Genome-Wide Association Studies for Growth and Meat Production Traits in Sheep

PLoS ONE

Volumn 8, Issue 6, 2013, Pages

  Zhang, Li ^a   Liu, Jiasen ^a   Zhao, Fuping ^a   Ren, Hangxing ^a,b   Xu, Lingyang ^a   Lu, Jian ^a   Zhang, Shifang ^a   Zhang, Xiaoning ^a   Wei, Caihong ^a   Lu, Guobin ^a   Zheng, Youmin ^a,c   Du, Lixin ^a  

^a INSTITUTE OF PLANT PROTECTION   (China)

^b Chongqing Academy of Animal Sciences   (China)

^c National Animal Husbandry Service   (China)

Author keywords

[No Author keywords available]

Indexed keywords

ANIMAL EXPERIMENT; ANTHROPOMETRIC PARAMETERS; ARTICLE; BIRTH WEIGHT; CAMKMT GENE; CHEST CIRCUMFERENCE; CONTROLLED STUDY; FEMALE; GENE; GENE IDENTIFICATION; GENETIC ASSOCIATION; GENETIC TRAIT; GENOTYPE; GRM1 GENE; MALE; MBD5 GENE; MEAT; MEF2B GENE; NONHUMAN; NUCLEOTIDE SEQUENCE; OAR3 GENE; OAR9 GENE; QUALITY CONTROL; QUANTITATIVE TRAIT LOCUS; RFXANK GENE; RIPK2 GENE; RPL7 GENE; SHEEP; SINGLE NUCLEOTIDE POLYMORPHISM; SMC2 GENE; STRUCTURAL GENE; TRHDE GENE; UBR2 GENE; WEANING; WEIGHT GAIN; ANIMAL; BODY WEIGHT; GENE LOCUS; GENETICS; GENOTYPING TECHNIQUE; GROWTH, DEVELOPMENT AND AGING; HUMAN; MUTATION; ORGAN SIZE; PHENOTYPE;

OVIS; OVIS ARIES;

ANIMALS; BODY WEIGHT; FEMALE; GENETIC LOCI; GENOME-WIDE ASSOCIATION STUDY; GENOTYPING TECHNIQUES; HUMANS; MALE; MEAT; MUTATION; ORGAN SIZE; PHENOTYPE; POLYMORPHISM, SINGLE NUCLEOTIDE; QUALITY CONTROL; SHEEP; WEANING;

EID: 84879337492     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0066569     Document Type: Article

References (67)

