Genomic scan of selective sweeps in thin and fat tail sheep breeds for identifying of candidate regions associated with fat deposition

BMC Genetics

Volumn 13, Issue , 2012, Pages

  Moradi, Mohammad Hossein ^a   Nejati Javaremi, Ardeshir ^a   Moradi Shahrbabak, Mohammad ^a   Dodds, Ken G ^b   McEwan, John C ^b  

^a UNIVERSITY OF TEHRAN   (Iran)

^b INVERMAY AGRICULTURAL CENTRE   (New Zealand)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; BEEF; BREED; BREED DIFFERENCE; CHROMOSOME 5; CHROMOSOME 7; DAIRY CATTLE; DOMESTICATION; FAT TAIL SHEEP; GENE IDENTIFICATION; GENE LOCATION; GENE MAPPING; GENE MUTATION; HAPLOTYPE MAP; HOMOZYGOSITY; IRAN; LIPID STORAGE; MATHEMATICAL MODEL; NONHUMAN; QUANTITATIVE TRAIT LOCUS; SHEEP; SINGLE NUCLEOTIDE POLYMORPHISM; THIN TAIL SHEEP; X CHROMOSOME; ADIPOSE TISSUE; ANIMAL; ANIMAL DISEASE; BREEDING; CHROMOSOME MAP; GENETIC SELECTION; GENETICS; GENOTYPE; TAIL;

ANIMALIA; BOS; OVIS; OVIS ARIES;

ADIPOSE TISSUE; ANIMALS; BREEDING; CHROMOSOME MAPPING; GENOTYPE; POLYMORPHISM, SINGLE NUCLEOTIDE; QUANTITATIVE TRAIT LOCI; SELECTION, GENETIC; SHEEP, DOMESTIC; TAIL;

EID: 84857348874     PISSN: None     EISSN: 14712156     Source Type: Journal    
DOI: 10.1186/1471-2156-13-10     Document Type: Article

References (75)

