Mapping QTL affecting resistance to Marek's disease in an F6 advanced intercross population of commercial layer chickens

详细信息    查看全文

• 作者：Eliyahu M Heifetz (1) (2)
  Janet E Fulton (3)
  Neil P O'Sullivan (3)
  James A Arthur (3)
  Hans Cheng (4)
  Jing Wang (1) (5)
  Morris Soller (6)
  Jack CM Dekkers (1)
  
• 刊名：BMC Genomics
• 出版年：2009
• 出版时间：December 2009
• 年：2009
• 卷：10
• 期：1
• 全文大小：1248KB
• 参考文献：1. Baigent SJ, Petherbridge LJ, Howes K, Smith LP, Currie RJW, Nair VK: Absolute quantitation of Marek's disease virus genome copy number in chicken feather and lymphocyte samples using real-time PCR. / J Virol Methods 2005, 123:53-4. CrossRef
  2. Osterrieder N, Kamil JP, Schumacher D, Tischer BK, Trapp S: Marek's disease virus: from miasma to model. / Nature Reviews Microbiology 2006, 4:283-4. CrossRef
  3. Morrow C, Fehler F: Marek's disease: a worldwide problem. / Marek's Disease, An Evolving Problem / (Edited by: Davison F, Nair V). Elsevier Ltd, Oxford, U.K 2004, 49-1. CrossRef
  4. Burgess SC, Young JR, Baaten BJ, Hunt L, Ross LN, Parcells MS, Kumar PM, Tregaskes CA, Lee LF, Davison TF: Marek's disease is a natural model for lymphomas overexpressing Hodgkin's disease antigen (CD30). / Proc Natl Acad Sci U S A 2004,101(38):13879-384. CrossRef
  5. Baigent SJ, Smith LP, Nair VK, Currie RJ: Vaccinal control of Marek's disease: current challenges, and future strategies to maximize protection. / Vet Immunol Immunopathol 2006, 112:78-6. CrossRef
  6. Nair V: Evolution of Marek's disease -a paradigm for incessant race between the pathogen and the host. / The Veterinary Journal 2005, 170:175-83.
  7. Liu HC, Kung HJ, Fulton JE, Morgan RW, Cheng HH: Growth hormone interacts with the Marek's disease virus SORF2 protein and is associated with disease resistance in chicken. / Proc Natl Acad Sci USA 2001, 98:9203-208. CrossRef
  8. Liu HC, Cheng HH, Tirunagaru V, Sofer L, Burnside J: A strategy to identify positional candidate genes conferring Marek's disease resistance by integrating DNA microarrays and genetic mapping. / Anim Genet 2001, 32:351-59. CrossRef
  9. Liu HC, Niikura M, Fulton J, Cheng HH: Identification of chicken stem lymphocyte antigen 6 complex, locus E (LY6E, alias SCA2) as a putative Marek's disease resistance gene via a virus-host protein interaction screen. / Cytogenet Genome Res 2003, 102:304-08. CrossRef
  10. Niikura M, Liu HC, Dodgson JB, Cheng HH: A comprehensive screen for chicken proteins that interact with proteins unique to virulent strains of Marek's disease virus. / Poult Sci 2004, 83:1117-123.
  11. Smith C, Smith DB: The need for close linkages in marker-assisted selectionfor economic merit in livestock. / Animal Breeding Abstracts 1993, 61:197-03.
  12. Darvasi A, Weinreb A, Minke V, Weller JI, Soller M: Detecting marker-QTL linkage and estimating QTL gene effect and map location using a saturated genetic map. / Genetics 1993, 134:943-1.
  13. Darvasi A, Soller M: A simple method to calculate resolving power and confidence interval of QTL map location. / Behav Genet 1997, 27:125-32. CrossRef
  14. Weller JI, Soller M: An analytical formula to estimate confidence interval of QTL location with a saturated genetic map as a function of experimental design. / Theor Appl Genet 2003,109(6):1224-229. CrossRef
  15. Darvasi A, Soller M: Advanced intercross lines, an experimental population for fine genetic mapping. / Genetics 1995, 141:1199-207.
  16. Iraqi F, Clapcott SJ, Kumari P, Haley CS, Kemp SJ, Teale AJ: Fine mapping of trypanosomiasis resistance loci in murine advanced intercross lines. / Mamm Genome 2000, 11:645-48. CrossRef
