Incorporating selfing to purge deleterious alleles in a cassava genomic selection program

Authors: SOMO, MOHAMED - Cornell University; Jannink, Jean-Luc

Submitted to: bioRxiv
Publication Type: Other
Publication Acceptance Date: 4/2/2020
Publication Date: 4/5/2020
Citation: Somo, M., Jannink, J. 2020. Incorporating selfing to purge deleterious alleles in a cassava genomic selection program. bioRxiv. https://doi.org/10.1101/2020.04.04.025841.
DOI: https://doi.org/10.1101/2020.04.04.025841

Interpretive Summary: Mutations that negatively affect a crop, deleterious mutations, can be recessive. In that case, if they are together with the non-mutated wild-type gene, their effect is masked. Crops that outcross (that do not self-fertilize) often have high levels of recessive deleterious mutations. This makes the performance of these crops drop dramatically when they are self-fertilized, so called inbreeding depression. Breeders therefore consider specific approaches to decrease these mutations in varieties. Using self-fertilization to unmask deleterious recessive alleles and therefore accelerate their purging is one possibility. Before implementation of this approach we sought to understand better its consequences through simulation. Breeding program populations with many deleterious recessives were simulated. The populations were then subjected to five generations of selection in schemes that did or did not include a generation of selection on selfed progeny. We found that genomic selection was less effective under the directional dominance model than under the additive models that have commonly been used in simulations. While selection did increase favorable allele frequencies, increased inbreeding during selection caused decreased gain in genotypic values under the directional dominance. Purging selection on selfed individuals was effective in the first breeding cycle but not effective in later cycles. We found that selection on individuals partially inbred by one generation of selfing did increase mean genetic value of the partially inbred population, but that this gain was accompanied by a relatively small increase in favorable allele frequencies such that improvement in the outbred population was lower than might have been intuited.

Technical Abstract: Cassava has been found to carry high levels of recessive deleterious mutations and it is known to suffer from inbreeding depression. Breeders therefore consider specific approaches to decrease cassava’s genetic load. Using self fertilization to unmask deleterious recessive alleles and therefore accelerate their purging is one possibility. Before implementation of this approach we sought to understand better its consequences through simulation. Founder populations with high directional dominance were simulated using a natural selection forward simulator. The founder population was then subjected to five generations of genomic selection in schemes that did or did not include a generation of phenotypic selection on selfed progeny. We found that genomic selection was less effective under the directional dominance model than under the additive models that have commonly been used in simulations. While selection did increase favorable allele frequencies, increased inbreeding during selection caused decreased gain in genotypic values under the directional dominance. While purging selection on selfed individuals was effective in the first breeding cycle, it was not effective in later cycles, an effect we attributed to the fact that the generation of selfing decreased the relatedness of the genomic prediction training population from selection candidates. That decreased relatedness caused genomic prediction accuracy to be lower in schemes incorporating selfing. We found that selection on individuals partially inbred by one generation of selfing did increase mean genetic value of the partially inbred population, but that this gain was accompanied by a relatively small increase in favorable allele frequencies such that improvement in the outbred population was lower than might have been intuited.