Livestock and the promise of genomics

Genome

Volumn 56, Issue 10, 2013, Pages 556-566

  Ludu, Jagjit S ^a   Plastow, Graham S ^a  

^a UNIVERSITY OF ALBERTA   (Canada)

Author keywords

Cattle; Genomic selection; Genomics; Livestock; Single nucleotide polymorphisms; Swine

Indexed keywords

ANIMAL; ANIMAL WELFARE; CANADA; CATTLE; COMPUTER PROGRAM; ECONOMICS; GENETIC VARIABILITY; GENETICS; GENOME; GENOMICS; HUMAN; LIVESTOCK; PHENOTYPE; REVIEW; SINGLE NUCLEOTIDE POLYMORPHISM; STANDARD; SWINE;

ANIMAL WELFARE; ANIMALS; CANADA; CATTLE; GENETIC VARIATION; GENOME; GENOMICS; HUMANS; LIVESTOCK; PHENOTYPE; POLYMORPHISM, SINGLE NUCLEOTIDE; SOFTWARE; SWINE;

EID: 84889825044     PISSN: 08312796     EISSN: None     Source Type: Journal    
DOI: 10.1139/gen-2013-0080     Document Type: Review

References (60)

1. Abler, D. 2010. Demand growth in developing countries. OECD Food, Agriculture and Fisheries Papers, No. 29, OECD Publishing. 10.1787/5km91p2xcsd4- en.
2. Agriculture and Agri-Food Canada. 2013 a. Harper government helps boost exports in high-quality genetics. [Online.] Available from http://www.agr.gc.ca/ cb/index-e.php?s1=n&s2=2013&page=n130315a [accessed 15 April 2013].
3. Agriculture and Agri-Food Canada. 2013 b. An overview of the Canadian Agriculture and Agri-Food system 2013. [Online.] Available from http://www4.agr.gc.ca/AAFC-AAC/display-afficher.do?id=1331319696826&lang= eng [accessed 15 April 2013].
4. Alexandratos, N., Bruinsma, J., Bödeker, G., Schmidhuber, J., Broca, S., Shetty P., and Ottaviani M.G. 2012. World agriculture towards 2030/2050: ESA working paper No. 12-03, Agricultural Development Economics Division, Food and Agriculture Organization of the United Nations.
5. Allan G.M. Ellis J.A. 2000. Porcine circoviruses: a review. J. Vet. Diagn. Invest. 12: 3-14. 10.1177/104063870001200102. 10690769.
6. Basarab J.A. Baron V.S. López-Campos O. Aalhus J.L. Haugen-Kozyra K. Okine E.K. 2012. Greenhouse gas emissions from calf-and yearling-fed beef production systems, with and without the use of growth promotants. Animals, 2: 195-220. 10.3390/ani2020195.
7. Basarab J.A. Beauchemin K.A. Baron V.S. Ominski K.H. Guan L.L. Miller S.P. Crowley J.J. 2013. Reducing GHG emissions through genetic improvement for feed efficiency: effects on economically important traits and enteric methane production. Animals, 7 (s2): 303-315. 10.1017/S1751731113000888. 23739472.
8. Blair D.B. 2010. The benefits of genomics to the dairy industry. WCDS Advances in Dairy Technology, 22: 341-348.
9. Boddicker N. Waide E.H. Rowland R.R.R. Lunney J.K. Garrick D.J. Reecy J.M. Dekkers J.C.M. 2012. Evidence for a major QTL associated with host response to porcine reproductive and respiratory syndrome virus challenge. J. Anim. Sci. 90: 1733-1746. 10.2527/jas.2011-4464. 22205662.
10. Bonabeau E. 2002. Agent-based modeling: methods and techniques for simulating human systems. Proc. Natl. Acad. Sci. U.S.A. 99: 7280-7287. 10.1073/pnas.082080899. 12011407. (Pubitemid 34522724)
11. Canadian International Development Agency (CIDA). 2013. CIDA's Food Security Strategy. [Online.] Available from http://www.acdi-cida.gc.ca/acdi- cida/acdi-cida.nsf/eng/NAD-31210472-LHX [accessed 12 April 2013].
12. Canavez F.C. Luche D.D. Stothard P. Leite K.R.M. Sousa-Canavez J.M. Plastow G. et al 2012. Genome sequence and assembly of Bos indicus. J. Hered. 103: 342-348. 10.1093/jhered/esr153. 22315242.
13. eBiz Professionals, Inc. 2010. Analysis of the economic and animal production impact of porcine circovirus associated disease (PCVAD) on the Canadian and North American pork industries. Available from the Canadian Swine Health Board, Ottawa, Ont.
