The main aim of pig and poultry breeding programs is to improve crossbred performance. This project aims to develop and validate tools to further increase efficiency and accuracy of genomic prediction, in particular for crossbred performance. Implemented tools comprise derivation of breed-of-origin of alleles in crossbred animals and its use in genomic prediction, modelling of genetic groups and metafounders in genomic prediction, and rapid detection and verification of parents using genotypes in large datasets.

Published results in this project are:

Aldridge, M. N., J. Vandenplas, R. Bergsma, and M. P. L. Calus. 2020. Variance estimates are similar using pedigree or genomic relationships with or without the use of metafounders or the algorithm for proven and young animals. J. Anim. Sci. 98: https://academic.oup.com/jas/article/98/3/skaa019/5709619

Calus, M. P. L., J. Vandenplas, I. Hulsegge, R. Borg, J. M. Henshall, and R. Hawken. 2019. Assessment of sire contribution and breed-of-origin of alleles in a three-way crossbred broiler dataset. Poult. Sci. https://doi.org/10.3382/ps/pez458

Aldridge, M. N., J. Vandenplas, and M. P. L. Calus. 2019. Efficient and accurate computation of base generation allele frequencies. J. Dairy Sci. 102:1364-1373. https://doi.org/10.3168/jds.2018-15264

Sevillano, C. A., J. ten Napel, S. E. F. Guimarães, F. F. Silva, and M. P. L. Calus. 2018. Effects of alleles in crossbred pigs estimated for genomic prediction depend on their breed-of-origin. BMC Genom. 19:740. https://doi.org/10.1186/s12864-018-5126-7

Calus, M. P. L., and J. Vandenplas. 2018. SNPrune: an efficient algorithm to prune large SNP array and sequence datasets based on high linkage disequilibrium. Genet. Sel. Evol. 50:34. https://doi.org/10.1186/s12711-018-0404-z

Calus, M. P. L., M. E. Goddard, Y. C. J. Wientjes, P. J. Bowman, and B. J. Hayes. 2018. Multibreed genomic prediction using multitrait genomic residual maximum likelihood and multitask Bayesian variable selection. J. Dairy Sci. 101:4279-4294. https://doi.org/10.3168/jds.2017-13366

Vandenplas, J., M. P. L. Calus, and G. Gorjanc. 2018. Genomic prediction using individual-level data and summary statistics from multiple populations. Genetics. 210:53-69. https://doi.org/10.1534/genetics.118.301109

Vandenplas, J., M. P. L. Calus, and J. ten Napel. 2018. Sparse single-step genomic BLUP in crossbreeding schemes. J. Anim. Sci. 96:2060-2073. https://doi.org/10.1093/jas/sky136


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