1. Cassady JP, Johnson RK, Pomp D, Rohrer GA, Van Vleck LD, et al. (2001) Identification of quantitative trait loci affecting reproduction in pigs. J Anim Sci 79: 623-633.
2. Machado MBB, Alencar MM, Pereira AP, Oliveira HN, Casas E, et al. (2003) QTL affecting body weight in a candidate region of cattle chromosome 5. Genetics and Molecular Biology 26: 259-265.
3. Carlborg R, Hocking PM, Burt DW, Haley CS, (2004) Simultaneous mapping of epistatic QTL in chickens reveals clusters of QTL pairs with similar genetic effects on growth. Genetical Research 83: 197-209.
4. Walling GA, Visscher PM, Wilson AD, McTeir BL, Simm G, et al. (2004) Mapping of quantitative trait loci for growth and carcass traits in commercial sheep populations. Journal of Animal Science 82: 2234-2245.
5. Animal QTLdb. Available: http://www.animalgenome.org/cgi-bin/QTLdb/index permanent.
6. Matukumalli LK, Lawley CT, Schnabel RD, Taylor JF, Allan MF, et al. (2009) Development and characterization of a high density SNP genotyping assay for cattle. PLoS One 4: e5350.
7. Fan B, Onteru SK, Du ZQ, Garrick DJ, Stalder KJ, et al. (2011) Genome-wide association study identifies Loci for body composition and structural soundness traits in pigs. PLoS One 6: e14726.
8. Jiang L, Liu J, Sun D, Ma P, Ding X, et al. (2010) Genome wide association studies for milk production traits in Chinese Holstein population. PLoS One 5: e13661.
9. Klein RJ, Zeiss C, Chew EY, Tsai JY, Sackler RS, et al. (2005) Complement factor H polymorphism in age-related macular degeneration. Science 308: 385-389.
10. Scott J, Chant D, Andrews G, Martin G, McGrath J, (2007) Association between trauma exposure and delusional experiences in a large community-based sample. British Journal of Psychiatry 190: 339-343.
11. Lee YH, Kang ES, Kim SH, Han SJ, Kim CH, et al. (2008) Association between polymorphisms in SLC30A8, HHEX, CDKN2A/B, IGF2BP2, FTO, WFS1, CDKAL1, KCNQ1 and type 2 diabetes in the Korean population. Journal of Human Genetics 53: 991-998.
12. Lasky-Su J, Anney RJL, Neale BM, Franke B, Zhou K, et al. (2008) Genome-Wide Association Scan of the Time to Onset of Attention Deficit Hyperactivity Disorder. American Journal of Medical Genetics Part B-Neuropsychiatric Genetics 147B: 1355-1358.
13. Meuwissen TH, Hayes BJ, Goddard ME, (2001) Prediction of total genetic value using genome-wide dense marker maps. Genetics 157: 1819-1829.
14. Dong Y, Xie M, Jiang Y, Xiao N, Du X, et al. (2012) Sequencing and automated whole-genome optical mapping of the genome of a domestic goat (Capra hircus). Nat Biotechnol.
15. Sheep Genome v1.0. Available: http://www.livestockgenomics.csiro.au/sheep/oar1.0.php. permanent.
16. Danielle M, Gorbach BF, Onteru SK, Zhao X, Du ZQ, et al. (2010) Genome-Wide Association Studies for Important Economic Traits in Domestic Animals Using High Density SNP Genotyping. Iowa State University Animal Industry Report.
17. Purdie AC, Plain KM, Begg DJ, de Silva K, Whittington RJ, (2011) Candidate gene and genome-wide association studies of Mycobacterium avium subsp paratuberculosis infection in cattle and sheep: A review. Comparative Immunology Microbiology and Infectious Diseases 34: 197-208.
18. Zhao X, Dittmer KE, Blair HT, Thompson KG, Rothschild MF, et al. (2011) A novel nonsense mutation in the DMP1 gene identified by a genome-wide association study is responsible for inherited rickets in Corriedale sheep. PLoS One 6: e21739.
19. García-Gámez E, Gutiérrez-Gil B, Sahana G, Sánchez JP, Bayón Y, et al. (2012) GWA Analysis for Milk Production Traits in Dairy Sheep and Genetic Support for a QTN Influencing Milk Protein Percentage in the LALBA Gene. PLoS ONE 7(10): e47782 doi:10.1371/journal.pone.0047782.
20. Jonas E, Thomson PC, Raadsma HW (2009) Genome-Wide Association Study And Fine Mapping Of QTL On OAR 21 For Body Weight In Sheep. BioScience: 0-3.
21. Marcq F, Detilleux J, Leroy PL, (1999) Growth performance of texel lambs in Belgium: estimation of non genetic and genetic parameters. Annales De Medecine Veterinaire 143(2): 125-130.
