Genome-Wide Association Identifies Multiple Genomic Regions Associated with Susceptibility to and Control of Ovine Lentivirus

PLoS ONE

Volumn 7, Issue 10, 2012, Pages

  White, Stephen N ^a,b   Mousel, Michelle R ^a   Herrmann Hoesing, Lynn M ^b   Reynolds, James O ^a   Leymaster, Kreg A ^c   Neibergs, Holly L ^b   Lewis, Gregory S ^a   Knowles, Donald P ^a,b  

^a AGRICULTURAL RESEARCH SERVICE   (United States)

^b WASHINGTON STATE UNIVERSITY   (United States)

^c U S MEAT ANIMAL RESEARCH CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ANIMAL CELL; ANIMAL EXPERIMENT; ARTICLE; CONTROLLED STUDY; DLG1 GENE; DLGAP1 GENE; GENE CLUSTER; GENE FREQUENCY; GENE IDENTIFICATION; GENE LINKAGE DISEQUILIBRIUM; GENE LOCUS; GENE MUTATION; GENETIC ASSOCIATION; GENETIC SUSCEPTIBILITY; GENETIC VARIABILITY; LENTIVIRINAE; NONHUMAN; PHENOTYPE; PROTEIN BINDING; RAB27A GENE; SEROLOGY; SHEEP; SINGLE NUCLEOTIDE POLYMORPHISM; SYTL3 GENE; TMEM154 GENE; VIRUS GENE; VIRUS REPLICATION; ZNF165 GENE; ZNF192 GENE; ZNF389 GENE; ZSCAN16 GENE; ANIMAL; BLOOD; CAPRINE ARTHRITIS ENCEPHALITIS VIRUS; GENETIC PREDISPOSITION; GENETICS; GENOME; GENOTYPE; HUMAN; LENTIVIRUS INFECTION; MUTATION; PHYSIOLOGY; PROVIRUS; VIROLOGY;

ANIMALS; GENETIC PREDISPOSITION TO DISEASE; GENOME; GENOME-WIDE ASSOCIATION STUDY; GENOTYPE; HUMANS; LENTIVIRUS; LENTIVIRUS INFECTIONS; LENTIVIRUSES, OVINE-CAPRINE; LINKAGE DISEQUILIBRIUM; MUTATION; PHENOTYPE; PROVIRUSES; SHEEP, DOMESTIC;

EID: 84867650518     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0047829     Document Type: Article

References (59)