1. Chessa B, Pereira F, Arnaud F, Amorim A, Goyache F, Mainland I, Kao RR, Pemberton JM, Beraldi D, Stear MJ, et al. Revealing the history of Sheep domestication using retrovirus integrations. Science 2009, 324(5926):532-536. 10.1126/science.1170587, 3145132, 19390051.
2. Meadows JRS, Cemal I, Karaca O, Gootwine E, Kijas JW. Five Ovine mitochondrial lineages identified from Sheep breeds of the Near East. Genetics 2007, 175(3):1371-1379. 1840082, 17194773.
3. Ryder ML. Sheep and Man 1983, 17-92. London: Duckworth press.
4. Handley LJL, Byrne K, Santucci F, Townsend S, Taylor M, Bruford MW, Hewitt GM. Genetic structure of European sheep breeds. Heredity 2007, 99:620-631. 10.1038/sj.hdy.6801039, 17700634.
5. Zeder MA. Animal domestication in the Zagros: a review of past and current research. Pale'orient 1999, 25:11-26.
6. Kijas JW, Townley D, Dalrymple BP, Heaton MP, Maddox JF, McGrath A, Wilson P, Ingersoll RG, McCulloch R, McWilliam S, Tang D, McEwan J, et al. A Genome Wide Survey of SNP Variation Reveals the Genetic Structure of Sheep Breeds. PLoS ONE 2009, 4(3):e4668. 10.1371/journal.pone.0004668, 2652362, 19270757.
7. Davidson A. The Oxford Companion to Food. 2006, 293-294. Oxford University Press, Tom Jaine, 2.
8. Ryder M. Evolution of domesticated animals 1981, 63-85. Longman: London and New York.
9. Ermias E, Yami A, Rege JEO. Fat deposition in tropical sheep as adaptive attribute to periodic feed fluctuation. J Anim Breed Genet 2002, 119:235-246.
10. Gokdal O, Ulker H, Karakus F, Cengiz F, Temur C, Handil H. Growth, feedlot performance and carcass characteristics of Karakas and crossbred lambs (F1) (Ile de France × Akkaraman (G1) × Karakas) under rural farm conditions in Turkey. South African Journal of Animal Science 2004, 34(4):223-232.
11. Kashan NEJ, Manafi-Azar GH, Afzalzadeh A, Salehi A. Growth performance and carcass quality of fattening lambs from fat-tailed and tailed sheep breeds. Small Ruminant Research 2005, 60:267-271.
12. Nejati-Javaremi A, Izadi F, Rahmati G, Moradi M. Selection in fat-tailed sheep based on two traits of fat-tail and body weight versus single-trait total body weight. Int J Agri Biol 2007, 9(4):645-648.
13. Güney O. Commercial crossbreeding between Ile-de-France, Rambouillet, Chios and local fat-tail Awassi for market lamb production. Small Ruminant Research 1990, 3(6):449-456.
14. Farid A. Slaughter and carcass characteristics of three fat-tailed sheep breeds and their crosses with Corriedale and Targhee rams. Small Ruminant Research 1991, 5(3):255-271.
15. Momani-Shaker M, Abdullah AY, Kridli RT, Blaha J, Sada I, Sovjak R. Fattening performance and carcass value of Awassi ram lambs, F1 crossbreds of Romanov × Awassi and Charollais × Awassi in Jordan. Czech J Anim Sci 2002, 47(10):429-438.
16. Unal N, Akcapinar H, Aytac M, Atasoy F. Fattening performance and carcass traits in crossbred ram lambs. Medycyna Wet 2006, 62(2):401-404.
17. Khaldari M, Kashan NEJ, Afzalzadeh A, Salehi A. Growth and carcass characteristics of crossbred progeny from lean tailed and fat tailed sheep breeds. South African Journal of Animal Science 2007, 37(1):51-56.
18. Marai IFM, Daader AH, Bahgat LB. Performance traits of purebred Ossimi and Rahmani lambs and their crosses with Finnsheep born under two accelerated mating systems. Arch Tierz 2009, 52:497-51.
19. Akey JM. Constructing genomic maps of positive selection in humans: Where do we go from here. Genome Res 2009, 19(5):711-722. 10.1101/gr.086652.108, 19411596.
20. Qanbari S, Pimentel ECG, Tetens J, Thaller G, Lichtner P, Sharifi AR, Simianer H. A genome-wide scan for signatures of recent selection in Holstein cattle. Anim Genet 2010, 41(4):377-89.