22. Marcq F, Larzul C, Marot V, Bouix J, Eychenne F, et al. (2002) Preliminary results of a whole-genome scan targeting QTL for carcass traits in a Texel× Romanov intercross. Institut National de la Recherche Agronomique (INRA): 0-4.
23. Marcq F, Elsen JM, Grobet L, Royo L, Leroy P, et al. (1998) Investigating the role of myostatin in the determinism of double muscling characterizing Belgian Texel sheep. Animal Genetics 29suppl. 1: 75.
24. Shay TL, Berghmans S, Segers K, Meyers S, Beever JE, et al. (2001) Fine-mapping and construction of a bovine contig spanning the ovine callipyge locus. Mammalian Genome 12: 141-149.
25. Jopson NB, Stevenson-Barry J, Duncan S, Greer G, Bain W, et al. (2001) Mode of inheritance and effects on meat quality of the rib eye muscling (REM) QTL in sheep.
26. Clop A, Marcq F, Takeda H, Pirottin D, Tordoir X, et al. (2006) A mutation creating a potential illegitimate microRNA target site in the myostatin gene affects muscularity in sheep. Nat Genet 38(7): 813-818.
27. Cockett NE, Jackson SP, Shay TL, Farnir F, Berghmans S, et al. (1996) Polar overdominance at the ovine callipyge locus. Science 273: 236-238.
28. Fahrenkrug SC, Freking BA, Rexroad CE, Leymaster KA, Kappes SM, et al. (2000) Comparative mapping of the ovine clpg locus. Mammalian Genome 11: 871-876.
29. Nicoll GB, Burkin HR, Broad TE, Jopson NB, Greer GJ, et al. (1998) Genetic linkage of microsatellite markers to the carwell locus for rib-wye muscling in sheep. VI World Conference of Genetic Applied to Livestock Production 26: 529-532.
30. McEwan JC, Gerard EM, Jopson NB, Nicoll GB, Greer GJ, et al. (1998) Localization of a QTL for rib-eye muscling on OAR 18. Animal Genetics 29(Suppl).
31. Walling GA, Wilson AD, McTeir BL, Visscher PM, Simm G, et al. (2002) A candidate region approach allows efficient QTL detection in UK Suffolk and Texel populations Proceedings of the 7th World Congress on Genetics Applied to Livestock ProductionMontpellier, France.
32. Matukumalli LK, Lawley CT, Schnabel RD, Taylor JF, Allan MF, et al. (2009) Development and Characterization of a High Density SNP Genotyping Assay for Cattle. PLoS One 4.
33. Maxa J, Norberg E, Berg P, Pedersen J, (2007) Genetic parameters for carcass traits and in vivo measured muscle and fat depth in Danish Texel and Shropshire. Acta Agriculturae Scandinavica Section a-Animal Science 57: 49-54.
34. Patterson N, Price AL, Reich D, (2006) Population structure and eigenanalysis. PLoS Genet 2: e190.
35. Price K, Patterson E, Hegney D, (2006) Being strategic: utilising consumer views to better promote an expanded role for nurses in Australian general practice. Collegian 13: 16-21.
36. Pearson TA, Manolio T, (2008) How to interpret a genome-wide association study. Jama 299: 1335-1344.
37. UCSC Genome Bioinformatics.Available: http://genome.ucsc.edu, permanent.
38. National Center for Biotechnology Information. Availble: http://www.ncbi.nlm.nih.gov/. permanent.
39. Sheep Genome v3.1. Available: http://www.livestockgenomics.csiro.au/sheep/oar3.1.php permanent.
40. Bradbury PJ, Zhang Z, Kroon DE, Casstevens TM, Ramdoss Y, et al. (2007) TASSEL: software for association mapping of complex traits in diverse samples. Bioinformatics 23: 2633-2635.
41. Zhang Z, Ersoz E, Lai CQ, Todhunter RJ, Tiwari HK, et al. (2010) Mixed linear model approach adapted for genome-wide association studies. Nat Genet 42: 355-360.
42. Edmondson DG, Lyons GE, Martin JF, Olson EN, (1994) Mef2 gene expression marks the cardiac and skeletal muscle lineages during mouse embryogenesis. Development 120: 1251-1263.
43. Lilly B, Zhao B, Ranganayakulu G, Paterson BM, Schulz RA, et al. (1995) Requirement of MADS domain transcription factor D-MEF2 for muscle formation in Drosophila. Science 267: 688-693.
44. Ranganayakulu G, Zhao B, Dokidis A, Molkentin JD, Olson EN, et al. (1995) A series of mutations in the D-MEF2 transcription factor reveal multiple functions in larval and adult myogenesis in Drosophila. Dev Biol 171: 169-181.
45. Subramanian SV, Nadal-Ginard B, (1996) Early expression of the different isoforms of the myocyte enhancer factor-2 (MEF2) protein in myogenic as well as non-myogenic cell lineages during mouse embryogenesis. Mech Dev 57: 103-112.
