Evolutionary computing to assemble standing genetic diversity and achieve long‐term genetic gain

• Published in: The plant genome Vol. 17; no. 2; pp. e20467 - n/a
• Main Authors: Villiers, Kira, Voss‐Fels, Kai P., Dinglasan, Eric, Jacobs, Bertus, Hickey, Lee, Hayes, Ben J.
• Format: Journal Article
• Language: English
• Published: United States Wiley 01-06-2024
• ISSN: 1940-3372; 1940-3372
• DOI: 10.1002/tpg2.20467

Loss of genetic diversity in elite crop breeding pools can severely limit long‐term genetic gains and limit ability to make gains in new traits, like heat tolerance, that are becoming important as the climate changes. Here, we investigate and propose potential breeding program applications of optimal haplotype stacking (OHS), a selection method that retains useful diversity in the population. OHS selects sets of candidates containing, between them, haplotype segments with very high segment breeding values for the target trait. We compared the performance of OHS, a similar method called optimal population value (OPV), truncation selection on genomic estimated breeding values (GEBVs), and optimal contribution selection (OCS) in stochastic simulations of recurrent selection on founder wheat genotypes. After 100 generations of intercrossing and selection, OCS and truncation selection had exhausted the genetic diversity, while considerable diversity remained in the OHS population. Gain under OHS in these simulations ultimately exceeded that from truncation selection or OCS. OHS achieved faster gains when the population size was small, with many progeny per cross. A promising hybrid strategy, involving a single cycle of OHS in the first generation followed by recurrent truncation selection, substantially improved long‐term gain compared with truncation selection and performed similarly to OCS. The results of this study provide initial insights into where OHS could be incorporated into breeding programs.
Core Ideas
We investigate potential uses of a haplotype‐stacking strategy, optimal haplotype stacking (OHS).
Several selection strategies were compared in stochastic simulations of recurrent selection in wheat.
OHS maintained more useful diversity than optimal cross selection or truncation‐based genomic selection.
Rates of gain from OHS are competitive in small populations.
One generation of OHS in a truncation selection program can increase short‐ and long‐term genetic gain.
Plain Language Summary
Breeders use selection strategies based on genetic and phenotypic information to choose parents that will improve agriculturally relevant traits (e.g., grain yield) in their progeny. Generally, this involves estimating breeding values (scores) for each candidate parent. This study investigated an alternative “haplotype stacking” approach called optimal haplotype stacking (OHS), which instead estimates breeding values for each unique genome segment in the population, then selects a group of parents who, between them, carry the haplotypes with the highest estimated breeding value at each chromosomal segment. In simulations, OHS gives improvements close to existing methods when populations are small and outperforms them in the long term (100+ generations). Using just one generation of OHS boosts the performance of other methods in the short and long term. Breeders might consider adopting haplotype stacking in their programs, once techniques to do so are established.