[en] Cow fertility traits are key factors that influence beef production profitability, and is particularly important in tropical environments where achieving high reproductive rates is challenging. Genomic selection (GS) has the potential to improve genetic gain rates for reproduction, if genomic estimated breeding values (GEBV) for these traits are sufficiently accurate. Several Bayesian models have already been proposed for GS, but the benchmarks used to compare them are still scarce, mainly for age at first calving (AFC) in Nellore cattle. A total of 714 AFC records of Nellore cows and 70 K SNPs were used to compare five models, Bayes A (BA), Bayes B (BB), Bayes Cπ (BCπ), Bayesian LASSO (BL) and Bayesian Ridge Regression (BRR). These models were compared by cross validation, randomly partitioning the whole population into 7 subsets (7-fold) and replicated 15 times. The prediction accuracy were 0.24 (0.11), 0.23 (0.11), 0.33 (0.13), 0.24 (0.11) and 0.38 (0.13), for BA, BB, BCπ, BL and BRR, respectively. Thus, BRR resulted in 14%, 15%, 5% and 14% additional prediction accuracy compared to BA, BB, BCπ and BL, respectively. Pearson and Spearman correlations between GEBVs obtained from BRR and BB models were, 0.97 and 0.94, respectively. It suggested that little difference in terms of animal selection would result from these methods. A more parsimonious model, such as BRR, can be successfully used in breeding programs to generate GEBVs which further enable consistent selection decisions. Although moderate accuracies of GEBV for AFC can be achieved, we found low efficiency of GS for AFC in the present population due to the small sample size and low heritability, reinforcing that GS efficiency is highly dependent upon these factors.
Disciplines :
Animal production & animal husbandry
Author, co-author :
REIS MOTA, Rodrigo ; Université de Liège - ULiège > Agronomie, Bio-ingénierie et Chimie (AgroBioChem) > Ingénierie des productions animales et nutrition
Fonseca e Silva, Fabyano
Facioni Guimarães, Simone Eliza
Hayes, Ben
Rufino Salinas Fortes, Marina
Kelly, Matthew John
Domingos Guimarães, José
Penitente-Filho, Jurandy Mauro
Torres Ventura, Henrique
Moore, Stephen
Language :
English
Title :
Benchmarking Bayesian genome enabled-prediction models for age at first calving in Nellore cows
Publication date :
May 2018
Journal title :
Livestock Science
ISSN :
1871-1413
eISSN :
1878-0490
Publisher :
Elsevier, Netherlands
Volume :
211
Pages :
75-79
Peer reviewed :
Peer Reviewed verified by ORBi
Funders :
CAPES - Coordenação de Aperfeicoamento de Pessoal de Nível Superior [BR]
Boddhireddy, P., Pragaya, K., Barros, P., Lobo, R., DeNise, S., Genomic Predictions of Economically Important Traits in Nelore Cattle of Brazil (2014) 10th World Congr. Genet. Appl. to Livest. Prod., 32, pp. 1-10
Boligon, A.A., Albuquerque, L.G.D., Mercadante, M.E.Z., Lôbo, R.B., Study of relations among age at first calving, average weight gains and weights from weaning to maturity in Nellore cattle (2010) Rev. Bras. Zootec., 39, pp. 746-751
Chud, T.C.S., Caetano, S.L., Buzanskas, M.E., Grossi, D.A., Guidolin, D.G.F., Nascimento, G.B., Rosa, J.O., Munari, D.P., Genetic analysis for gestation length, birth weight, weaning weight, and accumulated productivity in Nellore beef cattle (2014) Livest. Sci., 170, pp. 16-21
Costa, R.B., Irano, N., Diaz, I.D.P.S., Takada, L., Carvalheiro, R., Baldi, F., Oliveira, H.N., Albuquerque, L.G., Prediction of Genomic Breeding Values for Reproductive Traits in Nellore Heifers (2014) Proceedings, 10th World Congr. Genet. Appl. to Livest. Prod
De Los Campos, G., Naya, H., Gianola, D., Crossa, J., Legarra, A., Manfredi, E., Weigel, K., Cotes, J.M., Predicting quantitative traits with regression models for dense molecular markers and pedigree (2009) Genetics, 182, pp. 375-385
Farah, M.M., Swan, A.A., Fortes, M.R.S., Fonseca, R., Moore, S.S., Kelly, M.J., Accuracy of genomic selection for age at puberty in a multi-breed population of tropically adapted beef cattle (2016) Anim. Genet., 47, pp. 3-11
