Genetic analysis of diverse potato diseases using association genetics, SMRT-AgRenSeq-d

• Funding – self-funded/externally sponsored applicants (PhD Fees can be found here)
• Applications are accepted year round
• Standard Entry dates – January and September
• Applicants are expected to have a degree (equivalent of Honours or Masters) in a relevant discipline.

Potato is the third most important food crop and consumed by over a billion people around the world. More than 375 million tonnes of potato were produced in 2021 but it’s estimated that approximately 25% are lost to diseases. Since many diseases can be controlled by members of the nucleotide-binding, leucine-rich-repeat family of disease resistance genes (NLRs), we have developed targeted enrichment sequencing (RenSeq) to specifically study these genes in potatoes.

The application of RenSeq to over 1000 potato varieties and breeding clones, including those grown in the UK, USA, China, Europe and South Korea, has provided insights into the historical and geographical deployment of useful resistance genes. In addition, these data combined with phenotypic data enable powerful association genetic studies (AgRenSeq) as initially described in wheat. To significantly improve the representation of NLRs for AgRenSeq, and to reliably ascertain the NLRome of potatoes, we have successfully implemented PacBio-based sequencing of long (4-7 kb) RenSeq-enriched genomic DNA samples. Used in combination with AgRenSeq to identify NLRs associated with the resistance traits, and dRenSeq to confirm the presence or absence of full-length candidates, we refer to this development as SMRT-AgRenSeq-d.

Objectives:

The Objectives of this project are to further develop and apply SMRT-AgRenSeq-d to potato tuber diseases such as wart disease, common and powdery scab, as well as Spraing, which have been relatively intractable until recently.

We will combine existing RenSeq data with phenotypic observations to:

1. predict candidate genes for the resistances, 
2. demonstrate functionality of NLRs using CRISPR/CAS9 knockout in resistant cultivars and complementation via transgenic lines,
3. develop markers for breeding

Impact:

By elucidating the genes responsible for resistances against diverse pathogens of potato and understanding their individual mechanisms, we will achieve significant scientific impact but also provide new means for industry to protect potatoes from diseases. Thus, this project bridges fundamental research with immediately applied research. Importantly, the findings of this PhD project can be used in diploid and tetraploid potato breeding through the developed markers. Further, this research offers opportunities to develop resistant plants through gene editing or cis-genic approaches as the political framework of GE technology is shifting. 

Our research community thrives on the diversity of students and staff which helps to make the University of Dundee a UK university of choice for postgraduate research.  We welcome applications from all talented individuals and are committed to widening access to those who have the ability and potential to benefit from higher education.

2nd Supervisor:  Dr Micha Bayer