 247 254 10.1016/j.livprodsci.2005.01.005 (Pubitemid 41129129)
48. METAPOP-A software for the management and analysis of subdivided populations in conservation programs. Perez-Figueroa A, Saura M, Fernández J, Toro MA, Caballero A, Conserv Genet 2009 10 1097 1099 10.1007/s10592-008-9718-7
49. Analysis of genetic diversity for the management of conserved subdivided populations. Caballero A, Toro MA, Conserv Genet 2002 3 289 299 10.1023/A:1019956205473
50. Origins and genetic diversity of New World Creole cattle: inferences from mitochondrial and Y chromosome polymorphisms. Ginja C, Penedo MC, Melucci L, Quiroz J, Matrinez Lopez OR, Revidatti MA, Martinez AM, Delgado JV, Gama L, Anim Genet 2010 41 128 141 10.1111/j.1365-2052.2009.01976.x 19817725
51. Complete sequence of bovine mitochondrial DNA. Conserved features of the mammalian mitochondrial genome. Anderson S, de Bruijn MH, Coulson AR, Eperon IC, Sanger F, Young IG, J Mol Biol 1982 156 683 717 10.1016/0022-2836(82)90137-1 7120390 (Pubitemid 12055132)
52. Arlequin ver. 2.000: A software for population genetics data analysis. Schneider S, Roessli D, Excoffier L, Genetics and Biometry Laboratory, University of Geneva 2000
53. Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees. Tamura K, Nei M, Mol Biol Evol 1993 10 512 526 8336541 (Pubitemid 23157236)
54. Median-joining networks for inferring intraspecific phylogenies. Bandelt HJ, Forster P, Rohl A, Mol Biol Evol 1999 16 37 48 10331250 (Pubitemid 29024937)
55. Detecting wildlife poaching: Identifying the origin of individuals with Bayesian Assignment tests and multilocus genotypes. Manel S, Berthier P, Luikart G, Conserv Biol 2002 16 650 659 10.1046/j.1523-1739.2002.00576.x (Pubitemid 34592919)
56. Predominant African-derived mtDNA in Caribbean and Brazilian Creole cattle is also found in Spanish cattle (Bos taurus). Miretti MM, Dunner S, Naves M, Contel EP, Ferro JA, J Hered 2004 95 450 453 10.1093/jhered/esh070 15388773 (Pubitemid 39304782)
57. Conservation genetics of UK livestock: from molecules to management. Bruford MW, Farm animal genetic resources Nottingham: Nottingham University Press, Simm G, Villanueva B, Townsend S, 2004 151 169
58. Prioritization for conservation of northern European cattle breeds based on analysis of microsatellite data. Tapio I, Varv S, Bennewitz J, Maleviciute J, Fimland E, Grislis Z, Meuwissen TH, Miceikiene I, Olsaker I, Viinalass H, Vilkki J, Kantanen J, Conserv Biol 2006 20 1768 1779 10.1111/j.1523-1739.2006. 00488.x 17181812 (Pubitemid 44912632)
59. A novel method for the estimation of the relative importance of breeds in order to conserve the total genetic variance. Bennewitz J, Meuwissen TH, Genet Sel Evol 2005 37 315 337 10.1186/1297-9686-37-4-315 15823238 (Pubitemid 40589282)
60. Heat stress intensification in the Mediterranean climate change hotspot. Diffenbaugh NS, Pal JS, Giorgi F, Gao X, Geophys Res Lett 2007 34 doi:10.1029/2007GL030000 10.1029/2007GL030000 (Pubitemid 47272412)
61. Management of genetic diversity of subdivided populations in conservation programmes. Caballero A, Rodriguez-Ramilo ST, Avila V, Fernandez J, Conserv Genet 2010 11 409 419 10.1007/s10592-009-0020-0
62. Population genetic structure of and inbreeding in an insular cattle breed the Jersey and its implications for genetic resource management. Chikhi L, Goossens B, Treanor A, Bruford MW, Heredity 2004 92 396 401 10.1038/sj.hdy. 6800433 15014423 (Pubitemid 38673705)
63. Prioritization for conservation of northern European cattle breeds based on analysis of microsatellite data. Tapio I, Varv S, Bennewitz J, Maleviciute J, Fimland E, Grislis Z, Meuwissen TH, Miceikiene I, Olsaker I, Viinalass H, Vilkki J, Kantanen J, Conserv Biol 2006 20 1768 1779 10.1111/j.1523-1739.2006. 00488.x 17181812 (Pubitemid 44912632)
64. Characterization and conservation of genetic diversity in subdivided populations. Toro MA, Caballero A, Philos Trans R Soc Lond B Biol Sci 2005 360 1367 1378 10.1098/rstb.2005.1680 16048780 (Pubitemid 43138540)
65. The population genetic effects of ancestry and admixture in a subdivided cattle breed. Bray TC, Chikhi L, Sheppy AJ, Bruford MW, Anim Genet 2009 40 393 400 10.1111/j.1365-2052.2009.01850.x 19397525
66. Analysis of genetic diversity and conservation priorities in Iberian pigs based on microsatellite markers. Fabuel E, Barragan C, Silio L, Rodriguez MC, Toro MA, Heredity 2004 93 104 113 10.1038/sj.hdy.6800488 15150539 (Pubitemid 38965204)
67. Genetic and morphometric characterization of a local Vietnamese swamp buffalo population. Berthouly C, Rognon X, Nhu Van T, Berthouly A, Thanh Hoang H, Bed'Hom B, Laloe D, Vu Chi C, Verrier E, Maillard JC, J Anim Breed Genet 127 74 84 10.1111/j.1439-0388.2009.00806.x 20074189
68. Notas sobre Portugal-Industria Pecuária. Tierno J, Lisboa: Imprensa Nacional 1 1908