14. Fix J.S. Cassady J.P. van Heugten E. Hanson D.J. See M.T. 2010. Differences in lean growth performance of pigs sampled from 1980 and 2005 commercial swine fed 1980 and 2005 representative feeding programs. Livest. Sci. 128: 108-114. 10.1016/j.livsci.2009.11.006.
15. Food and Agriculture Organization of the United Nations (UNFAO). 2002. World agriculture: towards 2015/2030 summary report. Rome.
16. Forsberg C.W. Meidinger R.G. Liu M. Cottrill M. Golovan S. Phillips J.P. 2013. Integration, stability and expression of the E. coli phytase transgene in the Cassie line of Yorkshire Enviropig™. Transgenic Res. 22: 379-389. 10.1007/s11248-012-9646-7.
17. Gillespie J. Opriessnig T. Meng X.J. Pelzer K. Buechner-Maxwell V. 2009. Porcine circovirus type 2 and porcine circovirus-associated disease. J. Vet. Intern. Med. 23: 1151-1163. 10.1111/j.1939-1676.2009.0389.x. 19780932.
18. Grant J.R. Arantes A.S. Liao X. Stothard P. 2011. In-depth annotation of SNPs arising from resequencing projects using NGS-SNP. Bioinformatics, 27: 2300-2301. 10.1093/bioinformatics/btr372. 21697123.
19. Groenen M.A.M. Archibald A.L. Uenishi H. Tuggle C.K. Takeuchi Y. Rothschild M.F. et al 2012. Analyses of pig genomes provide insight into porcine demography and evolution. Nature, 491: 393-398. 10.1038/nature11622. 23151582.
20. Harding, J.C. 1996. Postweaning multisystemic wasting syndrome: preliminary epidemiology and clinical findings. In Proceedings of the Western Canadian Association of Swine Practitioners, Saskatoon, Sask. 1996:21.
21. Holtkamp D.J. Kliebenstein J.B. Neumann E.J. Zimmerman J.J. Rotto H.F. Yoder T.K. et al 2013. Assessment of the economic impact of porcine reproductive and respiratory syndrome virus on United States pork producers. J. Swine Health Prod. 21: 72-84.
22. International Livestock Research Institute. 2011. CGIAR research program 3.7: More meat, milk and fish by and for the poor. [Online.] Available from http://livestockfish.cgiar.org/resources/[accessed 12 April 2013].
23. Keirstead N.D. Hayes M.A. Vandervoort G.E. Brooks A.S. Squires E.J. Lillie B.N. 2011. Single nucleotide polymorphisms in collagenous lectins and other innate immune genes in pigs with common infectious diseases. Vet. Immunol. Immunopathol. 142: 1-13. 10.1016/j.vetimm.2011.02.011. 21570129.
24. Kinghorn B.P. 2011. An algorithm for efficient constrained mate selection. Genet. Sel. Evol. 43: 4. 10.1186/1297-9686-43-4. 21251244.
25. Kinghorn B.P. 2012. The use of genomics in the management of livestock. Anim. Prod. Sci. 52: 78-91. 10.1071/AN11092.
26. Kosseim P. Chapman S. 2011. Science and society: Some "made-in-Canada" options for improving integration. Account. Res. 18: 194-216. 21574074.
27. Lane, A.S., and Schaer, L. 2010. The real dirt on farming II. The Ontario Farm Animal Council.
28. Liao, X., Peng, F., Forni, S., McLaren, D., Plastow, G., and Stothard, P. 2013. Whole genome sequencing of Gir cattle for identifying polymorphisms and loci under selection. Genome, 56. This issue. 10.1139/gen-2013-0082.
29. Lim W.S. Thomson A. Little P. 2007. Preparing for the next flu pandemic. Br. Med. J. 334: 268. 10.1136/bmj.39101.628715.80.
30. Lu, D., Sargolzaei, M., Li, C., Abo-Ismail, M., Vander Voort, G., Wang, Z., et al. 2013. Association analysis for feed efficiency traits in beef cattle using preserved haplotypes. Genome, 56. This issue. 10.2527/jas.2012-5716.