21. Sabeti PC, Schaffner SF, Fry B, Lohmueller J, Varilly P, Shamovsky O, Palma A, Mikkelsen TS, Altshuler D, Lande ES. Positive natural selection in the human lineage. Science 2006, 3129(5780):1614-1620.
22. Biswas S, Akey JM. Genomic insights into positive selection. TRENDS in Genetics 2006, 22(8):437-436. 10.1016/j.tig.2006.06.005, 16808986.
23. McRae K. Signatures of selective sweeps in parasite selection flocks 2011, University of Otago, Zoology department: MSc thesis.
24. Akey JM, Zhang G, Zhang K, Jin L, Shriver MD. Interrogating a high density SNP map for signatures of natural selection. Genome Res 2002, 12(12):1805-14. 10.1101/gr.631202, 187574, 12466284.
25. Pollinger JP, Bustamante CD, Fledel-Alon A, Schmutz S, Gray MM, Wayne RK. Selective sweep mapping of genes with large phenotypic effects. Genome Research 2005, 15:1809-1819. 10.1101/gr.4374505, 1356119, 16339379.
26. Worley K, Carey J, Veitch A, Coltman DW. Detecting the signature of selection on immune genes in highly structured populations of wild sheep (Ovis dalli). Mol Ecol 2006, 15(3):623-637. 10.1111/j.1365-294X.2006.02829.x, 16499690.
27. Hayes BJ, Lien S, Nilsen H, Olsen HG, Berg P, MacEachern S, Potter S, Meuwissen THE. The origin of selection signatures on bovine chromosome six. Anim Genet 2008, 39(2):105-111. 10.1111/j.1365-2052.2007.01683.x, 18241301.
28. Prasad A, Schnabel RD, McKay SD, Murdoch B, Stothard P, Kolbehdari D, Wang Z, Taylor JF, Moore SS. Linkage disequilibrium and signatures of selection on chromosomes 19 and 29 in beef and dairy cattle. Anim Genet 2008, 39:597-605. 10.1111/j.1365-2052.2008.01772.x, 2659388, 18717667.
29. Barendse W, Harrison BE, Bunch RJ, Thomas MB, Turner LB. Genome wide signatures of positive selection: The comparison of independent samples and the identification of regions associated to traits. BMC Genomics 2009, 10:178. 10.1186/1471-2164-10-178, 2681478, 19393047.
30. Dayo GK, Thevenon S, Berthier D, Moazami-Goudarzi K, Denis C, Cuny G, Eggen A, Gautier M. Blackwell Publishing Ltd Detection of selection signatures within candidate regions underlying trypanotolerance in outbred cattle populations. Molecular Ecology 2009, 18:1801-1813. 10.1111/j.1365-294X.2009.04141.x, 19302350.
31. Flori L, Fritz S, Jaffre zic F, Boussaha M, Gut I, Heath S, Foulley JL, Gautier M. The genome response to artificial selection: a case study in dairy cattle. PLoS ONE 2009, 4(8):e6595. 10.1371/journal.pone.0006595, 2722727, 19672461.
32. Gu J, Orr N, Park SD, Katz LM, Sulimova G, MacHugh DE, Hill EW. A genome scan for positive selection in thoroughbred horses. PLoS ONE 2009, 4(6):e5767. 10.1371/journal.pone.0005767, 2685479, 19503617.
33. Hayes BJ, Chamberlain AJ, Maceachern S, Savin K, McPartlan H, MacLeod I, Sethuraman L, Goddard ME. A genome map of divergent artificial selection between Bos taurus dairy cattle and Bos taurus beef cattle. Anim Genet 2009, 40(2):176-184. 10.1111/j.1365-2052.2008.01815.x, 19067671.
34. MacEachern S, Hayes B, McEwan J, Goddard M. An examination of positive selection and changing effective population size in Angus and Holstein cattle populations (Bos taurus) using a high density SNP genotyping platform and the contribution of ancient polymorphism to genomic diversity in Domestic cattle. BMC Genomics 2009, 10:181. 10.1186/1471-2164-10-181, 2681480, 19393053.
35. Pariset L, Joost S, Ajmone-Marsan P, Valentini A. Econogene Consortium(EC): Landscape genomics and biased FST approaches reveal single nucleotide polymorphisms under selection in goat breeds of North-East Mediterranean. BMC Genetics 2009, 10:7. 2663570, 19228375.
36. The Bovine HapMap Consortium Genome wide survey of SNP variation uncovers the genetic structure of cattle breeds. Science 2009, 324(5926):528-532. 2735092, 19390050, The Bovine HapMap Consortium.
