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Increased and stable plant production requires further genetic progress. To maintain this, breeders must preserve genetic diversity in their programs, even though it is depleted by breeding. Over the last century, large collections of genetic resources have been organized, representing significant diversity. However, their use for variety development has remained an unsolved problem because of their performance gap with elite varieties. Advances in genotyping and statistical methods now allow their effective use through linkage schemes based on genomic prediction and diversity monitoring. Our study provides a demonstration of a series of new tools incorporated into new breeding schemes to effectively utilize donor genetic resources, allowing them to contribute to the improvement of quantitative traits in elite populations.

Abstract

Genetic progress in crop plants is necessary to cope with human population growth and to ensure production stability under increasingly unstable environmental conditions. Selection is accompanied by a loss of genetic diversity, which limits genetic gain in the medium to long term. Methodologies based on molecular marker information have been developed to manage diversity and have proven effective in increasing long-term genetic gain. However, with realistically sized plant breeding populations, diversity depletion in closed programs seems inescapable, requiring the introduction of relevant diversity donors. Although maintained through considerable effort, genetic resource collections remain underutilized, due to a large performance gap with elite germplasm. Crossing genetic resources with elite lines to create a bridging population before their introduction into elite programs can effectively manage this gap. To improve this strategy, we explored, using simulations, different options for genomic prediction and genetic diversity management in a global program including an intermediate component (bridging population) and an elite component. We analyzed the dynamics of fixation of quantitative trait loci and followed the fate of allele donors after their introduction into the breeding program. Allocating 25% of the total experimental resources to the creation of a bridge population appears to be highly beneficial. We have shown that potential diversity donors should be selected on the basis of their phenotype rather than genomic predictions calibrated with the current breeding program. We recommend incorporating improved donors into the elite program using global calibration of the genomic prediction model and selection to maintain consistent diversity. These approaches effectively use genetic resources to support genetic gain and maintain neutral diversity, thereby improving flexibility to meet future breeding goals.

Contact:

• Alain Charcosset alain.charcosset@inrae.fr
• Génétique Quantitative et Evolution (GQE) Le Moulon, 91190, Gif sur Yvette France