31. Lunney J.K. Steibel J.P. Reecy J.M. Fritz E. Rothschild M.F. Kerrigan M. et al 2011. Probing genetic control of swine responses to PRRSV infection: current progress of the PRRS host genetics consortium. BMC Proc. 5 (Suppl. 4): S30. 10.1186/1753-6561-5-S4-S30.
32. Lyall J. Irvine R.M. Sherman A. McKinley T.J. Núñez A. Purdie A. et al 2011. Suppression of avian influenza transmission in genetically modified chickens. Science, 331: 223-226. 10.1126/science.1198020. 21233391.
33. McAfee A.J. McSorley E.M. Cuskelly G.J. Moss B.W. Wallace J.M.W. Bonham M.P. Fearon A.M. 2010. Red meat consumption: an overview of the risks and benefits. Meat Sci. 84: 1-13. 10.1016/j.meatsci.2009.08.029. 20374748.
34. Meijerink E. Fries R. Vogell P. Masabanda J. Wigger G. Stricker C. et al 1997. Two α(1,2) fucosyltransferase genes on porcine chromosome 6q11 are closely linked to the blood group inhibitor (S) and Escherichia coli F18 receptor (ECF18R) loci. Mamm. Genome, 8: 736-741. 10.1007/s003359900556. (Pubitemid 27439814)
35. Miglior, F., Chesnais, J., and van Doormaal, B.J. 2012. Genetic improvement: a major component of increased dairy farm profitability. [Online.] Available from http://cgil.uoguelph.ca/dcbgc/Agenda%201209/ Genetic%20Improvement%20-%20Miglior%20et%20al.pdf [accessed 2 April 2013].
36. Miller G.Y. Liu X. McNamara P.E. Barber D.A. 2005. Influence of Salmonella in pigs preharvest and during pork processing on human health costs and risks from pork. J. Food Protect. 68: 1788-1798. (Pubitemid 41446108)
37. Ministry of Agriculture and Agri-Food. 2012. Agriculture and agri-food market access report: re-opening, maintaining, and expanding markets. Government of Canada.
38. Nkrumah J.D. Okine E.K. Mathison G.W. Schmid K. Li C. Basarab J.A. et al 2006. Relationships of feedlot feed efficiency, performance and feeding behaviour with metabolic rate, methane production, and energy partitioning in beef cattle. J. Anim. Sci. 84: 145-153. 16361501. (Pubitemid 44405737)
39. Ontario Livestock & Poultry Council. 2012. Livestock on-farm biosecurity information guide, Ontario. Report. [Online.] Available from http://www.ontlpc.ca/pdfs/downloads/olpc-livestock-web.pdf [accessed 2 April 2013].
40. Psouni E. Janke A. Garwicz M. 2012. Impact of carnivory on human development and evolution revealed by a new unifying model of weaning in mammals. PLoS One, 7: e32452. 10.1371/journal.pone.0032452. 22536316.
41. Ramos A.M. Crooijmans R.P.M.A. Affara N.A. Amaral A.J. Archibald A.L. Beever J.E. et al 2009. Design of a high density SNP genotyping assay in the pig using SNPs identified and characterized by next generation sequencing technology. PLoS One, 4: e6524. 10.1371/journal.pone.0006524. 19654876.
42. Ren J. Yan X. Ai H. Zhang Z. Huang X. Ouyang J. et al 2012. Susceptibility towards enterotoxigenic Escherichia coli F4ac diarrhea is governed by the MUC13 gene in pigs. PLoS One, 7: e44573. 10.1371/journal.pone. 0044573. 22984528.
43. Statistics Canada. 2013. Population and dwelling counts for census metropolitan areas and census agglomerations, 2011 and 2006 censuses. [Online.] Available from http://www12.statcan.gc.ca/census-recensement/2011/dp-pd/hlt-fst/ pd-pl/Table-Tableau.cfm?LANG=Eng&T=201&S=3&O=D&RPP=150 [accessed 2 April 2013].
44. Stephens T.P. McAllister T.A. Stanford K. 2009. Perineal swabs reveal effect of super shedders on the transmission of Escherichia coli O157:H7 in commercial feedlots. J. Anim. Sci. 87: 4151-4160. 10.2527/jas.2009-1967. 19684276.
