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. We have recently developed a new high-resolution haplotyping approach in wheat which opens 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, provide the backdrop for this CASE PhD project in partnership with major breeding companies BASF and Limagrain.

The aim of this PhD will be to investigate and implement methodologies to identify and exploit novel haplotypes for disease resistance breeding in wheat. To achieve this, we will identify haplotypes across resistance gene clusters in the wheat pangenome. The student will investigate strategies to use the datasets to develop and validate haplotype-specific markers across breeding germplasm. They will work with BASF and Limagrain to perform marker-trait association studies in available populations. They 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.

The project provides multiple tracks which complementary approaches that allow room for the student to take ownership of the project and expand into their areas of interest and according to results. The student will receive mentoring and outstanding training in modern crop genetics, genomics, data analysis and bioinformatics, alongside essential core scientific and transferable skills.


Brinton J, Ramirez-Gonzalez RH, Simmonds J, Wingen L, Orford S, Griffiths S, 10 Wheat Genome Project, Haberer G, Spannagl M, Walkowiak S, Pozniak C, Uauy C. 2020. A haplotype-led approach to increase the precision of wheat breeding. Communications Biology 3:712

Walkowiak et al. 2020. Multiple wheat genomes reveal global variation in modern breeding. Nature 588: 277–283