مقایسه روش‌های آماری مختلف در انتخاب ژنومی بر اساس معیار اثربخشی انتخاب

Atefi A., Shadparvar A. A. and Ghavi Hossein-Zadeh N. 2016. Comparison of whole genome prediction accuracy across generations using parametric and semi parametric methods. Acta Scientiarum. Animal Sciences, 38(4): 447-453.

Atefi A., Shadparvar A. A. and Ghavi Hossein-Zadeh N. 2018. Accuracy of genomic prediction under different genetic architectures and estimation methods.  Iranian Journal of Applied Animal Science, 8(1): 43-52.

Brito F. V., Neto J. B., Sargolzaei M., Cobuci J. A. and Schenkel F. S. 2011. Accuracy of genomic selection in simulated populations mimicking the extent of linkage disequilibrium in beef cattle. BMC Genetics, 12(1): 80-90.

Calus M. P. L., Goddard M. E., Wientjes Y. C. J., Bowman P. J. and Hayes B. J. 2018. Multibreed genomic prediction using multitrait genomic residual maximum likelihood and multitask Bayesian variable selection. Journal of Dairy Science, 101(5): 4279-4294.

Calus M. P. L., Meuwissen T. H. E., De Roos A. P. W. and Veerkamp R. F. 2008. Accuracy of genomic selection using different methods to define haplotypes. Genetics, 178(1): 553-561.

Clark S. A., Hickey J. M. and Van Der Werf J. H. 2011. Different models of genetic variation and their effect on genomic evaluation. Genetics Selection Evolution, 43(1): 1-9.

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. Genetics, 193(2): 347-365.

Daetwyler H. D., Kemper K. E., Van Der Werf J. H. J. and Hayes B. J. 2012. Components of the accuracy of genomic prediction in a multi-breed sheep population. Journal of Animal Science, 90(10): 3375-3384.

Daetwyler H. D., Villanueva B., Bijma P. and Woolliams J. A. 2007. Inbreeding in genome-wide selection. Journal of Animal Breeding and Genetics, 124(6): 369-376.

De Los Campos G. and Perez-Rodriguez P. 2012. BGLR: Bayesian Generalized Linear Regression. R Package.

De Los Campos G., Hickey J. M., Pong-Wong R., Daetwyler H. D. and Calus M. P. 2013. Whole-genome regression and prediction methods applied to plant and animal breeding. Genetics, 193(2): 327-345.

Dekkers J. C. M. 2004. Commercial application of marker-and gene-assisted selection in livestock: strategies and lessons. Journal of Animal Science, 82(13): 313-328.

Falconer D. S. and Mackay F. C. T. 1996. Introduction to Quantitative Genetics. Third edition. Longman Group. pp. 100-143.

Fernando R. L. and Grossman M. 1989. Marker assisted selection using best linear unbiased prediction. Genetics Selection Evolution, 21(4): 467-481.

Goddard M. 2009. Genomic selection: prediction of accuracy and maximization of long term response. Genetica, 136(2): 245-257.

Goddard M. E. and Hayes B. J. 2007. Genomic selection. Journal of Animal Breeding and Genetics, 124(6): 323-330.

Gowane G. R., Lee S. H., Clark S., Moghaddar N., Al-Mamun H. A. and Van Der Werf J. H. 2019. Effect of selection and selective genotyping for creation of reference on bias and accuracy of genomic prediction. Journal of Animal Breeding and Genetics, 136(5): 390-407.

Habier D., Fernando R. L. and Dekkers J. C. M. 2007. The impact of genetic relationship information on genome-assisted breeding values. Genetics, 177(4): 2389-2397.

Habier D., Tetens J., Seefried F. R., Lichtner P. and Thaller G. 2010. The impact of genetic relationship information on genomic breeding values in German Holstein cattle. Genetics Selection Evolution, 42(1): 5-17.

Haley C. S. and Visscher P. M. 1998. Strategies to utilize marker-quantitative trait loci associations. Journal of Dairy Science, 81(2): 85-97.

Hayes B. J., Phillip J. B., Chamberlain A. C., Verbyla K. and Goddard M. E. 2009. Accuracy of genomic breeding values in multi-breed dairy cattle populations. Genetics Selection Evolution, 41(1): 1-9.

