Genetic structure of European sheep breeds

Heredity

Volumn 99, Issue 6, 2007, Pages 620-631

  Lawson Handley, L J ^a,c   Byrne, K ^b   Santucci, F ^a,d   Townsend, S ^b   Taylor, M ^a,e   Bruford, M W ^b,f   Hewitt, G M ^a  

^a UNIVERSITY OF EAST ANGLIA   (United Kingdom)

^b INSTITUTE OF ZOOLOGY   (United Kingdom)

^c UNIVERSITY OF CAMBRIDGE   (United Kingdom)

^d UNIVERSITY OF PERUGIA   (Italy)

^e BANGOR UNIVERSITY   (United Kingdom)

^f CARDIFF UNIVERSITY   (United Kingdom)

Author keywords

Bayesian cluster analysis; Domestic breeds; Genetic diversity; Heterozygote deficit; Livestock conservation; Null alleles

Indexed keywords

MICROSATELLITE DNA;

BAYESIAN ANALYSIS; BREEDING; CLUSTER ANALYSIS; DIVERGENCE; GENETIC DIFFERENTIATION; GENETIC DRIFT; GENETIC MARKER; GENETIC STRUCTURE; GEOGRAPHICAL DISTRIBUTION; HETEROZYGOSITY; LIVESTOCK; SHEEP; SPECIES CONSERVATION;

ANIMAL; ARTICLE; CLASSIFICATION; EUROPE; GENETIC VARIABILITY; GENETICS; SHEEP; SPECIES DIFFERENCE;

ANIMALS; EUROPE; MICROSATELLITE REPEATS; SHEEP, DOMESTIC; SPECIES SPECIFICITY; VARIATION (GENETICS);

OVIS ARIES;

EID: 36349022023     PISSN: 0018067X     EISSN: 13652540     Source Type: Journal    
DOI: 10.1038/sj.hdy.6801039     Document Type: Article

References (76)

