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Genome-wide association study for growth traits in Nelore cattle

Published online by Cambridge University Press:  16 November 2017

A. P. N. Terakado ,
R. B. Costa ,
G. M. F. de Camargo ,
N. Irano ,
T. Bresolin ,
L. Takada ,
C. V. D. Carvalho ,
H. N. Oliveira ,
R. Carvalheiro  and
F. Baldi
...Show all authors
A. P. N. Terakado
Affiliation:
Departamento de Zootecnia, Universidade Estadual Paulista (Unesp), Faculdade de Ciências Agrárias e Veterinárias, Jaboticabal-SP, Brazil
R. B. Costa*
Affiliation:
Escola de Medicina Veterinária e Zootecnia, Universidade Federal da Bahia (UFBA), Salvador-BA, Brazil
G. M. F. de Camargo
Affiliation:
Escola de Medicina Veterinária e Zootecnia, Universidade Federal da Bahia (UFBA), Salvador-BA, Brazil
N. Irano
Affiliation:
Departamento de Zootecnia, Universidade Estadual Paulista (Unesp), Faculdade de Ciências Agrárias e Veterinárias, Jaboticabal-SP, Brazil
T. Bresolin
Affiliation:
Departamento de Zootecnia, Universidade Estadual Paulista (Unesp), Faculdade de Ciências Agrárias e Veterinárias, Jaboticabal-SP, Brazil
L. Takada
Affiliation:
Departamento de Zootecnia, Universidade Estadual Paulista (Unesp), Faculdade de Ciências Agrárias e Veterinárias, Jaboticabal-SP, Brazil
C. V. D. Carvalho
Affiliation:
Escola de Medicina Veterinária e Zootecnia, Universidade Federal da Bahia (UFBA), Salvador-BA, Brazil
H. N. Oliveira
Affiliation:
Departamento de Zootecnia, Universidade Estadual Paulista (Unesp), Faculdade de Ciências Agrárias e Veterinárias, Jaboticabal-SP, Brazil
R. Carvalheiro
Affiliation:
Departamento de Zootecnia, Universidade Estadual Paulista (Unesp), Faculdade de Ciências Agrárias e Veterinárias, Jaboticabal-SP, Brazil
F. Baldi
Affiliation:
Departamento de Zootecnia, Universidade Estadual Paulista (Unesp), Faculdade de Ciências Agrárias e Veterinárias, Jaboticabal-SP, Brazil
L. G. de Albuquerque
Affiliation:
Departamento de Zootecnia, Universidade Estadual Paulista (Unesp), Faculdade de Ciências Agrárias e Veterinárias, Jaboticabal-SP, Brazil
*
†E-mail: raphaelbcosta@gmail.com
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Abstract

The objective of this study was to investigate the association of single nucleotide polymorphisms (SNPs) with birth weight, weight gain from birth to weaning and from weaning to yearling, yearling height and cow weight in Nelore cattle. Data from 5064 animals participating in the DeltaGen and PAINT breeding programs were used. The animals were genotyped with a panel of 777 962 SNPs (Illumina BovineHD BeadChip) and 412 993 SNPs remained after quality control analysis of the genomic data. A genome-wide association study was performed using a single-step methodology. The analyses were processed with the BLUPF90 family of programs. When applied to a genome-wide association studies, the single-step GBLUP methodology is an iterative process that estimates weights for the SNPs. The weights of SNPs were included in all analyses by iteratively applying the single-step GBLUP methodology and repeated twice so that the effect of the SNP and the effect of the animal were recalculated in order to increase the weight of SNPs with large effects and to reduce the weight of those with small effects. The genome-wide association results are reported based on the proportion of variance explained by windows of 50 adjacent SNPs. Considering the two iterations, only windows with an additive genetic variance >1.5% were presented in the results. Associations were observed with birth weight on BTA 14, with weight gain from birth to weaning on BTA 5 and 29, with weight gain from weaning to yearling on BTA 11, and with yearling height on BTA 8, showing the genes TMEM68 (transmembrane protein 8B) associated with birth weight and yearling height, XKR4 (XK, Kell blood group complex subunit-related family, member 4) associated with birth weight, NPR2 (natriuretic peptide receptor B) associated with yearling height, and REG3G (regenerating islet-derived 3-gamma) associated with weight gain from weaning to yearling. These genes play an important role in feed intake, weight gain and the regulation of skeletal growth.

