Fine mapping of QTL and genomic prediction using allele-specific expression SNPs demonstrates that the complex trait of genetic resistance to Marek's disease is predominantly determined by transcriptional regulation

BMC Genomics

Volumn 16, Issue 1, 2015, Pages

  Cheng, Hans H ^a   Perumbakkam, Sudeep ^a,b   Pyrkosz, Alexis Black ^a   Dunn, John R ^a   Legarra, Andres ^c   Muir, William M ^d  

^a AGRICULTURAL RESEARCH SERVICE   (United States)

^b Michigan State University Microbiology and Molecular Genetics ^*  (United States)

^c CEMAGREF   (France)

^d PURDUE UNIVERSITY   (United States)

Author keywords

Allele specific expression; Complex traits; Disease resistance; Genetic architecture; Genomic selection; Transcriptional regulation

Indexed keywords

ACCURACY; ALLELE; ARTICLE; CHICKEN; GENETIC ASSOCIATION; GENETIC RESISTANCE; GENETIC SELECTION; GENOME; GENOTYPE; HUMAN; MAREK DISEASE; MORBIDITY; PEDIGREE; PHENOTYPE; PREDICTION; PROGENY; QUANTITATIVE TRAIT LOCUS MAPPING; SINGLE NUCLEOTIDE POLYMORPHISM; TRANSCRIPTION REGULATION; ANIMAL; DISEASE RESISTANCE; FEMALE; GENE EXPRESSION; GENETICS; GENOME-WIDE ASSOCIATION STUDY; MALE; MAREK'S DISEASE VIRUS 1; PATHOGENICITY; QUANTITATIVE TRAIT LOCUS; REGULATORY SEQUENCE; VIROLOGY;

ALLELES; ANIMALS; CHICKENS; DISEASE RESISTANCE; FEMALE; GENE EXPRESSION; GENOME-WIDE ASSOCIATION STUDY; GENOTYPE; HERPESVIRUS 2, GALLID; MALE; MAREK DISEASE; PHENOTYPE; POLYMORPHISM, SINGLE NUCLEOTIDE; QUANTITATIVE TRAIT LOCI; REGULATORY ELEMENTS, TRANSCRIPTIONAL;

EID: 84945198517     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/s12864-015-2016-0     Document Type: Article

References (28)

1. Muir WM, Wong GK, Zhang Y, Wang J, Groenen MAM, Crooijmans RPMA, et al. Genome-wide assessment of world-wide chicken SNP genetic diversity indicates significant absence of rare alleles in commercial breeds. Proc Natl Acad Sci USA. 2008;105:17312-7.
2. Osterrieder N, Kamil JP, Schumacher D, Tischer BK, Trapp S. Marek's disease virus: from miasma to model. Nat Rev Microbiol. 2006;4:283-94.
3. Witter RL. Protective efficacy of Marek's disease vaccines. Curr Top Microbiol Immunol. 2001;255:57-90.
4. Witter RL. Increased virulence of Marek's disease virus field isolates. Avian Dis. 1997;41:149-63.
5. Davison F, Nair V. Use of Marek's disease vaccines: could they be driving the virus to increasing virulence? Expert Rev. Vaccines. 2005;4:77-88.
6. Atkins KE, Read AF, Savill NJ, Renz KG, Islam AF, Walkden-Brown SW, et al. Vaccination and reduced cohort duration can drive virulence evolution: Marek's disease virus and industrialized agriculture. Evolution. 2013;67:851-60.
7. Read AF, Baigent SJ, Powers C, Kgosana LB, Blackwell L, Smith LP, et al. Imperfect vaccination can enhance the transmission of highly virulent pathogens. PLoS Biol. 2015;13, e1002198.
8. Cheng HH, Kaiser P, Lamont SJ. Integrated genomics approaches to enhance genetic resistance in chickens. Ann Rev Anim Vet Biosci. 2013;1:239-60.
9. Maurano MT, Humbert R, Rynes E, Thurman RE, Haugen E, Sheffield NC, et al. Systematic localization of common disease-associated variation in regulatory DNA. Science. 2012;337:1190-5.
10. Robinson MR, Wray NR, Visscher PM. Explaining additional genetic variation in complex traits. Trends Genet. 2014;30:124-32.
11. Schaub MA, Boyle AP, Kundaje A, Batzoglou S, Snyder M. Linking disease associations with regulatory information in the human genome. Genome Res. 2012;22:1748-59.
12. Hasin-Brumshtein Y, Hormozdiari F, Martin L, van Nas A, Eskin E, Lusis AJ, et al. Allele-specific expression and eQTL analysis in mouse adipose tissue. BMC Genomics. 2014;15:471.
13. MacEachern S, Muir WM, Crosby S, Cheng HH. Genome-wide identification and quantification of cis- and trans-regulated genes responding to Marek's disease virus infection via analysis of allele-specific expression. Frontier Live Gen. 2012;2:113.
14. Perumbakkam S, Muir WM, Black-Pyrkosz A, Okimoto R, Cheng HH. Comparison and contrast of genes and biological pathways responding to Marek's disease virus infection using allele-specific expression and differential expression in broiler and layer chickens. BMC Genomics. 2013;14:64.
15. International Chicken Genome Sequencing Consortium. Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature. 2004;432:695-716.
16. Legarra A. http://snp.toulouse.inra.fr/~alegarra/. 2013.
17. Liu H-C, Kung H-J, 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;98:9203-8.
18. 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. Cytogen Genome Res. 2003;102:304-8.
19. Niikura M, Liu H-C, Dodgson JB, Cheng HH. A comprehensive screen for chicken proteins that interact with proteins unique to virulent strains of Marek's disease virus. Poultry Sci. 2004;83:1117-23.
20. Gusev A et al. Partitioning heritability of regulatory and cell-type-specific variants across 11 common diseases. Am J Human Genet. 2014;95:535-52.
21. Muir WM. Comparison of genomic and traditional BLUP-estimated breeding value accuracy and selection response under alternative trait and genomic parameters. J Anim Breed Genet. 2007;124:342-55.
22. 2 intercross chickens. Genetics. 1998;148:349-60.
23. Subramaniam S, Johnston J, Preeyanon L, Brown CT, Kung HJ, Cheng HH. Integrated analyses of genome-wide DNA occupancy and expression profiling identify key genes and pathways involved in cellular transformation by Marek's disease oncoprotein. Meq J Virology. 2013;87:9016-29.
24. Subramaniam S, Preeyanon L, Cheng HH. Transcriptional profiling of Meq-dependent genes in Marek's disease resistant and susceptible inbred chicken lines. PLoS One. 2013;8:e78171.
25. Preeyanon L, Brown CT, Cheng HH. Transcriptome variation in response to Marek's disease virus acute infection. Cytogenet Genome Res. 2015;145:154-63.
26. Albert FW, Kruglyak L. The role of regulatory variation in complex traits and disease. Nat Rev Genet. 2015;16:197-212.
27. Habier D, Fernando RL, Kizilkaya K, Garrick DJ. Extension of the Bayesian alphabet for genomic selection. BMC Bioinfo. 2011;12:186.
28. Legarra A, Croiseau P, Sanchez MP, Teyssèdre S, Sallé G, Allais S, et al. A comparison of methods for whole-genome QTL mapping using dense markers in four livestock species. Genet Select Evol. 2015;47:6.