45. Stothard P. Choi J.W. Basu U. Sumner-Thomson J.M. Meng Y. Liao X. Moore S. 2011. Whole genome resequencing of black Angus and Holstein cattle for SNP and CNV discovery. BMC Genomics, 12: 559. 10.1186/1471-2164-12-559. 22085807.
46. Tan W.S. Carlson D.F. Walton M.W. Fahrenkrug S.C. Hackett P.B. 2012. Precision editing of large animal genomes. Adv. Genet. 80: 37-97. 10.1016/B978-0-12-404742-6.00002-8. 23084873.
47. Tang G. Stewart-Smith J. Plastow G. Moore S. Basarab J. MacNeil M.D. Wang Z. 2011. Optimizing a beef production system using specialized sire and dam lines. Can J. Anim. Sci. 91: 353-361. 10.4141/cjas10073.
48. The Bovine Genome Sequencing and Analysis Consortium, Elsik C.G. Tellam R.L. Worley K.C. 2009. The genome sequence of Taurine cattle: a window to ruminant biology and evolution. Science, 324: 522-528. 10.1126/science.1169588. 19390049.
49. The Livestock, Environment, and Development Initiative. 2006. Livestock's long shadow: environmental issues and options. Available from the United Nations Food and Agriculture Organization, Rome, Italy.
50. Thompson-Crispi K.A. Mallard B.A. 2012. Type 1 and type 2 immune response profiles of commercial dairy cows in 4 regions across Canada. Can. J. Vet. Res. 76: 120-128. 23024454.
51. Tuggle C.K. Bearson S.M. Uthe J.J. Huang T.H. Couture O.P. Wang Y.F. et al 2010. Methods for transcriptomic analyses of the porcine host immune response: application to Salmonella infection using microarrays. Vet. Immunol. Immunopathol. 138: 280-291. 10.1016/j.vetimm.2010.10.006. 21036404.
52. Uthe J.J. Wang Y. Qu L. Nettleton D. Tuggle C.K. Bearson S.M.D. 2009. Correlating blood immune parameters and a CCT7 genetic variant with the shedding of Salmonella enterica serovar Typhimurium in swine. Vet. Microbiol. 135: 384-388. 10.1016/j.vetmic.2008.09.074. 18996651.
53. van der Steen, H.A.M., Prall, G.F.W., and Plastow, G.S. 2005. Application of genomics to the pork industry. J. Anim. Sci. 83 (E. Suppl.): E1-E8.
54. van Eenennaam A.L. Muir W.M. 2011. Transgenic salmon: a final leap to the grocery shelf? Nat. Biotechnol. 29: 706-710. 10.1038/nbt.1938. 21822244.
55. van Tassell C.P. Smith T.P.L. Matukumalli L.K. Taylor J.F. Schnabel R.D. Lawley C.T. et al 2008. SNP discovery and allele frequency estimation by deep sequencing of reduced representation libraries. Nat. Methods, 5: 247-252. 10.1038/nmeth.1185. (Pubitemid 351325649)
56. Wang Y. Qu L. Uthe J.J. Bearson S.M.D. Kuhar D. Lunney J.K. et al 2007. Global transcriptional response of porcine mesenteric lymph nodes to Salmonella enterica serovar Typhimurium. Genomics, 90: 72-84. 10.1016/j.ygeno.2007.03.018. 17499962. (Pubitemid 46891742)
57. Wang Y. Cai Z. Stothard P. Moore S.S. Goebel R. Wang L. Lin G. 2012. Fast accurate missing SNP genotype local imputation. BMC Res. Notes, 5: 404. 10.1186/1756-0500-5-404.
58. Wang. Z., Nascimento, M.A., and MacGregor, M.H. 2011. Towards end-to-end routing for periodic mobile objects. In Proceedings of the First ACM International Symposium on Design and Analysis of Intelligent Vehicular Networks and Applications (DIVANet'11), Miami Beach, Florida, USA. 10.1145/2069000. 2069012.
59. Wang Z. Basarab J.A. Goonewardene L.A. Colazo M.G. Ambrose D.J. Marques E. et al 2012. Impact of selection for residual feed intake on breeding soundness and reproductive performance of bulls on pasture-based multi-sire mating. J. Anim. Sci. 90: 2963-2969. 10.2527/jas.2011-4521. 22585812.
60. Wetterstrand, K.A. 2013. DNA sequencing costs: data from the NHGRI genome sequencing program (GSP). [Online.] Available from www.genome.gov/ sequencingcosts [accessed 15 April 2013].