Rapidly increasing training populations require efficient genomic evaluations. In this project, we develop the MiXBLUP (www.mixblup.eu) genomic evaluation software based on the latest scientific developments, that is easy to use, fast, suitable for simultaneous analyses of a large number of traits, and able to fit complex models. With this software, a single-step genomic multi-trait evaluation using 1.5 million genotyped animals, 10 million animals in the pedigree, and 3.5 million data records, was successfully completed within 2 days of computing time.
Published results in this project are:
Vandenplas J., M.P.L. Calus, H. Eding, and C. Vuik. 2019. A second-level diagonal preconditioner for single-step SNPBLUP. Genet. Sel. Evol. 51:30. https://doi.org/10.1186/s12711-019-0472-8
Vandenplas, J., H. Eding, M. P. L. Calus, and C. Vuik. 2018. Deflated preconditioned conjugate gradient method for solving single-step BLUP models efficiently. Genet. Sel. Evol. 50:51. https://doi.org/10.1186/s12711-018-0429-3
Napel, J. t., A. Cromie, G. Schopen, J. Vandenplas, and R. F. Veerkamp. 2018. Towards routine estimation of breeding values using one million genotyped animals. Page 905 in Proceedings of the 11th World Congress on Genetics Applied to Livestock Production. http://www.wcgalp.org/system/files/proceedings/2018/towards-routine-estimation-breeding-values-using-one-million-genotyped-animals.pdf