  17. Song JZ, Soller M, Genizi A: The full-sib intercross line (FSIL) design: A QTL mapping design for outcrossing species. / Genetical Research 1999, 73:61-3. CrossRef
  18. Heifetz EM, Fulton JE, O'Sullivan NP, Arthur JA, Wang J, Dekkers JCM, Soller M: Mapping Quantitative Trait Loci Affecting Susceptibility to Marek's Disease Virus in a Backcross Population of Layer Chickens. / Genetics 2007, 177:2417-431. CrossRef
  19. Parslickova D, Sharif S, Sarson A, Abdul-Careem MF, Zadworny D, Kulenkamp A, Ansah G, Kuhnlein U: Association of a marker in the vitamin D receptor gene with Marek's disease resistance in poultry. / Poult Sci 2008, 87:1112-119. CrossRef
  20. McElroy JP, Zhang W, Koehler KJ, Lamont SJ, Dekkers JCM: Comparison of methods for analysis of selective genotyping survival data. / Genet Sel Evol 2006,38(6):637-55.
  21. Yonash N, Bacon LD, Witter RL, Cheng HH: High resolution mapping and identification of new quantitative trait loci (QTL) affecting susceptibility to Marek's disease. / Anim Genet 1999, 30:126-35. CrossRef
  22. Bagnato A, Schiavini F, Rossoni A, Maltecca C, Dolezal M, Medugorac I, S?lkner J, Russo V, Friedman A, Soller M, Lipkin E: Quantitative Trait Loci Affecting Milk Yield and Protein Percent in a three Countries Brown Swiss Population. / J Dairy Sci 2008, 91:767-83. CrossRef
  23. Longenecker BM, Pazderka F, Gavora JS, Spencer JL, Ruth RF: Lymphoma induced by herpesvirus: Resistance associated with a major histocompatibility gene. / Immunogenetics 1976, 3:401-07. CrossRef
  24. Bacon LD: Influence of the major histocompatibility complex on disease resistance and productivity. / Poult Sci 1987, 66:802-11.
  25. Hartmann W: Evaluation of "major genes" affecting disease resistance in poultry in respect to their potential for commercial breeding in recent advances. / Recent Advances in Avian immunology research / (Edited by: Boghal BS, Koch G, Alan R). Liss, Inc. New York, NY 1989, 221-31.
  26. Soller M, Brody T, Genizi A: On the power of experimental designs for the detection of linkage between marker loci and quantitative loci in crosses between inbred lines. / Theoretical and Applied Genetics 1976, 47:35-9. CrossRef
  27. Cheng HH, Zhang Y, Muir WM: Evidence for widespread epistatic interactions influencing Marek's disease virus viremia levels in chicken. / Cytogenet Genome Res 2007, 117:313-18. CrossRef
  28. Stone HA: Use of highly inbred chickens in research. [http://animalscience.ucdavis.edu/AvianResources/Files/Use%20of%20Highly%20Inbred%20Chickens.pdf] / U.S. Department of Agriculture, ARS, Tech. Bull 1975, 1514:1-2.
  29. Korol A, Frenkel Z, Cohen L, Lipkin U, Soller M: Fractioned DNA pooling: A new cost effective strategy for fine QTL mapping. / Genetics 2007, 176:2611-625. CrossRef
  30. Witter RL: Increased virulence of Marek's disease virus field isolates. / Avian Dis 1997, 41:149-63. CrossRef
  31. Darvasi A, Soller M: Selective DNA pooling for determination of linkage between a molecular marker and a quantitative trait locus. / Genetics 1994, 138:1365-373.
  32. Lipkin E, Mosig MO, Darvasi A, Ezra E, Shalom A, Friedmann A, Soller M: Mapping loci controlling milk protein percentage in dairy cattle by means of selective milk DNA pooling using dinucleotide microsatellite markers. / Genetics 1998, 149:1557-567.
  33. Lipkin E, Fulton J, Cheng H, Yonash N, Soller M: Quantitative trait locus mapping in chicken by selective DNA pooling with dinucleotide microsatellite markers using purified DNA, and fresh or frozen red blood cells with application to marker assisted selection. / Poult Sci 2001,81(3):283-92.
  34. Lamont SJ: The chicken major histocompatibility complex in disease resistance and poultry breeding. / J Dairy Sci 1989, 72:1328-333. CrossRef
