Genomic mate selection for clonally propagated crops: improving the chance of breeding top ranking clones by predicted variance in total genetic merit
Diverse crops ranging from staples (e.g., cassava) to cash crops (e.g., cacao) are both outbred and clonally propagated. In these crops, exceptional genotypes can be immortalized and commercialized as clonal varieties. Genomic truncation selection (TS) evaluates parents based on breeding value (i.e. the mean value of their unselected offspring). Predictions can include non-additive effects in clonal crops to select candidates with high total genetic merit for variety development (Wolfe et al. 2016). Improvements over truncation selection are possible by selecting crosses instead of parents. By predicting the variance in a cross using a genetic map, phased haplotypes, and genome-wide marker effects (Lehermeier et al. 2017; Allier et al. 2019; Bijma et al. 2020) mate-selection criteria like the mean of selected offspring (aka the “usefulness criterion”, UC) can be derived.
Our overall objective is to develop improvements on truncation selection targeted at clonal crop breeding by deriving optimizing schemes for population improvement (mating) and clone testing efforts (variety development).
As a first contribution, in this poster, we: (1) Retrospectively analyze empirical data comparing predicted and realized variances from a cassava genomic selection program. (2) Prospectively evaluate the interest of possible future crosses in terms of additive and total merit.