Hill W. G. and Robertson A. 1968. Linkage disequilibrium in finite populations. Theoretical and Applied Genetics, 38(6): 226-231.

Jimenez-Montero J. A., Gianola D., Weigel K., Alenda R. and Gonzalez-Recio O. 2013. Assets of imputation to ultra-high density for productive and functional traits. Journal of Dairy Science, 96(9): 6047-6058.

Lund M. S., Sahana G., De Koning D. J., Su G. and Carlborg Ö. 2009. Comparison of analyses of the QTLMAS XII common dataset. I: Genomic selection. BMC Proceedings, 3(1): 1-8.

Meuwissen T. H. 2003. Genomic selection: the future of marker assisted selection and animal breeding. In: MAS: a fast track to increase genetic gain in plants and animal breeding?, FAO, Session II: Marker assisted selection in animals, electronic forum on biotechnology in food and agriculture, 17–18 Oct. Turin, Italy, pp. 54-59.

Meuwissen T. H., Hayes B. J. and Goddard M. E. 2001. Prediction of total genetic value using genome-wide dense marker maps. Genetics, 157(4): 1819-1829.

Muir W. M. 2007. Comparison of genomic and traditional BLUP-estimated breeding value accuracy and selection response under alternative trait and genomic parameters. Journal of Animal Breeding and Genetics, 124(6): 342-355.

Nejati-Javaremi A., Smith C. and Gibson J. P. 1997. Effect of total allelic relationship on accuracy of evaluation and response to selection. Journal of Animal Science, 75(7): 1738-1745.

Neves H. H., Carvalheiro R., O’brien A. M. P., Utsunomiya Y. T., Do Carmo A. S., Schenkel F. S., Sölkner J., McEwan J. C., Van Tassell C. P., Cole J. B. and Da Silva M. V. 2014. Accuracy of genomic predictions in Bos indicus (Nellore) cattle. Genetics Selection Evolution, 46(1): 1-13.

Ornella L., Pérez P., Tapia E., González-Camacho J. M., Burgueño J., Zhang X., Singh S., Vicente F. S., Bonnett D., Dreisigacker S., Singh R., Long N. and Crossa J. 2014. Genomic-enabled prediction with classification algorithms. Heredity, 112(6): 616-626.

R Core Team. 2018. R: a language and environment for statistical computing, R Foundation for Statistical Computing, Vienna, Austria, V 3.5.1.

Saatchi M., Miraei-Ashtiani S. R., Nejati-Javaremi A., Moradi-Shahrbabak M. and Mehrabani-Yeghaneh H. 2010. The impact of information quantity and strength of relationship between training set and validation set on accuracy of genomic estimated breeding values. African Journal of Biotechnology, 9(4): 438-442.

Sargolzaei M. and Schenkel F. S. 2009. QMSim: a large-scale genome simulator for livestock. Bioinformatics, 25(5): 680-681.

Schaeffer L. R. 2006. Strategy for applying genome-wide selection in dairy cattle. Journal of Animal Breeding and Genetics, 123(4): 218-223.

Solberg T. R., Sonesson A. K., Woolliams J. A. and Meuwissen T. H. E. 2008. Genomic selection using different marker types and densities. Journal of Animal Science, 86(10): 2447-2454.

VanRaden P. M. 2008. Efficient methods to compute genomic predictions. Journal of Dairy Science, 91(11): 4414-4423.

VanRaden P. M. and Sullivan P. G. 2010. International genomic evaluation methods for dairy cattle. Genetics Selection Evolution, 42(1): 1-7.

Vitezica Z. G., Aguilar I., Misztal I. and Legarra A. 2011. Bias in genomic predictions for populations under selection. Genetics Research, 93(5): 357-366.

Wientjes Y. C., Veerkamp R. F., Bijma P., Bovenhuis H., Schrooten C. and Calus M. P. 2015. Empirical and deterministic accuracies of across-population genomic prediction. Genetics Selection Evolution, 47(1): 1-14.

Zhang Z., Ding X. D., Liu J., De Koning D. J. and Zhang Q. 2011. Genomic selection for QTL-MAS data using a trait-specific relationship matrix. BMC Proceedings, 5(3): 1-4.