Fernandes Júnior, G.A., Rosa, G.J.M., Valente, B.D., Carvalheiro, R., Baldi, F., Garcia, D.A., Gordo, D.G.M., de Albuquerque, L.G., Genomic prediction of breeding values for carcass traits in Nellore cattle (2016) Genet. Sel. Evol., 48, p. 7
Fortes, M.R.S., Reverter, A., Zhang, Y., Collis, E., Nagaraj, S.H., Jonsson, N.N., Prayaga, K.C., Hawken, R.J., Association weight matrix for the genetic dissection of puberty in beef cattle (2010) Proc. Natl. Acad. Sci. USA, 107, pp. 13642-13647
Garrick, D.J., Taylor, J.F., Fernando, R.L., Deregressing estimated breeding values and weighting information for genomic regression analyses (2009) Genet. Sel. Evol., 41, p. 55
Gianola, D., Priors in whole-genome regression: the Bayesian alphabet returns (2013) Genetics, 194, pp. 573-596
Gianola, D., de los Campos, G., Hill, W.G., Manfredi, E., Fernando, R., Additive genetic variability and the Bayesian alphabet (2009) Genetics, 183, pp. 347-363
Grossi, D.A., Berton, M.P., Buzanskas, M.E., Chud, T.C.S., Grupioni, N.V., de Paz, C.C.P., Lbo, R.B., Munari, D.P., Genetic analysis on accumulated productivity and calving intervals in Nelore cattle (2016) Trop. Anim. Health Prod., 48, pp. 207-210
Grossi, D.A., Frizzas, O.G., Paz, C.C.P., Bezerra, L.A.F., Lobo, R.B., Oliveira, J.A., Munari, D.P., Genetic associations between accumulated productivity, and reproductive and growth traits in Nelore cattle (2008) Livest. Sci., 117, pp. 139-146
Grossi, D.A., Venturini, G.C., Paz, C.C.P., Bezerra, L.A.F., Lobo, R.B., Oliveira, J.A., Munari, D.P., Genetic associations between age at first calving and heifer body weight and scrotal circumference in Nelore cattle (2009) J. Anim. Breed. Genet., 126, pp. 387-393
Guo, Z., Tucker, D.M., Lu, J., Kishore, V., Gay, G., Evaluation of genome-wide selection efficiency in maize nested association mapping populations (2012) Theor. Appl. Genet., 124, pp. 261-275
Habier, D., Fernando, R.L., Dekkers, J.C.M., The impact of genetic relationship information on genome-assisted breeding values (2007) Genetics, 177, pp. 2389-2397
Habier, D., Fernando, R.L., Kizilkaya, K., Garrick, D.J., Extension of the Bayesian alphabet for genomic selection (2011) BMC Bioinform., 12, p. 1
Johnston, D.J., Genetic Improvement of Reproduction in Beef Cattle (2014) Proc. 10th World Congr. Genet. Appl. to Livest. Prod
Malhado, C.H.M., Malhado, A.C.M., Filho, M., Carneiro, R., P.L.S., P., Adrián, A., Carrillo, J., Age at first calving of Nellore cattle in the semi-arid region of northeastern Brazil using linear, threshold, censored and penalty models (2013) Livest. Sci., 154, pp. 28-33
Meuwissen, T.H.E., Hayes, B.J., Goddard, M.E., Prediction of total genetic value using genome-wide dense marker maps (2001) Genetics, 157, pp. 1819-1829. , doi:11290733
Neves, H.H., Carvalheiro, R., O Brien, A.M., Utsunomiya, Y.T., do Carmo, A.S., Schenkel, F.S., Sölkner, J., Garcia, J.F., Accuracy of genomic predictions in Bos indicus (Nellore) cattle (2014) Genet. Sel. Evol., 46, p. 17
Nogueira, G.P., Puberty in South American Bos indicus (Zebu) cattle (2004) Anim. Reprod. Sci., 82-83, pp. 361-372
Park, T., Casella, G., The bayesian lasso (2008) J. Am. Stat. Assoc., 103, pp. 681-686
Pérez, P., (2013), de los Campos, G. BGLR: A Statistical Package for Whole Genome Regression and Prediction
Valente, T.S., Sant'Anna, A.C., Baldi, F., Albuquerque, L.G., da Costa, M.J.R.P., Genetic association between temperament and sexual precocity indicator traits in Nellore cattle (2014) J. Appl. Genet., 56, pp. 349-354
Wise, A.L., Gyi, L., Manolio, T.A., eXclusion: toward integrating the X chromosome in genome-wide association analyses (2013) Am. J. Hum. Genet., 92, pp. 643-647
Zhang, Y.D., Johnston, D.J., Bolormaa, S., Hawken, R.J., Tier, B., Genomic selection for female reproduction in Australian tropically adapted beef cattle (2014) Anim. Prod. Sci., 54, pp. 16-24