37. Stella A, Ajmone-Marsan P, Lazzari B. Boettcher Paul: Identification of selection signatures in cattle breeds selected for dairy production. Genetics 2010, 185:1451-1461. 10.1534/genetics.110.116111, 2927769, 20479146.
38. Qanbari S, Gianola D, Hayes B, Schenkel F, Miller S, Moore S, Thaller G, Simianer H. Application of site and haplotype-frequency based approaches for detecting selection signatures in cattle. BMC Genomics 2011, 12:318. 10.1186/1471-2164-12-318, 3146955, 21679429.
39. Vatankhah M, Talebi MA. Heritability estimates and correlations between production and reproductive traits in Lori-Bakhtiari sheep in Iran. South African Journal of Animal Science 2008, 38(2):110-118.
40. Kamalzadeh A, Rajabaigy M, Kiasat A. Livestock production systems and trends in livestock industry in Iran. J Agri Soc Sci 2008, 04:183-88.
41. Dalrymple BP, Kirkness EF, Nefedov M, McWilliam S, Ratnakumar A, Barris W, Zhao S, Shetty J, Maddox JF, O'Grady M, et al. Using comparative genomics to reorder the human genome sequence into a virtual sheep genome. Genome Biology 2007, 8(7):R152. 10.1186/gb-2007-8-7-r152, 2323240, 17663790.
42. Weir BS, Cockerham CC. Estimating F-statistics for the analysis of population structure. Evolution 1984, 38(6):1358-1370.
43. The UCSC Genome Browser. , http://genome.ucsc.edu/
44. Casas E, Stone RT, Keele JW, Shackelford SD, Kappes SM, Koohmaraie M. A comprehensive search for quantitative trait loci affecting growth and carcass composition of cattle segregating alternative forms of the myostatin gene. J Anim Sci 2001, 79:854-860.
45. McClure MC, Morsci NS, Schnabel RD, Kim JW, Yao P, Rolf MM, McKay SD, Gregg SJ, Chapple RH, Northcutt SL, Taylor JF. A genome scan for quantitative trait loci influencing carcass, post-natal growth and reproductive traits in commercial Angus cattle. Animal Genetics 2010, 41:597-607. 10.1111/j.1365-2052.2010.02063.x, 20477797.
46. Casas E, Shackelford SD, Keele JW, Stone RT, Kappes SM, Koohmaraie M. Quantitative trait loci affecting growth and carcass composition of cattle segregating alternate forms of myostatin. J Anim Sci 2000, 78:560-569.
47. MacNeil MD, Grosz MD. Genome-wide scans for QTL affecting carcass traits in Hereford × composite double. J Anim Sci 2002, 80:2316-2324.
48. Casas E, Shackelford SD, Keele JW, Koohmaraie M, Smith TPL, Stone RT. Detection of quantitative trait loci for growth and carcass composition in cattle. J Anim Sci 2003, 81:2976-2983.
49. Li C, Basarab J, Snelling WM, Benkel B, Murdoch B, Hansen C, Moore SS. Assessment of positional candidate genes MYF5 and IGF1 for growth on bovine chromosome 5 in commercial lines of Bos taurus. J Anim Sci 2004, 82:1-7.
50. Schrooten C, Bink MCAM, Bovenhuis H. Whole genome scans to detect chromosomal regions affecting multiple traits in dairy cattle. J Dairy Sci 2004, 87:3550-3560. 10.3168/jds.S0022-0302(04)73492-X, 15377635.
51. Ashwell MS, Heyen DW, Weller JI, Ron M, Sonstegard TS, Van Tassell CP, Lewin HA. Detection of quantitative trait loci influencing conformation traits and calving ease in Holstein-Friesian cattle. J Dairy Sci 2005, 88:4111-4119. 10.3168/jds.S0022-0302(05)73095-2, 16230715.
52. Weicker JJ, Brumfield RT, et al. Estimating the unbiased estimator θ for population genetic survey data. Evolution 2001, 55(12):2601-2605.
53. Falconer DS, Mackay TFC. Introduction to quantitative genetics 1996, 72-73. Addison Wesley Longman, Harlow, Essex, UK, 3.
54. Stephens JC, Reich DE, Goldstein DB, Shin HD, Smith MW, Carrington M, Winkler C, Huttley GA, Allikmets R, Schriml L, et al. Dating the origin of the CCR5-D32 AID-resistance allele by the coalescence of haplotypes. Am J Hum Genet 1998, 62:1507-1515. 10.1086/301867, 1377146, 9585595.
55. Tecofsky RTJ, Gemmell NJ, Johnson PL, McEwan J. Searching for genetic markers for yellow fat in New Zealand sheep [abstract]. In proceedings of the ComBio Conference 2009,
