Plants are constantly assaulted by pathogens, which have the potential to result in devastating crop losses. However, plants have several mechanisms to protect themselves. One key mechanism of resistance is mediated by R genes, particularly the NLR class of genes. These genes typically reside in difficult to study, repeat rich regions of the genome. Fortunately, their conserved domain structure of Nucleotide Binding domains and Leucine Rich Repeat regions has allowed for the development of enrichment sequencing methods, termed RenSeq. In Arabidopsis, this methodology has previously been used to study the full complement of NLRs across the species, termed the Pan-NLRome (Van de Weyer et al., 2019). Potato is a crucial food crop that is consumed by over a billion people worldwide. In 2020, 350 million tons of potato were produced, though it is estimated around 25% of the potential yield is lost to diseases. This project will focus on studying the resistance gene complement in cultivated tetraploid potato to produce a Pan-NLRome in this important crop.
This will involve the student learning and applying techniques including classical genetics, population genomics and k-mer based diversity assessment methods. The student will benefit from access to the crop diversity HPC system. This will allow the performing of bioinformatic analyses utilising high-accuracy PacBio HiFi reads for SMRT-RenSeq (Witek et al., 2016) and other analyses of large RenSeq datasets. The student will join a multi-disciplinary team who are actively developing novel methods to investigate the NLR complement of potato, such as the recent release of automated workflows for SMRT-AgRenSeq-d with HISS (Adams et al., 2022). The student will also have access to training opportunities through the University of Dundee.
This project aims to improve the understanding of the NLR complement in cultivated potato, providing insights into the diversity currently exploited in breeding programmes and reveal targets for future breeding efforts. The work will also provide insights into the action of selection in this key gene class.
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