CTP-SAI-037

Controlling meiotic recombination in diploid potato

This PhD will be based in the Department of Plant Sciences at the University of Cambridge. The student will be registered with the University of Cambridge.

CTP-SAI-037

Controlling meiotic recombination in diploid potato

Prof. Ian Henderson (Department of Plant Sciences, University of Cambridge), Dr Edwin van der Vossen (Solynta) and Dr Ernst-Jan Eggers (Solynta)

BACKGROUND

Meiosis and recombination remain a major tool for crop breeding and improvement. Independent chromosome segregation and recombination provide a powerful means to combine variation from different sources. However, there are limitations on recombination that can slow or hinder crop improvement. For example, most plant species show pronounced regions of recombination suppression surrounding the centromeres that extend far into the chromosome arms. In situations where a gene or QTL of interest are located in such non-recombining intervals, further mapping of the locus can be impossible. During breeding, recombination suppression can manifest as linkage drag between deleterious alleles and target loci of choice that are under recurrent selection.

OBJECTIVES AND APPROACHES

It is therefore desirable to develop technologies to increase or relocate recombination events in the genomes of crop species. The overall objective of this project is to develop technologies that increase or control recombination in crop genomes. The focus will be to achieve recombination changes in diploid potato lines developed by the project industrial partner Solynta. The long-term strategic goal of the project is to provide proof-of-concept data for controlling recombination that can be built into future diploid potato breeding activities.

We have identified genetic approaches that are sufficient to, (i) increase global crossover numbers, and (ii) remodel the recombination landscape and unlock silent regions. In this project, the student will translate our understanding into diploid potato, in order to both increase and remodel recombination, in ways that accelerate breeding and variety improvement. The student will explore three main strategies to manipulate the recombination landscape.


Objective 1. Overexpression of HEI10 to promote potato crossovers. A conserved set of 'ZMM' pathway proteins are required for the majority of crossovers in plants. A single gene within this pathway, HEI10, which encodes an E3 ubiquitin ligase, is a dosage-sensitive modulator of crossovers. Specifically, by increasing HEI10 gene copy number (and expression) using transformation it is possible to quantitatively increase crossover numbers. The student will transform diploid potato with additional copies of potato HEI10, and then confirm mRNA and protein overexpression in the transformants. These transgenics will be crossed to a polymorphic potato line, and F1 hybrids generated, followed by F2 or backcross (BC) population development. Genotyping of these populations, compared to controls, will then be performed, to quantify levels and the chromosomal distribution of crossovers. Viral methods of gene over expression will also be explored.


Objective 2. Removal of RECQ4 anti-crossover factors in diploid potato. In parallel to the action of the HEI10, a set of at least three anti-crossover pathways are active in plants. These include the DNA helicases RECQ4A and RECQ4B, which act to promote DSB repair as non-crossovers. Mutation of the anti-crossover genes causes a dramatic increase in crossovers. In this Objective the student will generate loss of function mutations in RECQ4 homologs in diploid potato using CRISPR/Cas9 gene editing. As recq4a recq4b mutations are recessive, these will be obtained in both mapping parents. The mutants will then be crossed together to make F1 hybrids and then F2or BC populations, and crossover number and location identified via genotyping. In the event that Objectives 1 and 2 are successful in diploid potato, the generated lines will be further combined to cause even higher crossover levels.


