# Genomic-inferred cross-selection methods for multi-trait improvement in a recurrent selection breeding program

## TL;DR

This paper introduces a new method for genomic selection in breeding programs that balances short-term genetic gains with long-term genetic variance retention.

## Contribution

The study proposes an integrated index selection approach within the genomic inferred cross-selection framework for multi-trait improvement.

## Key findings

- The posterior mean variance method consistently outperformed other methods in enhancing genetic gain.
- Optimizing the number of parents, crosses, and progeny per cross can maximize both short- and long-term genetic gains.
- The method was evaluated over a 40-year simulated breeding program in pulse crops.

## Abstract

The major drawback to the implementation of genomic selection in a breeding program lies in long-term decrease in additive genetic variance, which is a trade-off for rapid genetic improvement in short term. Balancing increase in genetic gain with retention of additive genetic variance necessitates careful optimization of this trade-off. In this study, we proposed an integrated index selection approach within the genomic inferred cross-selection (GCS) framework to maximize genetic gain across multiple traits. With this method, we identified optimal crosses that simultaneously maximize progeny performance and maintain genetic variance for multiple traits. Using a stochastic simulated recurrent breeding program over a 40-years period, we evaluated different GCS methods along with other factors, such as the number of parents, crosses, and progeny per cross, that influence genetic gain in a pulse crop breeding program. Across all breeding scenarios, the posterior mean variance consistently enhances genetic gain when compared to other methods, such as the usefulness criterion, optimal haploid value, mean genomic estimated breeding value, and mean index selection value of the superior parents. In addition, we provide a detailed strategy to optimize the number of parents, crosses, and progeny per cross that can potentially maximize short- and long-term genetic gain in a public breeding program.

The online version contains supplementary material available at 10.1186/s13007-024-01258-4.