Keywords

beef cattleheightsingle-stepSNPweight

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Type
Research Article
Information
animal , Volume 12 , Issue 7 , July 2018 , pp. 1358 - 1362
Copyright
© The Animal Consortium 2017 

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References

Aguilar, I, Misztal, I, Johnson, DL, Legarra, A, Tsuruta, S and Lawlor, TJ 2010. Hot topic: a unified approach to utilize phenotypic, full pedigree, and genomic information for genetic evaluation of Holstein final score. Journal of Dairy Science 93, 743–752.CrossRefGoogle Scholar
Alexander, LJ, Geary, TW, Snelling, WM and MacNeil, MD 2007. Quantitative trait loci with additive effects on growth and carcass traits in a Wagyu-Limousin F2 population. Animal Genetics 38, 413–416.CrossRefGoogle Scholar
Baldi, F, Albuquerque, LG and Alencar, MM 2010. Random regression models on Legendre polynomials to estimate genetic parameters for weights from birth to adult age in Canchim cattle. Journal of Animal Breeding and Genetics 127, 289–299.CrossRefGoogle ScholarPubMed
Boligon, AA, Albuquerque, LG, Mercadante, MEZ and Lôbo, RB 2009. Herdabilidades e correlações entre pesos do nascimento à idade adulta em rebanhos da raça Nelore. Revista Brasileira de Zootecnia 38, 2320–2326.CrossRefGoogle Scholar
Bolormaa, S, Hayes, BJ, Savin, K, Hawken, R, Barendse, W, Arthur, PF, Herd, RM and Goddard, ME 2011. Genome-wide association studies for feedlot and growth traits in cattle. Journal of Animal Science 89, 1684–1697.CrossRefGoogle ScholarPubMed
Buzanskas, ME, Grossi, DA, Ventura, RV, Schenkel, FS, Sargolzaei, M, Meirelles, SLC, Mokry, FB, Higa, RH, Mudadu, MA, Silva, MVGB, Niciura, SCM, Torres Júnior, RAA, Alencar, MM, Regitano, LCA and Munari, DP 2014. Genome-wide association for growth traits in Canchim beef cattle. PLoS One 9, e94802.CrossRefGoogle ScholarPubMed
Comuzzie, AG, Cole, SA, Laston, SL, Voruganti, VS, Haack, K, Gibbs, RA and Butte, NF 2012. Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population. PLoS One 7, e51954.CrossRefGoogle ScholarPubMed
Everard, A, Lazarevic, V, Gaia, N, Johansson, M, Stahlman, M, Backhed, F, Delzenne, NM, Schrenzel, J, François, P and Cani, PD 2014. Microbiome of prebiotic-treated mice reveals novel targets involved in host response during obesity. Multidisciplinary Journal of Microbial Ecology 8, 2116–2130.Google ScholarPubMed
Ferraz Filho, PB, Ramos, AA, Silva, LOC, Souza, JC, Alencar, MM and Malhado, CHM 2002. Tendência genética dos efeitos direto e materno sobre os pesos à desmama e pós-desmama de bovinos da raça Tabapuã no Brasil. Revista Brasileira de Zootecnia 31, 635–640.CrossRefGoogle Scholar
Frizzas, OG, Grossi, DA, Buzanskas, ME, Paz, CCP, Bezerra, LAF, Lôbo, RB, Oliveira, JA and Munari, DP 2009. Heritability estimates and genetic correlations for body weight and scrotal circumference adjusted to 12 and 18 months of age for male Nellore cattle. Animal 3, 347–351.CrossRefGoogle ScholarPubMed
Gutiérrez-Gil, B, Williams, JL, Homer, D, Burton, D, Haley, CS and Wiener, P 2009. Search for quantitative trait loci affecting growth and carcass traits in a cross population of beef and dairy cattle. Journal of Animal Science 87, 24–36.CrossRefGoogle Scholar
Lindholm-Perry, AK, Sexten, AK, Kuehn, LA, Smith, TPL, King, DA, Shackelford, SD, Wheeler, TL, Ferrell, CL, Jenkins, TG, Snelling, WM and Freetly, HC 2011. Association, effects and validation of polymorphisms within the NCAPG – LCORL locus located on BTA6 with feed intake, gain, meat and carcass traits in beef cattle. BMC Genetics 12, 103.CrossRefGoogle ScholarPubMed
