Single Step GBLUP (SS-GBLUP): case study using beef cattle genomic data

Single step genomic selection method (SS-GBLUP) with combining genomic relationship matrix and pedigree relationship matrix and simultaneous use of all genotyped and ungenotyped animals has been used widely in estimating genomic breeding values (GEBV) in recent years. The purpose of the present study was to compare genomic selection accuracy of traditional BLUP, SNP-BLUP, G-BLUP and SS-GBLUP for carcass weight in beef cattle. Results showed that genomic prediction accuracy for the above methods were 0.77±0.11, 0.88±0.21, 0.87±0.23 and 0.95±0.25 respectively. Genomic prediction accuracy of SS_BLUP was 0.08, 0.07 and 0.18 higher than SNP- BLUP, G_BLUP and traditional BLUP. Mean squared error of above methods was 3.46, 2.21, 2.22 and 1.76 respectively. In general, the performance of single step method was better than other studied genomic evaluation methods. Moreover, the regression coefficient of corrected phenotype on GEBV was 0.81, 0.82 and 0.90 for SNP- BLUP, G-BLUP and single step method, respectively. Thus, the bias of GEBV for single step method was less than G-BLUP and SNP-BLUP.