Exploiting novel haplotypes to improve disease resistance in wheat

Wheat is a major cereal crop providing 20% of global calorie and protein intake for humans. While a 50% increase in wheat yield is required by 2050, diseases reduce yields by ~25% globally and thus pose a major threat to global food security. To address this threat, breeders select for genetic resistance to pest and pathogens which helps reduce crop losses in the field. Genomics provides a powerful means to define trait-associated haplotypes and implement targeted approaches to identify and exploit novel genetic variation. The recent development of a new high-resolution haplotyping approach in wheat has openend up the opportunity to implement this directly within pre-breeding programs. The recent resequencing of >1,000 wheat landraces/cultivars, alongside the potential impact in crop breeding, provides the backdrop for this project in partnership with major breeding companies BASF and Limagrain.

The aim of this project will be to investigate and implement methodologies to identify and exploit novel haplotypes for disease resistance breeding in wheat. To achieve this: haplotypes across resistance gene clusters will be identified in the wheat pangenome; strategies to use datasets to develop and validate haplotype-specific markers across breeding germplasm will be investigated; and marker-trait association studies in available populations will be performed by working with the non-academic partner organisations. The project will also aim to identify the allelic variation responsible for the novel disease resistance traits by performing targeted sequencing using in-vitro Cas9-enrichment followed by Oxford Nanopore sequencing.