1. Aberle KS, Hamann H, Drogemuller 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. Anim Genet 35: 270-277.
2. Arevalo E, Holder D, Derr JN, Bhebe E, Linn RA, Taylor JF et al. (1994). Caprine microsatellite dinucleotide repeat polymorphisms at the SRCRSP1, SRCRSP2, SRCRSP3, SRCRSP4 and SRCRSP5 loci. Anim Genet 25: 202.
3. Arranz J, Bayon Y, Primitivo FS (1998). Genetic relationships among Spanish sheep using microsatellites. Anim Genet 29: 435-440.
4. Bhebhe E, Kogi J, Holder D, Arevalo E, Derr JN, Linn RA et al. (1994). Caprine microsatellite dinucleotide repeat polymorphisms at the SRCRSP6, SRCRSP7, SRCRSP8, SRCRSP9 and SRCRSP10 loci. Anim Genet 25: 203.
5. Bishop MD, Kappes SM, Keele JW, Stone RT, Sunden S, Hawkins G et al. (1994). A genetic linkage map for cattle. Genetics 136: 619-639.
6. Brezinsky L, Kemp SJ, Teale AJ (1993). Five polymorphic bovine microsatellites (ILSTS010-014). Anim Genet 24: 75-76.
7. Bruford MW (2004). Conservation genetics of UK livestock: from molecules to management. In: Simm G, Villanueva B, Townsend S (eds). Farm Animal Genetic Resources. Nottingham University Press: Nottingham, UK, pp 151-169.
8. Bruford MW, Bradley DG, Luikart G (2003). DNA markers reveal the complexity of livestock domestication. Nat Rev Genet 4: 900-910.
9. Bruford MW, Townsend SJ (2006). Case studies in the genetics of animal domestication: sheep. In: Zeder M, Decker-Walters D, Bradley D, Smith BD (eds). Documenting Domestication: New Genetic and Archaeological Paradigms. California University Press: Berkeley, CA, USA.
10. Buchanan FC, Swarbrick PA, Crawford AM (1992). Ovine dinucleotide repeat polymorphism at the MAF65 locus. Anim Genet 23: 85.
11. Buchanan FC, Crawford AM (1992a). Ovine dinucleotide repeat polymorphism at the Maf70 locus. Anim Genet 23: 185.
12. Buchanan FC, Crawford AM (1992b). Ovine dinucleotide repeat polymorphism at the Maf209 locus. Anim Genet 23: 183.
13. Buchanan FC, Crawford AM (1992c). Ovine dinucleotide repeat polymorphism at the Maf214 Locus. Anim Genet 23: 394.
14. Buchanan FC, Crawford AM (1993). Ovine microsatellites at the OarFCB11, OarFCB128, OarFCB193, OarFCB266 and OarFCB304 loci. Anim Genet 24: 145.
15. Buchanan FC, Galloway S, Crawford AM (1994). Ovine microsatellites at the OarFCB5, OarFCB19, OarFCB20, OarFCB48, OarFCB129, and OarFCB226 loci. Anim Genet 25: 60.
16. Calvo JH, Bouzada JA, Jurado JJ, Serrano M (2006). Genetic substructure of the Spanish Manchega sheep breed. Small Rumin Res 64: 116-125.
17. Cañon J, Alexandrino P, Bessa I, Carleos C, Carretero Y, Dunner S et al. (2001). Genetic diversity measures of local European beef cattle breeds for conservation purposes. Genet Sel Evol 33: 311-332.
18. Cañon J, Checa ML, Carleos C, Vega-Pla JL, Vallejo M, Dunner S (2000). The genetic structure of Spanish Celtic horse breeds inferred from microsatellite data. Anim Genet 31: 39-48.
19. Cañon J, Garcia D, Garcia-Atance MA, Obexer-Ruff G, Lenstra JA, Ajmone-Marsan P et al. (2006). Geographical partitioning of goat diversity in Europe and the Middle East. Anim Genet 37: 327-334.
20. Chakraborty R, De Andrade M, Daiger SP, Budowle B (1992). Apparent heterozygote deficiencies observed in DNA typing data and their implications in forensic applications. Ann Hum Genet 56: 45-57.
21. Chapuis M-P, Estoup A (2007). Microsatellite null alleles and estimation of population differentiation. Mol Biol Evol 24: 621-631.
22. Coltman DW, Pilkington JG, Pemberton JM (2003). Fine-scale genetic structure in a free-living ungulate population. Mol Ecol 12: 733-742.
23. Coltman DW, Pilkington JG, Smith JA, Pemberton JM (1999). Parasite-mediated selection against inbred Soay sheep in a free-living, island population. Evolution 53: 1259-1267.
24. Crawford A, Dodds K, Ede A, Pierson CA, Montgomery GW, Garmonsway HG et al. (1995). An autosomal genetic linkage map of the sheep genome. Genetics 140: 703-724.
25. Dakin EE, Avise JC (2004). Microsatellite null alleles in parentage analysis. Heredity 93: 504-509.
