Accuracy of Bayesian methods in genomic evaluation threshold traits with different genetic architecture


1- Abdollahi-Arpanahi R., Pakdel, A., and Zandi-Baghchehmaryam, MB. 2012. From infinitesimal model to Genomic Selection. Genetic-Novin. 29:105-121. (In Persian)
2- Calus, M., De Roos, A., and Veerkamp, R. 2008. Accuracy of genomic selection using different methods to define haplotypes. Journal of Genetics. 178: 553-561.
3- Daetwyler, H.D., Calus, M.P., Pong-Wong, R., de los Campos, G., and Hickey, J. M. 2013. Genomic prediction in animals and plants: simulation of data, validation, reporting, and benchmarking. Journal of Genetics. 193: 347-365.
4- Daetwyler, H.D., Villanueva, B., and Woolliams, J.A. 2008. Accuracy of predicting the genetic risk of disease using a genome-wide approach. PLoS One. 3: e3395.
5- De los Campos, G., and Perez Rodriguez, P. 2015. Package BGLR "Bayesian Generalized Linear Regression". Department of Biostatistics, University of Alabama-Birmingham.
6- De los Campos, G., Hickey, J., Pong-Wong, R., Daetwyler, H., and Calus, M. 2013. Whole-genome regression and prediction methods applied to plant and animal breeding. Journal of Genetics, 193(2): 327-345.
7- Gianola, D., and Foulley, J. 1983. Sire evaluation for ordered categorical data with a threshold model. Journal of Genetics Selection Evolution. 15: 201-224.
8- Goddard, M. 2009. Genomic selection- prediction of accuracy and maximisation of long term response. Journal of Genetics. 136: 245–257.
9- 1González-Recio, O., and Forni, S. 2011. Genome-wide prediction of discrete traits using Bayesian regressions and machine learning. Journal of Journal of Genetics Selection Evolution. 43: 7.
10- Habier, D., Fernando, R.L., Kizilkaya, K., and Garrick, D.J. 2011. Extension of the Bayesian alphabet for genomic selection. Journal of BMC Bioinformatics. 12: 186.
11- Haley, C., and Visscher, P. 1998. Strategies to utilize marker-quantitative trait loci associations. Journal of Dairy Science. 81: 85-97.
12- Hayes, B.J., Bowman, P.J., Chamberlain, A.C., Verbyla, K., and Goddard, M.E. 2009. Accuracy of genomic breeding values in multi-breed dairy cattle populations. Journal of Genetics Selection Evolution. 41: 51.
13- Kizilkaya, K., Fernando, R.L., and Garrick, D.J. 2014. Reduction in accuracy of genomic prediction for ordered categorical data compared to continuous observations. Journal of Genetics Selection Evolution. 46: 37.
14- Lande, R., and Thompson, R. 1990. Efficiency of marker-assisted selection in the improvement of quantitative traits. Journal of Genetics. 124: 743-756.
15- Lepori Honeyman, A. 2014. Genomic selection for traits of economic importance in sheep: a thesis presented
16- Mehraban, H., Nejati Javaremi, A., Mirayi Ashtiani, S., and Mehrabani Yeganeh, H. 2015. Simulation of base (historical) population and determining accuracy of linkage disequilibrium in genomic simulated studies. Journal of Agricultural Biotechnologies. 2: 45-51 (In Persian)
17- Meuwissen, T., Hayes, B., and Goddard, M. 2001. Prediction of total genetic value using genome-wide dense marker maps. Journal of Genetics. 157: 1819-1829.
18- Nejati-Javaremi, A., Smith, C., and Gibson, J. 1997. Effect of total allelic relationship on accuracy of evaluation and response to selection. Journal of Animal Science. 75 1738-1745.
19- Saatchi, M., McClure, M.C., McKay, S.D., Rolf, M.M., Kim, J., Decker, J.E., and Northcutt, S.L. 2011. Accuracies of genomic breeding values in American Angus beef cattle using K-means clustering for cross-validation. Journal of Genetics Selection Evolution. 43: 40.
20- Schaeffer, L. 2006. Strategy for applying genome‐wide selection in dairy cattle. Journal of Animal Breeding and Genetics. 123: 218-223.
21- Sved, J. 1971. Linkage disequilibrium and homozygosity of chromosome segments in finite populations. Theoretical population biology. 2: 125-141.
22- Silva, M., dos Santos, D., Boison, S., Utsunomiya, A., Carmo, A., Sonstegard, T., Cole, J., and Van Tassell, C. 2014. The development of genomics applied to dairy breeding. Livestock Science. 166: 66-75.
23- Solberg, T.R., Sonesson, A.K., Woolliams, J.A., Ødegard, J., and Meuwissen, T.H. 2009. Persistence of accuracy of genome-wide breeding values over generations when including a polygenic effect. Journal of Genetics Selection Evolution. 41: 53.
24- Technow, F. 2013. R Package hypred version 0.2: Simulation of genomic data in applied genetics. University of Hohenheim, Institute of Plant Breeding, Seed Science and Population Genetics, Stuttgart, Germany.
25- Van der Werf, J., and Hayes, B. 2013. Genome-wide association studies and genomic prediction. chapter 26, Genomic Selection in Animal Breeding Programs. Pp: 543-561, Humana Press.
26- Van Tassell, C., Van Vleck, L., and Gregory, K. 1998. Bayesian analysis of twinning and ovulation rates using a multiple-trait threshold model and Gibbs sampling. Journal of Animal Science. 76: 2048-2061.
27- Villanueva, B., Fernandez, J., Garcia-Cortes, L.A., Varona, L., Daetwyler, H.D., and Toro, M.A. 2011. Accuracy of genome-wide evaluation for disease resistance in aquaculture breeding programs. Journal of Animal. Science. 89: 3433-3442
28- Wang, C.L., Ding, X. D., Wang, J.Y., Liu, J.F., Fu, W.X., Zhang, Z., Jin, Z.J., and Zhang, Q. 2012. Bayesian methods for estimating GEBVs of threshold traits.Journal of Heredity. 110: 213-219.
29- Wimmer, V., Lehermeier, C., Albrecht, T., Auinger, H.J., Wang, Y., and Schon, C.C. 2013. Genome-wide prediction of traits with different genetic architecture through efficient variable selection. Journal of Genetics. 195: 573-587.
30- Zhang, Z., Zhang, Q., and Ding, X. 2011. Advances in genomic selection in domestic animals. Chinese Science Bulletin.56: 2655-2663.
31- Zhong, S., Dekkers, J.C., Fernando, R.L., and Jannink, J.L. 2009. Factors affecting accuracy from genomic selection in populations derived from multiple inbred lines: a Barley case study. Journal of Genetics. 182: 355-364.