Single nucleotide polymorphisms within the bovine DLK1-DIO3 imprinted domain are associated with economically important production traits in cattle

Journal of Heredity

Volumn 102, Issue 1, 2011, Pages 94-101

  Magee, David A ^a   Berry, Donagh P ^a   Berkowicz, Erik W ^a   Sikora, Klaudia M ^a   Howard, Dawn J ^a   Mullen, Michael P ^a   Evans, Ross D ^a   Spillane, Charles ^a   MacHugh, David E ^a  

^a UNIVERSITY COLLEGE DUBLIN   (Ireland)

Author keywords

Association; Bos; callipyge; DLK1 DIO3 domain; Genetic imprinting; Single nucleotide polymorphism

Indexed keywords

DEIODINASE IODOTHYRONINE TYPE III; DELTA LIKE 1 HOMOLOG 1 PROTEIN; MATERNALLY EXPRESSED 3 PROTEIN; MILK FAT; PATERNALLY EXPRESSED 11 PROTEIN; PROTEIN; RETROTRANSPOSON LIKE 1; UNCLASSIFIED DRUG;

ARTICLE; CARCASS; CONFORMATION; COW; DAIRY CATTLE; DNA SEQUENCE; ECONOMIC ASPECT; FERTILITY; GENE LINKAGE DISEQUILIBRIUM; GENE LOCUS; GENETIC SELECTION; GENETIC TRAIT; GENOTYPE; LIVESTOCK; MILK; NONHUMAN; NUCLEOTIDE SEQUENCE; PERINATAL MORTALITY; PHENOTYPE; PREGNANCY; PRIORITY JOURNAL; PROGENY; PROTEIN DOMAIN; SINGLE NUCLEOTIDE POLYMORPHISM; SUBCUTANEOUS FAT;

BOS; BOVINAE; FRIESIA; MAMMALIA; OVIS;

EID: 78650482165     PISSN: 00221503     EISSN: 14657333     Source Type: Journal    
DOI: 10.1093/jhered/esq097     Document Type: Article

References (44)

