Genomic selection for QTL-MAS data using a trait-specific relationship matrix

BACKGROUND: The genomic estimated breeding values (GEBV) of the young individuals in the XIV QTL-MAS workshop dataset were predicted by three methods: best linear unbiased prediction with a trait-specific marker-derived relationship matrix (TABLUP), ridge regression best linear unbiased prediction (RRBLUP), and BayesB. METHODS: The TABLUP method is identical to the conventional BLUP except that the numeric relationship matrix is replaced with a trait-specific marker-derived relationship matrix (TA). The TA matrix was constructed based on both marker genotypes and their estimated effects on the trait of interest. The marker effects were estimated in a reference population consisting of 2 326 individuals using RRBLUP and BayesB. The GEBV of individuals in the reference population as well as 900 young individuals were estimated using the three methods. Subsets of markers were selected to perform low-density marker genomic selection for TABLUP method. RESULTS: The correlations between GEBVs from different methods are over 0.95 in most scenarios. The correlations between BayesB using all markers and TABLUP using 200 or more selected markers to construct the TA matrix are higher than 0.98 in the candidate population. The accuracy of TABLUP is higher than 0.67 with 100 or more selected markers, which is nearly equal to the accuracy of BayesB with all markers. CONCLUSIONS: TABLUP method performed nearly equally to BayesB method with the common dataset. It also provides an alternative method to predict GEBV with low-density markers. TABLUP is therefore a promising method for genomic selection deserving further exploration.