Tuyển tập các báo cáo nghiên cứu về sinh học được đăng trên tạp chí sinh học quốc tế đề tài: Allele coding in genomic evaluation | Strandén and Christensen Genetics Selection Evolution 2011 43 25 http content 43 1 25 RESEARCH GSE Ge n et i cs Selection Evolution Open Access Allele coding in genomic evaluation Ismo Strandén1 and Ole F Christensen2 Abstract Background Genomic data are used in animal breeding to assist genetic evaluation. Several models to estimate genomic breeding values have been studied. In general two approaches have been used. One approach estimates the marker effects first and then genomic breeding values are obtained by summing marker effects. In the second approach genomic breeding values are estimated directly using an equivalent model with a genomic relationship matrix. Allele coding is the method chosen to assign values to the regression coefficients in the statistical model. A common allele coding is zero for the homozygous genotype of the first allele one for the heterozygote and two for the homozygous genotype for the other allele. Another common allele coding changes these regression coefficients by subtracting a value from each marker such that the mean of regression coefficients is zero within each marker. We call this centered allele coding. This study considered effects of different allele coding methods on inference. Both marker-based and equivalent models were considered and restricted maximum likelihood and Bayesian methods were used in inference. Results Theoretical derivations showed that parameter estimates and estimated marker effects in marker-based models are the same irrespective of the allele coding provided that the model has a fixed general mean. For the equivalent models the same results hold even though different allele coding methods lead to different genomic relationship matrices. Calculated genomic breeding values are independent of allele coding when the estimate of the general mean is included into the values. Reliabilities of estimated genomic breeding values calculated using elements of the inverse of the coefficient .
