Genomic selection strategies and their potential to maintain rare alleles and de-novo mutations: a long-term assessment.

backgroundSustainable breeding programs need to balance short-term genetic improvement with the conservation of genetic diversity. While genomic selection has considerably increased the genetic gain for many breeding programs, the consequences on diversity can be less desirable. This is particularly the case for rare alleles and de-novo mutations, as markers used in genomic selection are generally not strongly associated with rare alleles. Moreover, genomic selection allows for the selection of young individuals without records, thereby ignoring the effects of de-novo mutations. We aimed to evaluate various selection strategies in terms of long-term genetic gain and conservation of genetic variance, with a focus on the use and conservation of favorable rare alleles and de-novo mutations.

resultsTo study these selection strategies, we simulated populations of 1000 individuals subject to 50 generations of selection with a trait with only additive gene actions, a trait with additive and dominance gene actions, and a trait with additive, dominance and epistatic gene actions. For each trait, we evaluated five genomic selection strategies that balance between genetic improvement and diversity management, namely: truncation selection, which only focuses on short-term genetic gain; optimal contribution selection, which balances short-term genetic gain with a constraint on the relatedness of the selected individuals; two versions of allele-reweighted selection, which upscale the effect of rare alleles in the breeding values; and constrained allele loss selection, a novel strategy which balances short-term gain with a constraint on the reduction in frequency of rare alleles estimated to be favorable. Our results show that the allele-reweighted strategies provided an efficient trade-off between conserving genetic variance and achieving a higher genetic long-term gain, improving one or both metrics relative to truncation selection. Optimal contribution selection also improved the amount of genetic variance conserved and, for the trait with epistatic gene actions, also resulted in higher long-term genetic gain. On the other hand, the constrained allele loss did not show improvements over truncation selection.

conclusionsIntroducing into our genomic selection strategies a consideration for diversity management or the conservation of rare alleles can help in improving the long-term sustainability of breeding programs that use genomic selection.