46. Schomburg L, Turwitt S, Prescher G, Lohmann D, Horsthemke B, et al. (1999) Human TRH-degrading ectoenzyme cDNA cloning, functional expression, genomic structure and chromosomal assignment. Eur J Biochem 265: 415-422.
47. He B (2006) Culture, Identification and Biological Characteristics of Skeletal Muscle Satellite Cells of Pig and Preliminary Study about the Porcine MEF2B and MEF2C Gene. Master Thesis, Huazhong Agricultural University.
48. Reith W, Mach B, (2001) The bare lymphocyte syndrome and the regulation of MHC expression. Annu Rev Immunol 19: 331-373.
49. Rader K, Boyer AD, Farquhar MG, Arden KC, (2000) Assignment of ankyrin repeat, family A (RFXANK-like) 2 (ANKRA2) to human chromosome 5q12->q13 by radiation hybrid mapping and somatic cell hybrid PCR. Cytogenet Cell Genet 89: 164-165.
50. Magnani R, Dirk LM, Trievel RC, Houtz RL, (2010) Calmodulin methyltransferase is an evolutionarily conserved enzyme that trimethylates Lys-115 in calmodulin. Nat Commun 1: 43.
51. Hillier LW, Graves TA, Fulton RS, Fulton LA, Pepin KH, et al. (2005) Generation and annotation of the DNA sequences of human chromosomes 2 and 4. Nature 434: 724-731.
52. Freudenberg J, Lee HS, Han BG, Shin HD, Kang YM, et al. (2011) Genome-wide association study of rheumatoid arthritis in Koreans: population-specific loci as well as overlap with European susceptibility loci. Arthritis Rheum 63: 884-893.
53. Bowers PM, Cokus SJ, Elsenberg D, Yeates TO, (2004) Use of logic relationships to decipher protein network organization. Science 306: 2246-2249.
54. Cavanagh CR, Jonas E, Hobbs M, Thomson PC, Tammen I, et al. (2010) Mapping Quantitative Trait Loci (QTL) in sheep. III. QTL for carcass composition traits derived from CT scans and aligned with a meta-assembly for sheep and cattle carcass QTL. Genet Sel Evol 42: 36.
55. Meng Q, Zheng M, Liu H, Song C, Zhang W, et al. (2012) TRAF6 regulates proliferation, apoptosis, and invasion of osteosarcoma cell. Mol Cell Biochem 371: 177-186.
56. Bruzik KS, Tsai MD, (1994) Towards the mechanism of phosphonositide-specfic phospholipase Bioorg Med Chem. 2(2): 49-72.
57. Wang Y, Liu S-y, Han M, Li J-y, (2007) Cloning and sequence analysis of pol gene of the Inner Mongol ia strain of endogenous jaagsiekte sheep retrovirus. Chinese Journal of Veterinary Medicine 43: 8-10.
58. Pepin M, Vitu C, Russo P, Mornex JF, Peterhans E, (1998) Maedi-visna virus infection in sheep: a review. Vet Res 29: 341-367.
59. Straub OC, (2004) Maedi-Visna virus infection in sheep. History and present knowledge. Comp Immunol Microbiol Infect Dis 27: 1-5.
60. Payne LN, Nair V, (2012) The long view: 40 years of avian leukosis research. Avian Pathol 41: 11-19.
61. Qu Y, Sun H, Sun M, Li D, Qin L, et al. (2012) Sequence analysis for the complete proviral genome of avian leukosis virus subgroup J associated with haemangiomas, leiomyosarcomas and myelomas in layer flocks. Acta Vet Hung 60: 343-354.
62. Palmarini M, Sharp JM, Lee C, Fan H, (1999) In vitro infection of ovine cell lines by Jaagsiekte sheep retrovirus. J Virol 73: 10070-10078.
63. Talkowski ME, Rosenfeld JA, Blumenthal I, Pillalamarri V, Chiang C, et al. (2012) Sequencing chromosomal abnormalities reveals neurodevelopmental loci that confer risk across diagnostic boundaries. Cell 149: 525-537.
64. Du Y, Liu B, Guo F, Xu G, Ding Y, et al. (2012) The essential role of Mbd5 in the regulation of somatic growth and glucose homeostasis in mice. PLoS One 7: e47358.
65. Cukier HN, Lee JM, Ma D, Young JI, Mayo V, et al. (2012) The expanding role of MBD genes in autism: identification of a MECP2 duplication and novel alterations in MBD5, MBD6, and SETDB1. Autism Res 5: 385-397.
66. Strunnikov AV, Hogan E, Koshland D, (1995) SMC2, a Saccharomyces cerevisiae gene essential for chromosome segregation and condensation, defines a subgroup within the SMC family. Genes Dev 9: 587-599.
67. New York University (2007) How Different Species Can Use The Same Genes Yet Develop Distinct Features. Science Daily.