The genetic architecture of climatic adaptation of tropical cattle

PLoS ONE

Volumn 9, Issue 11, 2014, Pages

  Porto Neto, Laercio R ^a   Reverter, Antonio ^a   Prayaga, Kishore C ^b   Chan, Eva K F ^c   Johnston, David J ^d   Hawken, Rachel J ^e   Fordyce, Geoffry ^a   Garcia, Jose Fernando ^f   Sonstegard, Tad S ^g   Bolormaa, Sunduimijid ^h   Goddard, Michael E ^h   Burrow, Heather M ^a   Henshall, John M ^a   Lehnert, Sigrid A ^a   Barendse, William ^a  

^a UNIVERSITY OF QUEENSLAND   (Australia)

^b ZOETIS   (United States)

^c GARVAN INSTITUTE OF MEDICAL RESEARCH   (Australia)

^d UNIVERSITY OF NEW ENGLAND   (Australia)

^e Animal Genetics and Breeding Unit University of New England ^*  (United States)

^f SÃO PAULO STATE UNIVERSITY UNESP   (Brazil)

^g AGRICULTURAL RESEARCH SERVICE   (United States)

^h DEPARTMENT OF PRIMARY INDUSTRIES   (Australia)

Author keywords

[No Author keywords available]

Indexed keywords

ACCLIMATIZATION; ANGUS CATTLE; ARTICLE; BODY CONSTITUTION; BRAHMAN CATTLE; CATTLE; COAT COLOR; CONTROLLED STUDY; FECES ANALYSIS; FLIGHT TIME; GENETIC ASSOCIATION; GENETIC CORRELATION; GENETIC DIFFERENCE; GENETIC SELECTION; GENETIC TRAIT; GENETIC VARIABILITY; HAPLOTYPE; LESION DUE TO BITING BY BUFFALO FLY; NELLORE CATTLE; NONHUMAN; PENDULOUSNESS OF THE PENILE SHEATH; RECTUM TEMPERATURE; SINGLE NUCLEOTIDE POLYMORPHISM; TICK INFESTATION; TROPIC CLIMATE; YEARLING WEIGHT; ADAPTATION; ALGORITHM; ANIMAL; BOVINE; BREEDING; CLIMATE CHANGE; ENVIRONMENT; FEMALE; GENE EXPRESSION; GENE FREQUENCY; GENE LINKAGE DISEQUILIBRIUM; GENETICS; GENOME; GENOTYPE; MALE; PROCEDURES; QUANTITATIVE TRAIT;

BOS;

ADAPTATION, PHYSIOLOGICAL; ALGORITHMS; ANIMALS; BREEDING; CATTLE; CLIMATE CHANGE; ENVIRONMENT; FEMALE; GENE EXPRESSION; GENE FREQUENCY; GENETIC VARIATION; GENOME; GENOTYPE; HAPLOTYPES; LINKAGE DISEQUILIBRIUM; MALE; POLYMORPHISM, SINGLE NUCLEOTIDE; QUANTITATIVE TRAIT, HERITABLE; SELECTION, GENETIC; TROPICAL CLIMATE;

EID: 84913582594     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0113284     Document Type: Article

References (50)