  35. Bacon LD, Witter RL: B haplotype influence on the relative efficacy of Marek's disease vaccines in commercial chickens. / Poult Sci 1994, 73:481-87.
  36. Schat KA, Taylor RL Jr, Briles WE: Resistance to Marek's disease in chickens with recombinant haplotypes to the major histocompatibility (B) complex. / Poult Sci 1994, 73:502-08.
  37. ArkDB [http://www.thearkdb.org./]
  38. Chicken (Gallus Gallus) [http://www.ensembl.org/Gallus_gallus/index.html]
  39. Liu HC, Cheng HH: Genetic mapping of the chicken stem cell antigen 2 (SCA2) gene to chromosome 2 via PCR primer mutagenesis. / Anim Genet 2003, 34:158-60. CrossRef
  40. Wang J, Koehler KJ, Dekkers JCM: Interval mapping of quantitative trait loci with selective DNA pooling data. / Genet Sel Evol 2007,39(6):685-09. CrossRef
  41. Fernando RL, Nettleton D, Southey BR, Dekkers JC, Rothschild MF, Soller M: Controlling the proportion of false positives in multiple dependent tests. / Genetics 2004, 166:611-19. CrossRef
  42. Nettleton D, Hwang JTG, Caldo RA, Wise RP: Estimating the number of true null hypotheses from a histogram of p-values. [http://pubs.amstat.org/doi/pdfplus/10.1198/108571106X129135?cookieSet=1] / Journal of Agricultural, Biological, and Environmental Statistics 2006,11(3):337-56. CrossRef
  43. Storey JD, Tibshirani R: Statistical significance for genomewide studies. / Proc Natl Acad Sci USA 2003, 100:9440-445. CrossRef
  44. Lee HJ, Dekkers CM, Soller M, Malek M, Fernando RL, Rothschild MF: Application of the false positive rate to quantitative loci interval mapping with multiple traits. / Genetics 2002, 161:905-14.
  45. Hillier LW, Miller W, Birney E, Warren W, Hardison RC, Ponting CP, Bork P, Burt DW, Groenen MA, Delany ME, Dodgson JB, Chinwalla AT, Cliften PF, Clifton SW, Delehaunty KD, Fronick C, Fulton RS, Graves TA, Kremitzki C, Layman D, Magrini V, McPherson JD, Miner TL, Minx P, Nash WE, Nhan MN, Nelson JO, Oddy LG, Pohl CS, Randall-Maher J, Smith SM, Wallis JW, Yang SP, Romanov MN, Rondelli CM, Paton B, Smith J, Morrice D, Daniels L, Tempest HG, Robertson L, Masabanda JS, Griffin DK, Vignal A, Fillon V, Jacobbson L, Kerje S, Andersson L, Crooijmans RP, Aerts J, Poel JJ, Ellegren H, Caldwell RB, Hubbard SJ, Grafham DV, Kierzek AM, McLaren SR, Overton IM, Arakawa H, Beattie KJ, Bezzubov Y, Boardman PE, Bonfield JK, Croning MD, Davies RM, Francis MD, Humphray SJ, Scott CE, Taylor RG, Tickle C, Brown WR, Rogers J, Buerstedde JM, Wilson SA, Stubbs L, Ovcharenko I, Gordon L, Lucas S, Miller MM, Inoko H, Shiina T, Kaufman J, Salomonsen J, Skjoedt K, Wong GK, Wang J, Liu B, Wang J, Yu J, Yang H, Nefedov M, Koriabine M, Dejong PJ, Goodstadt L, Webber C, Dickens NJ, Letunic I, Suyama M, Torrents D, von Mering C, Zdobnov EM, Makova K, Nekrutenko A, Elnitski L, Eswara P, King DC, Yang S, Tyekucheva S, Radakrishnan A, Harris RS, Chiaromonte F, Taylor J, He J, Rijnkels M, Griffiths-Jones S, Ureta-Vidal A, Hoffman MM, Severin J, Searle SM, Law AS, Speed D, Waddington D, Cheng Z, Tuzun E, Eichler E, Bao Z, Flicek P, Shteynberg DD, Brent MR, Bye JM, Huckle EJ, Chatterji S, Dewey C, Pachter L, Kouranov A, Mourelatos Z, Hatzigeorgiou AG, Paterson AH, Ivarie R, Brandstrom M, Axelsson E, Backstrom N, Berlin S, Webster MT, Pourquie O, Reymond A, Ucla C, Antonarakis SE, Long M, Emerson JJ, Betrán E, Dupanloup I, Kaessmann H, Hinrichs AS, Bejerano G, Furey TS, Harte RA, Raney B, Siepel A, Kent WJ, Haussler D, Eyras E, Castelo R, Abril JF, Castellano S, Camara F, Parra G, Guigo R, Bourque G, Tesler G, Pevzner PA, Smit A, Fulton LA, Mardis ER, Wilson RK: Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. / Nature 2004, 432:695-16. CrossRef
  46. USCS Genome Browser Home [http://genome.ucsc.edu/]
  
