LWV25025 Sustainable onion breeding: Expanding the onion gene pool by bridging the Allium germplasm (TS-02-227-046)

The project aims to enhance sustainable onion breeding by unlocking genetic diversity from Allium relatives. Due to the limited genetic variation in cultivated onions, breeders face challenges in developing improved cultivars and are interested in exploiting the genomes of onion-related species with beneficial traits. The success of introgression breeding depends on meiotic recombination, a biological process by which genetic material from the donor into the recipient crop is introduced. The exchange of genetic material between parental chromosomes is commonly referred to as crossover (CO). As observed for many organisms, the distribution of COs in Allium is not random and appears genetically and strictly controlled. The development of Allium reference genomes will enable the assessment of genetic variation and inheritance, facilitating more efficient breeding strategies. By resolving Allium genomes at a chromosome complexity scale, this study provides a foundation for dissecting genetic variation, understanding recombination landscapes, and accelerating breeding efforts. Phasing haplotypes and mapping crossovers will allow for more precise tracking of beneficial alleles, especially in the context of introgression breeding, where homoeologous recombination, chromosome synapsis issues, and genome instability have previously hindered progress. Moreover, the high genomic resolution enables the identification of structural variants influencing agronomic traits, facilitating targeted selection strategies. This achievement paves the way for genetically diverse onion cultivars, ensuring the sustainable advancement of this globally important crop. The project will generate a high-quality nuclear genome assembly for the onion-related species Allium roylei, providing critical insights into its genetic landscape. In addition, full-length transcriptome sequences will be generated from a range of onion-related species that are crossable with onion or usable for introgression breeding using A. roylei as a bridge species. Outcomes include species-specific markers for breeding, recombination profiles for parental and hybrid populations, and a deeper understanding of genome (in)compatibility, using previously constructed hybrid plant material. These advances will contribute to new onion cultivars with improved traits, reducing dependency on pesticides and supporting sustainable agricultural practices. The project, a collaboration between WUR and breeding companies, ensures effective knowledge transfer from research to breeding. By integrating genomic technologies with applied strategies, the project will strengthen Dutch agricultural competitiveness, support food security, and foster environmentally friendly onion production.