1. Barrett JC, Fry B, Maller J, Daly MJ. 2005. Haploview: Analysis and visualization of LD and haplotype maps. Bioinformatics. 21:263-265.
2. Bartolomei MS, Tilghman SM. 1997. Genomic imprinting in mammals. Annu Rev Genet. 31:493-525.
3. Berry D, Kearney F, Harris B. 2009. Genomic selection in Ireland. In: Proceedings of the Interbull International Workshop. 2009 Jan 26-29; Uppsala, Sweden. Uppsala (Sweden): Interbull Publications. p. 29-34.
4. Berry DP, Buckley F, Dillon PG, Evans RD, Veerkamp RF. 2004. Genetic relationships among linear type traits, milk yield, body weight, fertility and somatic cell count in primiparous dairy cows. Irish J Agri Food Res. 43:161-176.
5. Berry DP, Shalloo L, Cromie AR, Veerkamp RF, Dillion P, Amer PR, Kearney JF, Evans RD, Wickham B. 2007. The economic breeding index: A generation on. Technical report to the Irish Cattle Breeding Federation. Feb 2007. p. 29-34. Available at: Http://www.icbf.com/publications/files /economic-breeding-index. pdf
6. Byrne K, Colgrave ML, Vuocolo T, Pearson R, Bidwell CA, Cockett NE, Lynn DJ, Fleming-Waddell JN, Tellam RL. 2010. The imprinted retrotransposon-like gene. PEG11 (Rtl1) is expressed as a full-length protein in skeletal muscle from callipyge sheep. PLoS One. 5:e8638.
7. Chen FY, Niu H, Wang JQ, Lei CZ, Lan XY, Zhang CL, Li MJ, Hua LS, Wang J, Chen H. 2010. Polymorphism of DLK1 and CLPG gene and their association with phenotypic traits in Chinese cattle. Mol Biol Rep. DOI: 10.1007/s11033-010-0101- 7.
8. Cheng HC, Zhang FW, Jiang CD, Li FE, Xiong YZ, Deng CY. 2008. Isolation and imprinting analysis of the porcine DLX5 gene and its association with carcass traits. Anim Genet. 39:395-399.
9. Cockett NE, Jackson SP, Shay TL, Farnir F, Berghmans S, Snowder GD, Nielsen DM, Georges M. 1996. Polar overdominance at the ovine callipyge locus. Science. 273:236-238.
10. Cockett NE, Smit MA, Bidwell CA, Segers K, Hadfield TL, Snowder GD, Georges M, Charlier C. 2005. The callipyge mutation and other genes that affect muscle hypertrophy in sheep. Genet Sel Evol. 1(37 Suppl):S65-S81.
11. Davis E, Caiment F, Tordoir X, Cavaille J, Ferguson-Smith A, Cockett N, Georges M, Charlier C. 2005. RNAi-mediated allelic trans-interaction at the imprinted Rtl1/Peg11 locus. Curr Biol. 15:743-749.
12. Davis E, Jensen CH, Schroder HD, Farnir F, Shay-Hadfield T, Kliem A, Cockett N, Georges M, Charlier C. 2004. Ectopic expression of DLK1 protein in skeletal muscle of padumnal heterozygotes causes the callipyge phenotype. Curr Biol. 14:1858-1862.
13. Da Rocha ST, Edwards CA, Ito M, Ogata T, Ferguson-Smith AC. 2008. Genomic imprinting at the mammalian Dlk1-Dio3 domain. Trends Genet. 24:306-316.
14. De Koning DJ, Rattink AP, Harlizius B, van Arendonk JA, Brascamp EW, Groenen MA. 2000. Genome-wide scan for body composition in pigs reveals important role of imprinting. Proc Natl Acad Sci U S A. 97: 7947-7950.
15. Dindot SV, Kent KC, Evers B, Loskutoff N, Womack J, Piedrahita JA. 2004. Conservation of genomic imprinting at the XIST, IGF2, and GTL2 loci in the bovine. Mamm Genome. 15:966-974.
16. Feil R. 2009. Epigenetic asymmetry in the zygote and mammalian development. Int J Dev Biol. 53:191-201.
17. Fleming-Waddell JN, Olbricht GR, Taxis TM, White JD, Vuocolo T, Craig BA, Tellam RL, Neary MK, Cockett NE, Bidwell CA. 2009. Effect of DLK1 and RTL1 but not MEG3 or MEG8 on muscle gene expression in callipyge lambs. PLoS One. 4:e7399.
18. Freking BA, Leymaster KA. 2006. Evaluation of the ovine callipyge locus: IV. Genotypic effects on reproductive traits. J Anim Sci. 84:311-316.
19. Freking BA, Murphy SK, Wylie AA, Rhodes SJ, Keele JW, Leymaster KA, Jirtle RL, Smith TP. 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.
20. Georges M, Charlier C, Cockett N. 2003. The callipyge locus: Evidence for the trans interaction of reciprocally imprinted genes. Trends Genet. 19:248-252.
21. Georgiades P, Watkins M, Surani MA, Ferguson-Smith AC. 2000. Parental origin-specific developmental defects in mice with uniparental disomy for chromosome 12. Development. 127:4719-4728.
22. Gilmour AR, Cullis BR, Gogel BJ, Welham SJ, Thompson R. 2006. ASReml Reference Manual. Hemel Hempstead (UK): VSN International Ltd.