• 作者单位：Eliyahu M Heifetz (1) (2)
  Janet E Fulton (3)
  Neil P O'Sullivan (3)
  James A Arthur (3)
  Hans Cheng (4)
  Jing Wang (1) (5)
  Morris Soller (6)
  Jack CM Dekkers (1)
  
  1. Department of Animal Science and Center for Integrated Animal Genomics, Iowa State University, 50011, Ames, IA, USA
  2. Department of Molecular Biology, Ariel University, 44837, Ariel, Israel
  3. Hy-Line International, Dallas Center, 50063, Hy-Line, IA, USA
  4. USDA-ARS-ADOL, Avian Disease and Oncology Laboratory,MI,USA, 48823, East Lansing, MI, USA
  5. Pioneer Hi-Bred International Inc, 50131, Johnston, IA, USA
  6. Department of Genetics, The Hebrew University of Jerusalem, 91904, Jerusalem, Israel
  

文摘

Background Marek's disease (MD) is a T-cell lymphoma of chickens caused by the Marek's disease virus (MDV), an oncogenic avian herpesvirus. MD is a major cause of economic loss to the poultry industry and the most serious and persistent infectious disease concern. A full-sib intercross population, consisting of five independent families was generated by crossing and repeated intercrossing of two partially inbred commercial White Leghorn layer lines known to differ in genetic resistance to MD. At the F6 generation, a total of 1615 chicks were produced (98 to 248 per family) and phenotyped for MD resistance measured as survival time in days after challenge with a very virulent plus (vv+) strain of MDV. Results QTL affecting MD resistance were identified by selective DNA pooling using a panel of 15 SNPs and 217 microsatellite markers. Since MHC blood type (BT) is known to affect MD resistance, a total of 18 independent pool pairs were constructed according to family × BT combination, with some combinations represented twice for technical reasons. Twenty-one QTL regions (QTLR) affecting post-challenge survival time were identified, distributed among 11 chromosomes (GGA1, 2, 3, 4, 5, 8, 9, 15, 18, 26 and Z), with about two-thirds of the MD resistance alleles derived from the more MD resistant parental line. Eight of the QTLR associated with MD resistance, were previously identified in a backcross (BC) mapping study with the same parental lines. Of these, 7 originated from the more resistant line, and one from the less resistant line. Conclusion There was considerable evidence suggesting that MD resistance alleles tend to be recessive. The width of the QTLR for these QTL appeared to be reduced about two-fold in the F6 as compared to that found in the previous BC study. These results provide a firm basis for high-resolution linkage disequilibrium mapping and positional cloning of the resistance genes.