More animals than markers: a study into the application of the single step T-BLUP model in large-scale multi-trait Australian Angus beef cattle genetic evaluation

Multi-trait single step genetic evaluation is increasingly facing the situation of having more individuals with genotypes than markers within each genotype. This creates a situation where the genomic relationship matrix (G) is not of full rank and its inversion is algebraically impossible. Recently, the SS-T-BLUP method was proposed as a modified version of the single step equations, providing an elegant way to circumvent the inversion of the G and therefore accommodate the situation described. SS-T-BLUP uses the Woodbury matrix identity, thus it requires an add-on matrix, which is usually the covariance matrix of the residual polygenic effet. In this paper, we examine the application of SS-T-BLUP to a large-scale multi-trait Australian Angus beef cattle dataset using the full BREEDPLAN single step genetic evaluation model and compare the results to the application of two different methods of using G in a single step model. Results clearly show that SS-T-BLUP outperforms other single step formulations in terms of computational speed and avoids approximation of the inverse of G.