Temporal and genomic analysis of additive genetic variance in plant breeding programs

This contribution demonstrates genomic and temporal analysis of genetic variance in different stages of aplant breeding programme. Traditionally we used specific experimental designs and recently the more general pedigree-based model to estimate genetic variance in various plant breeding populations. With the pedigree-based model we can estimate temporal changes in genetic variance by summarizing sampled realizations of genetic values from the fitted model. Here we extend this approach to a marker-based model to perform temporal and genomic analysis. We demonstrate the approach by analysing data from a simulated plant breeding programme involving a complex trait with additive and dominant gene actions.
We first fitted a marker-model with additive and dominance effects. Then we sampled realisations of marker effects to calculate realisations of genetic values encompassing the whole genome or genome regions. We then summarised these genetic values to analyse genomic and temporal trends in genetic variance. Results show good concordance with the real values in different stages of a breeding programme. Further, the results manifest the effects of genetic processes such as drift and the Bulmer effect. This contribution will help plant breeders to assess the amount of genetic variance in different stages of a programme and enhance its utilisation and management.