1. Leroux C, Cruz JC, Mornex JF, (2010) SRLVs: a genetic continuum of lentiviral species in sheep and goats with cumulative evidence of cross species transmission. Curr HIV Res 8: 94-100.
2. Blacklaws B, Harkiss GD, (2010) Small ruminant lentiviruses and human immunodeficiency virus: cousins that take a long view. Curr HIV Res 8: 26-52.
3. Cutlip RC, Lehmkuhl HD, Sacks JM, Weaver AL, (1992) Seroprevalence of ovine progressive pneumonia virus in sheep in the United States as assessed by analyses of voluntarily submitted samples. Am J Vet Res 53: 976-979.
4. InfoSheet (2003) Ovine Progressive Pneumonia: Awareness, Management, and Seroprevalence. USDA-APHIS-Veterinary Services. 1-4.
5. Narayan O, Kennedy-Stoskopf S, Zink MC, (1988) Lentivirus-host interactions: lessons from visna and caprine arthritis-encephalitis viruses. Ann Neurol 23 (Suppl): S95-100.
6. De Boer GF, Terpstra C, Houwers DJ, Hendriks J, (1979) Studies in epidemiology of maedi/visna in sheep. Res Vet Sci 26: 202-208.
7. Torsteinsdottir S, Andresdottir V, Arnarson H, Petursson G, (2007) Immune response to maedi-visna virus. Front Biosci 12: 1532-1543.
8. Blacklaws BA, (2012) Small ruminant lentiviruses: immunopathogenesis of visna-maedi and caprine arthritis and encephalitis virus. Comp Immunol Microbiol Infect Dis 35: 259-269.
9. Reina R, Berriatua E, Lujan L, Juste R, Sanchez A, et al. (2009) Prevention strategies against small ruminant lentiviruses: an update. Vet J 182: 31-37.
10. Gates NL, Winward LD, Gorham JR, Shen DT, (1978) Serologic survey of prevalence of ovine progressive pneumonia in Idaho range sheep. J Am Vet Med Assoc 173: 1575-1577.
11. Cutlip RC, Lehmkuhl HD, Brogden KA, Sacks JM, (1986) Breed susceptibility to ovine progressive pneumonia (maedi/visna) virus. Vet Microbiol 12: 283-288.
12. Houwers DJ, Visscher AH, Defize PR, (1989) Importance of ewe/lamb relationship and breed in the epidemiology of maedi-visna virus infections. Res Vet Sci 46: 5-8.
13. Snowder GD, Gates NL, Glimp HA, Gorham JR, (1990) Prevalence and effect of subclinical ovine progressive pneumonia virus infection on ewe wool and lamb production. J Am Vet Med Assoc 197: 475-479.
14. Keen JE, Hungerford LL, Wittum TE, Kwang J, Littledike ET, (1997) Risk factors for seroprevalence of ovine lentivirus in breeding ewe flocks in Nebraska, USA. Prev Vet Med 30: 81-94.
15. Herrmann-Hoesing LM, White SN, Mousel MR, Lewis GS, Knowles DP, (2008) Ovine progressive pneumonia provirus levels associate with breed and Ovar-DRB1. Immunogenetics 60: 749-758.
16. Heaton MP, Clawson ML, Chitko-McKown CG, Leymaster KA, Smith TP, et al. (2012) Reduced Lentivirus Susceptibility in Sheep with TMEM154 Mutations. PLoS Genet 8: e1002467.
17. Kijas JW, Lenstra JA, Hayes B, Boitard S, Porto Neto LR, et al. (2012) Genome-wide analysis of the world's sheep breeds reveals high levels of historic mixture and strong recent selection. PLoS Biol 10: e1001258.
18. Slatkin M, (2008) Linkage disequilibrium-understanding the evolutionary past and mapping the medical future. Nat Rev Genet 9: 477-485.
19. Herrmann-Hoesing LM, White SN, Lewis GS, Mousel MR, Knowles DP, (2007) Development and validation of an ovine progressive pneumonia virus quantitative PCR. Clin Vaccine Immunol 14: 1274-1278.
20. Herrmann-Hoesing LM, Noh SM, White SN, Snekvik KR, Truscott T, et al. (2009) Peripheral ovine progressive pneumonia provirus levels correlate with and predict histological tissue lesion severity in naturally infected sheep. Clin Vaccine Immunol 16: 551-557.
21. Kim ES, Kirkpatrick BW, (2009) Linkage disequilibrium in the North American Holstein population. Anim Genet 40: 279-288.
22. Qanbari S, Pimentel EC, Tetens J, Thaller G, Lichtner P, et al. (2010) The pattern of linkage disequilibrium in German Holstein cattle. Anim Genet 41: 346-356.
23. Badke YM, Bates RO, Ernst CW, Schwab C, Steibel JP, (2012) Estimation of linkage disequilibrium in four US pig breeds. BMC Genomics 13: 24.
24. Sutter NB, Eberle MA, Parker HG, Pullar BJ, Kirkness EF, et al. (2004) Extensive and breed-specific linkage disequilibrium in Canis familiaris. Genome Res 14: 2388-2396.
25. Consortium TIH, (2005) A haplotype map of the human genome. Nature 437: 1299-1320.
26. Slager RE, Li X, Meyers DA, Bleecker ER (2011) Recent developments in the genetics of asthma susceptibility and severity. In: Chung KF, Bel E H, Wenzel SE, editors. Difficult-to-Treat Severe Asthma. Plymouth, UK: European Respiratory Society. 82-96.
27. Du J, Lin G, Nie ZY, Lu GX, (2004) [Molecular cloning and characterization analysis of HPESCRG1, a novel gene expressed specifically in human embryonic stem cell]. Zhonghua Yi Xue Yi Chuan Xue Za Zhi 21: 542-547.
28. Madan B, Madan V, Weber O, Tropel P, Blum C, et al. (2009) The pluripotency-associated gene Dppa4 is dispensable for embryonic stem cell identity and germ cell development but essential for embryogenesis. Mol Cell Biol 29: 3186-3203.
29. Nakamura T, Nakagawa M, Ichisaka T, Shiota A, Yamanaka S, (2011) Essential roles of ECAT15-2/Dppa2 in functional lung development. Mol Cell Biol 31: 4366-4378.
30. Cortez-Romero C, Fieni F, Russo P, Pepin M, Roux C, et al. (2011) Presence of Maedi Visna virus (MVV)-proviral DNA in the genital tissues of naturally infected ewes. Reprod Domest Anim 46: e1-6.