Misztal, I 2012. BLUPF90 – a flexible mixed model program in Fortran 90, University of Georgia. Retrieved on 15 December 2014 from http://nce.ads.uga.edu/wiki/lib/exe/fetch.php?media=blupf90.pdf.Google Scholar
Olney, RC, Bükülmez, H, Bartels, CF, Prickett, TCR, Espiner, EA, Potter, LR and Warman, ML 2005. Heterozygous mutations in natriuretic peptide receptor-B (NPR2) are associated with short stature. Journal of Clinical Endocrinology and Metabolism 91, 1229–1232.CrossRefGoogle ScholarPubMed
Perez, R, Cañón, J and Dunner, S 2010. Genes associated with long-chain omega-3 fatty acids in bovine skeletal muscle 1010. Journal of Applied Genetics 51, 479–487.CrossRefGoogle Scholar
Peters, SO, Kizilkaya, K, Garrick, DJ, Fernando, RL, Reecy, JM, Weaber, RL, Silver, GA and Thomas, MG 2012. Bayesian genome wide association analyses of growth and yearling ultrasound measures of carcass traits in Brangus heifers. Journal of Animal Science 90, 3398–3409.CrossRefGoogle ScholarPubMed
Porto-Neto, LR, Bunch, RJ, Harrison, BE and Barendse, W 2012. Variation in the XKR4 gene was significantly associated with subcutaneous rump fat thickness in indicine and composite cattle. Animal Genetics 43, 785–789.CrossRefGoogle ScholarPubMed
Primeaux, SD, Braymer, HD and Bray, GA 2012. High fat diet differentially regulates the expression of olfactory receptors in the duodenum of obesity-prone and obesity-resistant rats. Digestive Diseases and Sciences 58, 72–78.CrossRefGoogle ScholarPubMed
Pryce, JE, Hayes, BJ, Bolormaa, S and Goddard, ME 2011. Polymorphic regions affecting human height also control stature in cattle. Genetics 187, 981–984.CrossRefGoogle ScholarPubMed
Ramayo-Caldas, Y, Ballester, M, Fortes, MRS, Esteve-Codina, A, Castelló, A, Noguera, JL, Fernández, AI, Pérez-Enciso, M, Reverter, A and Folch, JM 2014. From SNP co-association to RNA co-expression: novel insights into gene networks for intramuscular fatty acid composition in porcine. BMC Genomics 15, 232–246.CrossRefGoogle ScholarPubMed
R Core Team 2014. R: a language and environment for statistical computing. R Foundation for Statistical Computing, Vienna, Austria.Google Scholar
Utsunomiya, YT, Carmo, AS, Carvalheiro, R, Neves, HHR, Matos, MAC, Zavarez, LB, O’Brien, AMP, Sölkner, J, McEwan, JC, Cole, JB, Vantassel, CP, Schenkel, FS, Silva, MVGB, Porto-Neto, LR, Sonstegard, TS and Garcia, JF 2013. Genome-wide association study for birth weight in Nellore cattle points to previously described orthologous genes affecting human and bovine height. BMC Genetics 14, 52.CrossRefGoogle ScholarPubMed
Vanraden, PM 2008. Efficient methods to compute genomic predictions. Journal of Dairy Science 91, 4414–4423.CrossRefGoogle ScholarPubMed
Wang, H, Misztal, I, Aguilar, I, Legarra, A, Fernando, RL, Vitezica, Z, Okimoto, R, Wing, T, Hawken, R and Muir, WM 2014. Genome wide association mapping including phenotypes from relatives without genotypes in a single-step (ssGWAS) for 6 week body weight in broiler chickens. Frontiers in Genetics 5, 134.CrossRefGoogle Scholar
Wang, H, Misztal, I, Aguilar, I, Legarra, A and Muir, WM 2012. Genome-wide association mapping including phenotypes from relatives without genotypes. Genetic Research 94, 73–83.CrossRefGoogle ScholarPubMed
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