26. Dempster AP, Laird NM, Rubin DB (1977). Maximum like-lihood from incomplete data via the EM algorithm. J R Stat Soc B 39: 1-38.
27. Diez-Tascon C, Littlejohn RP, Almeida PAR, Crawford AM (2000). Genetic variation within the Merino sheep breed: analysis of closely related populations using microsatellites. Anim Genet 31: 243-251.
28. El Mousadik A, Petit RJ (1996). High level of genetic differentiation for allelic richness among populations of the argan tree Argania spinosa (L.) skeels endemic to Morocco. Theor Appl Genet 92: 832-839.
29. Excoffier L, Smouse PE, Quattro JM (1992). Analysis of molecular variance inferred from metric distances among DNA haplotypes: application to human mitochondrial DNA restriction data. Genetics 131: 479-491.
30. FAO (2000). Domestic Animal Diversity Information System (DAD-IS 2.0):http://www.fao.org/dad-is/.
31. Goudet J (2000). FSTAT, a programme to estimate and test gene diversities and fixation indices (version 2.9.1). Available from http://www.unil.ch/izea/ softwares/fstat.html (updated from Goudet 1995).
32. Guo J, Du LX, Ma YH, Guan WJ, Li HB, Zhao QJ et al. (2005). A novel maternal lineage revealed in sheep (Ovis aries). Anim Genet 36: 331-336.
33. Guo S, Thompson EA (1992). Performing the exact test of Hardy-Weinberg proportion for multiple alleles. Biometrics 48: 361-372.
34. 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. Proc R Soc London B 269: 893-904.
35. Hiendleder S, Mainz K, Plante Y, Lewalski H (1998). Analysis of mitochondrial DNA indicates that domestic sheep are derived from two different ancestral maternal sources: no evidence for contributions from Urial and Argali sheep. J Hered 89: 113-120.
36. Hoelzel AR, Dover G (1991). Molecular Genetic Ecology. Information Press: Oxford.
37. Katanen J, Olsaker I, Holm LE, Lien S, Vilkki J, Brusgaard K et al. (2000). Genetic diversity and population structure of 20 north European cattle breeds. J Hered 91: 446-457.
38. Kemp S, Hishida O, Wambugu J, Rink A, Longeri ML, Ma RZ et al. (1995). A panel of polymorphic bovine, ovine and caprine microsatellite markers. Anim Genet 26: 299-306.
39. Kim KS, Yeo JS, Choi CB (2002). Genetic diversity of north-east Asian cattle based on microsatellite data. Anim Genet 33: 201-204.
40. MacHugh D, Loftus RT, Cunningham P, Bradley DG (1998). Genetic structure of seven European cattle breeds assessed using 20 microsatellite markers. Anim Genet 29: 333-340.
41. Martín-Burriel I, Garcia-Muro E, Zargoza P (1999). Genetic diversity analysis of six Spanish native cattle breeds using microsatellites. Anim Genet 30: 177-182.
42. Martinez AM, Delgado JV, Rodero A, Vega-Pla JL (2000). Genetic structure of the Iberian pig breed using microsatellites. Anim Genet 31: 295-301.
43. Mason I (1967). Sheep Breeds of the Mediterranean. CAB: Slough, UK.
44. Mateus JC, Penedo MCT, Alves VC, Ramos M, Rangel-Figueiredo T (2004). Genetic diversity and differentiation in Portuguese cattle breeds using microsatellites. Anim Genet 35: 106-113.
45. Mendelsohn R (2003). The challenge of conserving indigenous domesticated animals. Ecol Econ 45: 501-510.
46. Paetkau D, Strobeck C (1995). The molecular basis and evolutionary history of a microsatellite null allele in bears. Mol Ecol 4: 519-520.
47. Pariset L, Savarese MC, Cappuccio I, Valentini A (2003). Use of microsatellites for genetic variation and inbreeding analysis in Sarda sheep flocks of central Italy. J Anim Breed Genet 120: 425-432.
48. Pedrosa S, Uzun M, Arranz JJ, Gutierrez-Gill B, Primitivo FS, Bayon Y (2005). Evidence of three maternal lineages in near eastern sheep supporting multiple domestication events. Proc R Soc London B 272: 2211-2217.
49. Peter C, Bruford MW, Perez T, Dalamitra S, Hewitt GM, Erhardt G, The Econogene Consortium (2007). Genetic diversity and subdivision of 57 European and Middle-Eastern sheep breeds. Anim Genet 38: 37-44.
50. Peter C, Prinzenberg EM, Erhardt G, The Econogene Consortium (2005). Null allele at the OarAE129 locus and corresponding allele frequencies in German sheep breeds. Anim Genet 36: 92.
