China Scholarship Council: Using state-of-the-art genomics and genetics to clone functional disease resistance genes in potato


   School of Life Sciences

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  Dr Ingo Hein, Dr M Bayer, Dr Thomas Adams  No more applications being accepted  Competition Funded PhD Project (Students Worldwide)

About the Project

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). 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.  

Training: 

The successful student will gain a comprehensive scientific skill set including bioinformatics, genomics, genetics, and molecular biology. In addition, transferable skills such as presentation and grant writing skills alongside a career development plan will be provided. 

Agriculture (1) Biological Sciences (4) Computer Science (8)

Funding Notes

In order to be eligible for these awards applicants must:
Be a Chinese national
Meet the requirements of the CSC – please see their website
Hold an unconditional offer to study for a PhD at the University of Dundee and meet our English language requirements
Have completed a bachelors or masters degree before the agreed start of PhD study.
Already have an IELTS score of 6.5 at time of applying
For further information on the CSC programme please visit https://www.dundee.ac.uk/phds/funding/china-scholarship-council-csc-programme and apply by completing our application form - https://dundee.onlinesurveys.ac.uk/csc-programme-2024-entry

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