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

Area of Science:

• Plant breeding and genetics
• Quantitative genetics
• Genomic selection

Background:

• Elite crop breeding pools face declining genetic diversity, hindering long-term genetic gains and adaptation to new traits like heat tolerance.
• Climate change necessitates the development of crop varieties with enhanced resilience and performance under adverse conditions.
• Maintaining genetic diversity is critical for sustained progress in crop improvement.

Purpose of the Study:

• To investigate and propose applications of optimal haplotype stacking (OHS) as a selection method to retain useful genetic diversity in crop breeding.
• To compare the performance of OHS against existing selection methods, including truncation selection and optimal contribution selection (OCS).
• To evaluate the potential of OHS in improving long-term genetic gains for important crop traits.

Main Methods:

• Stochastic simulations of recurrent selection were performed on founder wheat genotypes.
• Compared OHS with optimal population value (OPV), truncation selection on genomic estimated breeding values (GEBVs), and OCS.
• Evaluated selection methods over 100 generations of intercrossing and selection.

Main Results:

• Optimal contribution selection (OCS) and truncation selection exhausted genetic diversity after 100 generations, while OHS maintained considerable diversity.
• Optimal haplotype stacking (OHS) ultimately exceeded truncation selection and OCS in terms of genetic gain.
• A hybrid strategy combining one cycle of OHS with recurrent truncation selection significantly improved long-term gain compared to truncation selection alone.

Conclusions:

• Optimal haplotype stacking (OHS) is a promising selection method for preserving genetic diversity and enhancing long-term genetic gains in crop breeding programs.
• OHS demonstrates superior performance, especially in scenarios with smaller population sizes and more progeny per cross.
• Hybrid strategies incorporating OHS offer a viable approach to boost breeding program efficiency and achieve sustained genetic improvement for climate adaptation.