56. Becker D, Tetens J, Brunner A, Burstel D, Ganter M, Kijas J, Drogemuller C. Microphthalmia in Texel sheep is associated with a missense mutation in the paired-like homeodomain 3 PITX gene. PLoS ONE 2010, 5(1):e8689. 10.1371/journal.pone.0008689, 2805710, 20084168.
57. Voight BF, Kudaravalli S, Wen XQ, Pritchard JK. A map of recent positive selection in the human genome. PLoS Biology 2006, 4(3):e72. 10.1371/journal.pbio.0040072, 1382018, 16494531.
58. Sabeti PC, Varilly P, Fry B, Lohmueller J, Hostetter E, Cotsapas C, Xie XH, Byrne EH, McCarroll SA, Gaudet R, et al. Genome-wide detection and characterization of positive selection in human populations. Nature 2007, 449(7164):913-U912. 10.1038/nature06250, 2687721, 17943131.
59. Davies W, Isles AR, Wilkinson LS. Imprinted genes and mental dysfunction. Ann Med 2001, 33(6):428-436. 10.3109/07853890108995956, 11585104.
60. Helms C. Salting out Procedure for Human DNA extraction. The Donis-Keller Lab - Lab Manual Homepage , http://humgen.wustl.edu/hdk_lab_manual/dna/dna2.html
61. Kijas J, Lenstra JA, Hayes B, Boitard S, Neto LP, Cristobal MS, Servin B, McCulloch R, Whan V, Gietzen K, et al. Genome wide analysis of the world's sheep breeds reveals high levels of historic mixture and strong recent selection. PLoS Biology
62. The Wellcome Trust Case Control Consortium Genome-wide association study of 14,000 cases of seven common diseases and 3,000 shared controls. Nature 2007, 447(7145):661-78. 10.1038/nature05911, 2719288, 17554300, The Wellcome Trust Case Control Consortium.
63. Teo YY, Fry AE, Clark TG, Tai ES, Seielstad M. On the usage of HWE for identifying genotyping errors. Annals of Human Genetics 2007, 71:701-703. 10.1111/j.1469-1809.2007.00356.x, 17388941.
64. Abdi H. Bonferroni and Šidàk corrections for multiple comparisons. Encyclopedia of Measurement and Statistics 2007, 103-107. Sage: Thousand Oaks, Salkind N.
65. Maynard-Smith J, Haigh J. The hitch-hiking effect of a favourable gene. Genet Res 1974, 23:23-35. 10.1017/S0016672300014634, 4407212.
66. Wright S. The genetical structure of populations. Ann Eugen 1951, 15:323-354.
67. Fisher RA. Statistical Methods for Research Workers 1932, London: Oliver and Boyd.
68. Krumsiek J, Arnold R, Rattei T. Gepard: A rapid and sensitive tool for creating dotplots on genome scale. Bioinformatics 2007, 23(8):1026-1028. 10.1093/bioinformatics/btm039, 17309896.
69. The Ovine Genome Browser. , http://www.livestockgenomics.csiro.au/sheep/oar1.0.php
70. Maizel JV, Lenk RP. Enhanced graphic matrix analysis of nucleic acid and protein sequences. Proceedings of the National Academy of Sciences of the United States of America 1981, 78(12):7665-7669. 10.1073/pnas.78.12.7665, 349330, 6801656.
71. Scheet P, Stephens M. A fast and flexible statistical model for large-scale population genotype data: applications to inferring missing genotypes and haplotypic phase. Am J Hum Genet 2006, 78(4):629-644. 10.1086/502802, 1424677, 16532393.
72. Hill WG, Robertson A. Linkage disequilibrium in finite populations. Theoretical and Applied Genetics 1968, 38:226-231.
73. Hayes BJ, Visscher PM, McPartlan HC, Goddard ME. Novel multilocus measure of linkage disequilibrium to estimate past effective population size. Genome Res 2003, 13(4):635-643. 10.1101/gr.387103, 430161, 12654718.
74. Tenesa A, Navarro P, Hayes BJ, Duffy DL, Clarke GM, Goddard ME, Visscher PM. Recent human effective population size estimated from linkage disequilibrium. Genome Res 2007, 17(4):520-526. 10.1101/gr.6023607, 1832099, 17351134.
75. Villa-Angulo R, Matukumalli LM, Gill CA, Choi G, Van Tassle CP, Grefenstette JJ. High-resolution haplotype block structure in the cattle genome. BMC Genetics 2009, 10:19. 2684545, 19393054.