1. Foley JA, Ramankutty N, Brauman KA, Cassidy ES, Gerber JS, et al. (2011) Solutions for a cultivated planet. Nature 478: 337-342.
2. Herrero M, Thornton PK, Notenbaert AM, Wood S, Msangi S, et al. (2010) Smart investments in sustainable food production: Revisiting mixed crop-livestock systems. Science 327: 822-825.
3. Frisch JE, Vercoe JE (1977) Food intake, eating rate, weight gains, metabolic-rate and efficiency of feed utilization in Bos taurus and Bos indicus crossbred cattle. Animal Production 25: 343-358.
4. Frisch JE, Vercoe JE (1984) An analysis of growth of different cattle genotypes reared in different environments Journal of Agricultural Science 103: 137-153.
5. Davis GP (1993) Genetic parameters for tropical beef cattle in northern Australia: a review. Australian Journal of Agricultural Research 44: 179-198.
6. Menjo D, Bebe B, Okeyo A, Ojango J (2009) Analysis of early survival of Holstein-Friesian heifers of diverse sire origins on commercial dairy farms in Kenya. Tropical Animal Health and Production 41: 171-181.
7. Guis H, Caminade C, Calvete C, Morse AP, Tran A, et al. (2012) Modelling the effects of past and future climate on the risk of bluetongue emergence in Europe. Journal of the Royal Society Interface 9: 339-350.
8. Blackshaw JK, Blackshaw AW (1994) Heat stress in cattle and the effect of shade on production and behaviour: a review. Australian Journal of Experimental Agriculture 34: 285-295.
9. McLean RW, McCown RL, Little DA, Winter WH, Dance RA (1983) An analysis of cattle live-weight changes on tropical grass pasture during the dry and early wet seasons in northern Australia. 1. The nature of weight changes. Journal of Agricultural Science 101: 17-24.
10. Wharton RH, Utech KBW, Turner HG (1970) Resistance to the cattle tick, Boophilus microplus in a herd of Australian Illawarra Shorthorn cattle: its assessment and heritability. Australian Journal of Agricultural Research 21: 163-181.
11. Bock RE, Kingston TG, De Vos AJ (1999) Effect of breed of cattle on transmission rate and innate resistance to infection with Babesia bovis and B. bigemina transmitted by Boophilus microplus. Australian Veterinary Journal 77: 461-464.
12. Peacock FM, Koger M, Olson TA, Crockett JR (1981) Additive genetic and heterosis effects in crosses among cattle breeds of British, European and Zebu origin. Journal of Animal Science 52: 1007-1013.
13. Seifert GW (1971) Variations between and within breeds of cattle in resistance to field infestations of the cattle tick (Boophilus microplus). Australian Journal of Agricultural Research 22: 159-168.
14. Mayr E (1963) Animal Species and Evolution: Belknap Press of Harvard University Press, Cambridge, Massachusetts.
15. Dobzhansky T (1952) Nature and origin of heterosis. In: Gowen JW, editor. Heterosis. Ames, Iowa: Iowa State College Press.
16. Barendse W, Harrison BE, Hawken RJ, Ferguson DM, Thompson JM, et al. (2007) Epistasis between calpain 1 and its inhibitor calpastatin within breeds of cattle. Genetics 176: 2601-2610.
17. Hawken RJ, Zhang YD, Fortes MRS, Collis E, Barris WC, et al. (2012) Genome-wide association studies of female reproduction in tropically adapted beef cattle. Journal of Animal Science 90: 1398-1410.
18. Turner LB, Harrison BE, Bunch RJ, Porto Neto LR, Li YT, et al. (2010) A genome wide association study of tick burden and milk composition in cattle. Animal Production Science 50: 235-245.
19. 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. Proceedings of the National Academy of Sciences of the United States of America 106: 9362-9367.
20. Speliotes EK, Willer CJ, Berndt SI, Monda KL, Thorleifsson G, et al. (2010) Association analyses of 249,796 individuals reveal 18 new loci associated with body mass index. Nature Genetics 42: 937-U953.
21. Allen HL, Estrada K, Lettre G, Berndt SI, Weedon MN, et al. (2010) Hundreds of variants clustered in genomic loci and biological pathways affect human height. Nature 467: 832-838.
22. Sanders JO (1980) History and development of zebu cattle in the United States. Journal of Animal Science 50: 1188-1200.
23. Gibbs RA, Taylor JF, Van Tassell CP, Barendse W, Eversole KA, et al. (2009) Genome-wide survey of SNP variation uncovers the genetic structure of cattle breeds. Science 324: 528-532.
24. Bolormaa S, Pryce JE, Kemper K, Savin K, Hayes BJ, et al. (2013) Accuracy of prediction of genomic breeding values for residual feed intake and carcass and meat quality traits in Bos taurus, Bos indicus, and composite beef cattle. Journal of Animal Science 91: 3088-3104.