31. Peterson K, Brinkhof J, Houwers DJ, Colenbrander B, Gadella BM, (2008) Presence of pro-lentiviral DNA in male sexual organs and ejaculates of small ruminants. Theriogenology 69: 433-442.
32. Hu ZL, Fritz ER, Reecy JM, (2007) AnimalQTLdb: a livestock QTL database tool set for positional QTL information mining and beyond. Nucleic Acids Res 35: D604-609.
33. Hu ZL, Reecy JM, (2007) Animal QTLdb: beyond a repository. A public platform for QTL comparisons and integration with diverse types of structural genomic information. Mamm Genome 18: 1-4.
34. Marshall K, Maddox JF, Lee SH, Zhang Y, Kahn L, et al. (2009) Genetic mapping of quantitative trait loci for resistance to Haemonchus contortus in sheep. Anim Genet 40: 262-272.
35. Seldin MF, (2007) Admixture mapping as a tool in gene discovery. Curr Opin Genet Dev 17: 177-181.
36. Hulet CV, Ercanbrack SK, Knight AD, (1984) Development of the Polypay breed of sheep. J Anim Sci 58: 15-24.
37. Cockett NE, Jackson SP, Shay TL, Farnir F, Berghmans S, et al. (1996) Polar overdominance at the ovine callipyge locus. Science 273: 236-238.
38. Freking BA, Murphy SK, Wylie AA, Rhodes SJ, Keele JW, et al. (2002) Identification of the single base change causing the callipyge muscle hypertrophy phenotype, the only known example of polar overdominance in mammals. Genome Res 12: 1496-1506.
39. Kuroda TS, Fukuda M, Ariga H, Mikoshiba K, (2002) The Slp homology domain of synaptotagmin-like proteins 1-4 and Slac2 functions as a novel Rab27A binding domain. J Biol Chem 277: 9212-9218.
40. Fukuda M, Mikoshiba K, (2001) Synaptotagmin-like protein 1-3: a novel family of C-terminal-type tandem C2 proteins. Biochem Biophys Res Commun 281: 1226-1233.
41. Fraile-Ramos A, Cepeda V, Elstak E, van der Sluijs P, (2010) Rab27a is required for human cytomegalovirus assembly. PloS One 5: e15318.
42. Yokoyama K, Kaji H, He J, Tanaka C, Hazama R, et al. (2011) Rab27a negatively regulates phagocytosis by prolongation of the actin-coating stage around phagosomes. J Biol Chem 286: 5375-5382.
43. Ostrowski M, Carmo NB, Krumeich S, Fanget I, Raposo G, et al. (2010) Rab27a and Rab27b control different steps of the exosome secretion pathway. Nat Cell Biol 12: 19-30; sup 11-13.
44. Emerson RO, Thomas JH, (2009) Adaptive evolution in zinc finger transcription factors. PLoS Genet 5: e1000325.
45. Thomas JH, Schneider S, (2011) Coevolution of retroelements and tandem zinc finger genes. Genome Res 21: 1800-1812.
46. Zhu Y, Chen G, Lv F, Wang X, Ji X, et al. (2011) Zinc-finger antiviral protein inhibits HIV-1 infection by selectively targeting multiply spliced viral mRNAs for degradation. Proc Natl Acad Sci U S A 108: 15834-15839.
47. Heidtman M, Chen CZ, Collins RN, Barlowe C, (2005) Yos1p is a novel subunit of the Yip1p-Yif1p complex and is required for transport between the endoplasmic reticulum and the Golgi complex. Mol Biol Cell 16: 1673-1683.
48. Yamazaki D, Tabara Y, Kita S, Hanada H, Komazaki S, et al. (2011) TRIC-A channels in vascular smooth muscle contribute to blood pressure maintenance. Cell Metab 14: 231-241.
49. Satoh K, Yanai H, Senda T, Kohu K, Nakamura T, et al. (1997) DAP-1, a novel protein that interacts with the guanylate kinase-like domains of hDLG and PSD-95. Genes Cells 2: 415-424.
50. Kim E, Naisbitt S, Hsueh YP, Rao A, Rothschild A, et al. (1997) GKAP, a novel synaptic protein that interacts with the guanylate kinase-like domain of the PSD-95/SAP90 family of channel clustering molecules. J Cell Biol 136: 669-678.
51. Takeuchi M, Hata Y, Hirao K, Toyoda A, Irie M, et al. (1997) SAPAPs. A family of PSD-95/SAP90-associated proteins localized at postsynaptic density. J Biol Chem 272: 11943-11951.
52. Perugi F, Muriaux D, Ramirez BC, Chabani S, Decroly E, et al. (2009) Human Discs Large is a new negative regulator of human immunodeficiency virus-1 infectivity. Mol Biol Cell 20: 498-508.
53. Boon AC, deBeauchamp J, Hollmann A, Luke J, Kotb M, et al. (2009) Host genetic variation affects resistance to infection with a highly pathogenic H5N1 influenza A virus in mice. J Virol 83: 10417-10426.
54. Javier RT, Rice AP, (2011) Emerging Theme: Cellular PDZ Proteins as Common Targets of Pathogenic Viruses. J Virol 85: 11544-11556.
55. Herrmann LM, Cheevers WP, Marshall KL, McGuire TC, Hutton MM, et al. (2003) Detection of serum antibodies to ovine progressive pneumonia virus in sheep by using a caprine arthritis-encephalitis virus competitive-inhibition enzyme-linked immunosorbent assay. Clin Diagn Lab Immunol 10: 862-865.
56. Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MA, et al. (2007) PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet 81: 559-575.
57. Hindorff LA, Sethupathy P, Junkins HA, Ramos EM, Mehta JP, et al. (2009) Potential etiologic and functional implications of genome-wide association loci for human diseases and traits. Proc Natl Acad Sci U S A 106: 9362-9367.
58. Team RDC (2011) R: A Language and Environment for Statistical Computing. Vienna, Austria: R Foundation for Statistical Computing.
59. Terrill CE, (1958) Fifty Years of Progress in Sheep Breeding. J Anim Sci 17: 944-959.