51. Pritchard JK, Stephens M, Donnelly P (2000). Inference of population structure using multilocus genotype data. Genetics 155: 945-959.
52. Raymond M, Rousset F (1995). GENEPOP (version 1.2) population genetics software for exact tests and ecumenicism. J Hered 86: 248-249.
53. Rege JEO, Gibson JP (2003). Animal genetic resources and economic development: issues in relation to economic valuation. Ecol Econ 45: 319-330.
54. Rosenberg NA (2004). DISTRUCT: a program for the graphical display of population structure. Mol Ecol Notes 4: 137-138.
55. Rousset F, Raymond M (1995). Testing heterozygote excess and deficiency. Genetics 140: 1413-1419.
56. Ryder M (1981). Sheep. In: Mason I (ed). Evolution of Domesticated Animals. Longman: London and New York, pp 63-85.
57. Sage RD, Wolff JO (1986). Pleistocene glaciations, fluctuating ranges, and low genetic-variability in a large mammal (Ovis dalli). Evolution 40: 1092-1095.
58. Saitbekova N, Gaillard C, Obexer-Ruff G, Dolf G (1999). Genetic diversity in Swiss goat breeds based on microsatellite analysis. Anim Genet 30: 36-41.
59. Sambrook J, Fritsch EF, Maniatis T (1989). Molecular Cloning: a Laboratory Manual. Cold Spring Harbor Laboratory Press: Cold Spring Harbor, NY.
60. Santucci F, Ibrahim KM, Bruzzone A, Hewitt GM (2007). Selection on MHC-linked microsatellite loci in sheep populations. Heredity [E-pub ahead of print, 23 July 2007; http://dx.doi.org/10.1038/sj.hdy.6801006].
61. Schneider S, Roessli D, Excoffier L (2000). ARLEQUIN ver. 2.000: a Software for Population Genetic Data Analysis. Genetics and Biometry Laboratory, University of Geneva: Switzerland.
62. Scott P, Densmore LL (1991). Mitochondrial DNA isolation. In: Hoelzel AR (ed). Molecular Genetic Analysis of Populations: a Practical Approach. IRL Press: Oxford, UK, pp 29-58.
63. Signorello G, Pappalardo G (2003). Domestic animal biodiversity conservation: a case study of rural development plans in the European Union. Ecol Econ 45: 487-499.
64. Slatkin M (1995). A measure of population subdivision based on microsatellite allele frequencies. Genetics 139: 457-462.
65. Steffen P, Eggen A, Dietz A, Womack JE, Stranzinger G, Fries R (1993). Isolation and mapping of polymorphic microsatellites in cattle. Anim Genet 24: 121-124.
66. Tapio M, Miceikiene I, Vilkki J, Kantanen J (2003). Comparison of microsatellite and blood protein diversity in sheep: inconsistencies in fragmented breeds. Mol Ecol 12:2045-2056.
67. Tapio M, Tapio I, Grislis Z, Holm LE, Jeppsson S, Kantanen J et al. (2005). Native breeds demonstrate high contributions to the molecular variation in northern European sheep. Mol Ecol 14: 3951-3963.
68. Troy CS, MacHugh DE, Bailey JF, Magee DA, Loftus RT, Cunningham P et al. (2001). Genetic evidence for near-eastern origins of European cattle. Nature 410: 1088-1091.
69. Vaiman D, Mercier D, Moazami-Goudarzi K, Eggen A, Ciampolini R, Lepingle A et al. (1994). A set of 99 cattle microsatellites: characterisation, synteny mapping, and polymorphism. Mamm Genom 5: 288-297.
70. Walsh P, Metzger DA, Higuchi R (1991). Chelex 100 as a medium for simple extraction of DNA for PCR-based typing from forensic material. Biotechniques 10: 506-513.
71. Weir BS, Cockerham CC (1984). Estimating F-statistics for the analysis of population structure. Evolution 38: 1358-1370.
72. Weitzman ML (1992). On diversity. Quart J Econ CVII: 363-405.
73. Whittaker DG, Osterman SD, Boyce WM (2004). Genetic variability of reintroduced California bighorn sheep in Oregon. J Wildlife Manage 68: 850-859.
74. Wiener P, Burton D, Williams JL (2004). Breed relationships and definition in British cattle: a genetic analysis. Heredity 93: 597-602.
75. Wright S (1951). The genetic structure of populations. Ann Eugen 15: 323-354.
76. Wright S (1977). Evolution and the Genetics of Populations. Vol. 3: Experimental Results and Evolutionary Deductions. University of Chicago Press: Chicago.