25. Porto-Neto LR, Sonstegard TS, Liu GE, Bickhart DM, Silva MVB, et al. (2013) Genomic divergence of zebu and taurine cattle identified through high-density SNP genotyping. BMC Genomics 14: 876.
26. Burrow HM (1998) The effects of inbreeding on productive and adaptive traits and temperament of tropical beef cattle. Livestock Production Science 55: 227-243.
27. Sutherst RW, Bourne AS, Maywald GF, Seifert GW (2006) Prevalence, severity, and heritability of Stephanofilaria lesions on cattle in central and southern Queensland, Australia. Australian Journal of Agricultural Research 57: 743-750.
28. Prayaga KC, Corbet NJ, Johnston DJ, Wolcott ML, Fordyce G, et al. (2009) Genetics of adaptive traits in heifers and their relationship to growth, pubertal and carcass traits in two tropical beef cattle genotypes. Animal Production Science 49: 413-425.
29. Olson TA (1999) Genetics of color variation. In: Fries R, Ruvinsky A, editors. The genetics of cattle. Wallingford: CAB International. pp. 33-53.
30. Porto-Neto LR, Kijas JW, Reverter A (2014) The extent of linkage disequilibrium in beef cattle breeds using high-density SNP genotypes. Genetics Selection Evolution 46: 22.
31. Karim L, Takeda H, Lin L, Druet T, Arias JAC, et al. (2011) Variants modulating the expression of a chromosome domain encompassing PLAG1 influence bovine stature. Nature Genetics 43: 405-413.
32. Mariasegaram M, Chase CC, Chaparro JX, Olson TA, Brenneman RA, et al. (2007) The slick hair coat locus maps to chromosome 20 in Senepol-derived cattle. Animal Genetics 38: 54-59.
33. Fortes MRS, Kemper K, Sasazaki S, Reverter A, Pryce JE, et al. (2013) Evidence for pleiotropism and recent selection in the PLAG1 region in Australian Beef cattle. Animal Genetics 44: 636-647.
34. Hudson NJ, Reverter A, Wang YH, Greenwood PL, Dalrymple BP (2009) Inferring the transcriptional landscape of bovine skeletal muscle by integrating co-expression networks. PLoS ONE 4: e7249.
35. Lehnert SA, Byrne KA, Reverter A, Nattrass GS, Greenwood PL, et al. (2006) Gene expression profiling of bovine skeletal muscle in response to and during recovery from chronic and severe undernutrition. Journal of Animal Science 84: 3239-3250.
36. Heffernan C (2013) Introduction: special issue on animal health and climate change. Animal Health Research Reviews.
37. Running SW (2012) A measurable planetary boundary for the Biosphere. Science 337: 1458-1459.
38. Barwick SA, Johnston DJ, Burrow HM, Holroyd RG, Fordyce G, et al. (2009) Genetics of heifer performance in 'wet' and 'dry' seasons and their relationships with steer performance in two tropical beef genotypes. Animal Production Science 49: 367-382.
39. Barendse W, Reverter A, Bunch RJ, Harrison BE, Barris W, et al. (2007) A validated whole genome association study of efficient food conversion. Genetics 176: 1893-1905.
40. Matukumalli LK, Lawley CT, Schnabel RD, Taylor JF, Allan MF, et al. (2009) Development and characterization of a high density SNP genotyping assay for cattle. PLoS ONE 4: e5350.
41. Zimin AV, Delcher AL, Florea L, Kelley DR, Schatz MC, et al. (2009) A whole-genome assembly of the domestic cow, Bos taurus. Genome Biol 10: R42.
42. Browning SR, Browning BL (2010) High-Resolution Detection of Identity by Descent in Unrelated Individuals. American Journal of Human Genetics 86: 526-539.
43. Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MAR, et al. (2007) PLINK: A tool set for whole-genome association and population-based linkage analyses. American Journal of Human Genetics 81: 559-575.
44. Gibbs RA, Taylor JF, Van Tassell CP, Barendse W, Eversole KA, et al. (2009) Genome-wide survey of SNP variation uncovers the genetic structure of cattle breeds. Science 324: 528-532.
45. Akerman J (1982) American Brahman: a history of the American Brahman. Houston, Tex.: American Brahman Breeders Association. 384 p.
46. Felius M (1985) Genus Bos: Cattle Breeds of the World. Rahway, NJ: Merck and Co., Inc.
47. Alexander DH, Novembre J, Lange K (2009) Fast model-based estimation of ancestry in unrelated individuals. Genome Research 19: 1655-1664.
48. Perez-Enciso M, Misztal I (2011) Qxpak.5: Old mixed model solutions for new genomics problems. BMC Bioinformatics 12: 202.
49. Falconer DS, Mackay TFC (1996) Introduction to Quantitative Genetics. Harlow, Essex, UK: Longmans Green.
50. Bolormaa S, Pryce JE, Reverter A, Zhang Y, Barendse W, et al. (2014) A multi-trait, meta-analysis for detecting pleiotropic polymorphisms for stature, fatness and reproduction in beef cattle. PLoS Genetics 10: e1004198.