“In this paper, we review the performance of hidden Markov model-based imputation methods in animal breeding populations. Imputation is a technique that decreases the cost of genotyping animals, by allowing animal breeders to genotype most of their animals on a low-cost, low-density genotyping array, and a few of their animals on a higher-cost, higher-density genotyping...
Our group AlphaGenes focusses on the development and application of quantitative genetics methods and computational approaches for animal and plant breeding programs and human genetics. Currently our overarching research aim relates to the development of what we call “Genomic Selection 2.0“. We envisage that GS2.0 would be underpinned by huge quantities of sequence data generated at low cost and could enable several new ways of driving genetic improvement and biological insight. Specifically we are developing the algorithms, software and strategies for generating and analysing data on this scale and new breeding program designs to derive breeding benefit.