23. Goodall JJ, Schmutz SM. 2007. IGF2 gene characterization and association with rib eye area in beef cattle. Anim Genet. 38:154-161.
24. Hickey JM, Keane MG, Kenny DA, Cromie AR, Veerkamp RF. 2007. Genetic parameters for EUROP carcass traits within different groups of cattle in Ireland. J Anim Sci. 85:314-321.
25. Hill WG, Robertson A. 1968. Linkage disequilibrium in finite populations. Theor Applied Genet. 38:226-231.
26. Horsthemke B, Buiting K. 2008. Genomic imprinting and imprinting defects in humans. Adv Genet. 61:225-246.
27. Khatib H. 2007. Is it genomic imprinting or preferential expression? Bioessays. 29:1022-1028.
28. Kim KS, Kim JJ, Dekkers JC, Rothschild MF. 2004. Polar overdominant inheritance of a DLK1 polymorphism is associated with growth and fatness in pigs. Mamm Genome. 15:552-559.
29. Kurosawa K, Sasaki H, Sato Y, Yamanaka M, Shimizu M, Ito Y, Okuyama T, Matsuo M, Imaizumi K, Kuroki Y, et al. 2002. Paternal UPD14 is responsible for a distinctive malformation complex. Am J Med Genet. 110: 268-272.
30. Magee DA, Berkowicz EW, Sikora KM, Berry DP, Park SDE, Kelly AK, Sweeney T, Kenny DA, Evans RD, Wickham BW, et al. 2010. A catalogue of validated single nucleotide polymorphisms in bovine orthologs of mammalian imprinted genes and associations with beef production traits. Animal. DOI: 10.1017/ S1751731110001163.
31. McGrath J, Solter D. 1984. Completion of mouse embryogenesis requires both the maternal and paternal genomes. Cell. 37:179-183.
32. Mee JF, Berry DP, Cromie AR. 2008. Prevalance of, and risk factors associated with, perinatal calf mortality in pasture-based Holstein-Friesian cows. Animal. 2:613-620.
33. Murphy SK, Nolan CM, Huang Z, Kucera KS, Freking BA, Smith TP, Leymaster KA, Weidman JR, Jirtle RL. 2006. Callipyge mutation affects gene expression in cis: A potential role for chromatin structure. Genome Res. 16:340-346.
34. Nezer C, Moreau L, Brouwers B, Coppieters W, Detilleux J, Hanset R, Karim L, Kvasz A, Leroy P, Georges M. 1999. An imprinted QTL with major effect on muscle mass and fat deposition maps to the IGF2 locus in pigs. Nat Genet. 21:155-156.
35. Ruvinsky A. 1999. Basics of gametic imprinting. J Anim Sci. 2(77 Suppl): 228-237.
36. Sillence MN. 2004. Technologies for the control of fat and lean deposition in livestock. Vet J. 167:242-257.
37. Smit M, Segers K, Carrascosa LG, Shay T, Baraldi F, Gyapay G, Snowder G, Georges M, Cockett N, Charlier C. 2003. Mosaicism of Solid Gold supports the causality of a noncoding A-to-G transition in the determinism of the callipyge phenotype. Genetics. 163:453-456.
38. Surani MA, Barton SC, Norris ML. 1984. Development of reconstituted mouse eggs suggests imprinting of the genome during gametogenesis. Nature. 308:548-550.
39. Tamura K, Dudley J, Nei M, Kumar S. 2007. MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0. Mol Biol Evol. 24:1596-1599.
40. Uemoto Y, Sato S, Ohnishi C, Terai S, Komatsuda A, Kobayashi E. 2009. The effects of single and epistatic quantitative trait loci for fatty acid composition in a Meishan X Duroc crossbred population. J Anim Sci. 87:3470-3476.
41. Van Laere AS, Nguyen M, Braunschweig M, Nezer C, Collette C, Moreau L, Archibald AL, Haley CS, Buys N, Tally M, et al. 2003. A regulatory mutation in IGF2 causes a major QTL effect on muscle growth in the pig. Nature. 425:832-836.
42. Walling GA, Visscher PM, Wilson AD, McTeir BL, Simm G, Bishop SC. 2004. Mapping of quantitative trait loci for growth and carcass traits in commercial sheep populations. J Anim Sci. 82:2234-2245.
43. Waters SM, McCabe MS, Howard DJ, Giblin L, Magee DA, MacHugh DE, Berry DP. 2010. Associations between newly discovered polymorphisms in the Bos taurus growth hormone receptor gene and performance traits in Holstein- Friesian dairy cattle. Anim Genet. DOI: 10.1111/j.1365-2052.2010.02087.x.
44. Williams JL, Dunner S, Valentini A, Mazza R, Amarger V, Checa ML, Crisa A, Razzaq N, Delourme D, Grandjean F, et al. 2009. Discovery, characterization and validation of single nucleotide polymorphisms within 206 bovine genes that may be considered as candidate genes for beef production and quality. Anim Genet. 40:486-491.