Objective 3. Unlocking heterochromatic recombination using DNA methylation mutants. Many crops show extended regions of crossover suppression surrounding the centromeres. A major chromatin mark involved in heterochromatic silencing is DNA methylation, which occurs in both CG and non-CG (i.e. CHG and CHH, where H is any base apart from G) sequence contexts. Using mutants that disrupt either the CG or non-CG pathways we were able to show that non-CG mutants increased crossovers in the heterochromatic regions. Specifically, mutations in drm2 cmt2 cmt3 DNA methyltransferases were found to be most effective. The student will use CRISPR/Cas9 gene editing in diploid potato to obtain mutations in orthologs of DRM2, CMT2 and CMT3. The edited lines will be characterised for DNA methylation patterns genome-wide. Once DNA hypomethylated lines are obtained they will be used to generate F1hybrids, then F2 or BC populations, and crossovers mapped via genotyping. Ultimately, if all three strategies were successful, it will be possible to combine lines to achieve simultaneously increased and remodelled crossover landscapes in potato. For instance, by combining lines where HEI10is overexpressed, and non-CG DNA methylation is reduced simultaneously. DNA demethylating chemicals will also be explored as an alternative approach.

PRIMARY LOCATION OF THIS PHD

This PhD will be based in the Department of Plant Sciences at the University of Cambridge. The student will be registered with the University of Cambridge.

TRAINING

Students will have access to training opportunities through the University of Cambridge to complement their scientific development. This will be augmented by training in key bioscience areas, such as statistics, through the CTP-SAI.


There will be additional skills training to enhance employability and research capability. All CTP-SAI students will receive Graduate Training in Leadership and Management from MDS (www.mds-ltd.co.uk). Additionally, students will create their Personal Development Plan (PDP) to identify their development needs and areas of strength. Each student will receive individual coaching and mentoring pertinent to their career plans and skills development in addition to the scientific project supervision.

INDUSTRIAL PLACEMENT

Industrial placements are a key feature of CTP, and UKRI-BBSRC expects all doctoral candidates on a CTP programme to undertake a placement. Placements can be in the form of research placements (3-18 months duration) or used more flexibly for experiential learning of professional skills for business and/or entrepreneurship. All placements are developed in collaboration between the partners with input from the doctoral candidate. In this project the student will perform industrial placement with our partner Solynta.


Solynta is a hybrid potato breeding company based in Wageningen, the Netherlands. The Solynta Team is developing hybrid potato varieties with superior traits and performance at a speed that is faster than can be achieved by traditional breeding. The successful application of hybrid breeding allows for the use of Hybrid True Potato Seeds or HTPS. This revolution in breeding not only greatly enhances the speed of product development but also provides huge logistical and phytosanitary advantages. Although people have been breeding new potato varieties for centuries, the ability to use hybrid breeding is the ‘Holy Grail’ of potato improvement – something which many believed would not be possible. Together, the persistent team of Researchers, Breeders, Agronomists and many more at Solynta are Unlocking the True Potential of Potatoes.

APPLICATION AND ELIGIBILITY

Please contact Prof. Ian Henderson to initiate an informal discussion on the research content of this PhD.


Beginning in October 2023, the successful candidate should have (or expect to have) an Honours Degree (or equivalent) with a minimum of 2.1 in Plant Science, Molecular Biology, Genetics, Genomics, or other related science subjects. Students with a relevant Masters degree are particularly encouraged to apply.


We welcome UK, EU and international applicants. Candidates whose first language is not English must provide evidence that their English language is sufficient to meet the specific demands of their study. Candidates should check the requirements for each host organization they are applying to, but IELTS 6.5 (with no component below 6.0) or equivalent is usually the minimum standard.

This studentship is for four years and is fully funded in line with UKRI-BBSRC standard rates. These are an annual maintenance stipend of £17,668, fee support of £4,596, a research training support grant of £5,000, and conference and UK fieldwork expenses of £300.

To be classed as a home student, candidates must meet the following criteria: 

• Be a UK National (meeting residency requirements), or 

• Have settled status, or 

• Have pre-settled status (meeting residency requirements), or 

• Have indefinite leave to remain or enter 

If a candidate does not meet the criteria above, they would be classed as an international student and must demonstrate the ability to meet the supplement in fees required for an international student. 


Anyone interested should complete the online application form before the deadline of 6th January 2023. Interviews will take place at the end of January/beginning of February 2023.


Please contact recruitment-ctp-sai@niab.com for further application details.

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