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EASTBIO Genetic, Molecular and Bioinformatic Characterisation of Resistance to Root Knot Nematode in Rice


School of Biological Sciences

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Prof A Price , Prof J Jones , Dr I Hein No more applications being accepted Competition Funded PhD Project (Students Worldwide)

About the Project

Supervisors:

Professor Adam Price (University of Aberdeen)
www.abdn.ac.uk/sbs/people/profiles/a.price

Dr John Jones (The James Hutton Institute)
https://www.hutton.ac.uk/staff/john-jones

Dr Ingo Hein (The James Hutton Institute)
https://www.hutton.ac.uk/staff/ingo-hein

The overall aim is to characterise the gene(s) behind the very rare resistance to the root-knot nematode Meloidogyne graminicola recently mapped in three Asian rice cultivars. M. graminicola is considered the most important nematode pest of rice, is ubiquitous in tropical rice production and is well controlled by flooding. However, it is likely to be a major constraint when water-saving management that tackle poor sustainability credentials of much irrigated rice means rice fields are not permanently flooded. In addition, it has recently been reported in Italy (the first report in temperate rice production) where it is spreading rapidly, like due to climate change-induced spread of tropical pests into temperate regions.

In 2016 research at Aberdeen University reported two resistant Asian rice cultivars LD24 from Sri Lanka and Khao Pahk Maw (KPM) from Thailand (Dimkpa et al. 2016), and subsequent use of QTL-seq technique to map it to the last 6 million bases of chromosome 11 in both resistant cultivars (Lahari et al 2019). Concurrently, researchers at the James Hutton Institute (JHI) have been collaborating on a project that appears to map resistance from a third Asian rice cultivar (Zhongua 11 from China) to a similar region. This project aims to characterise this very rare resistance locus to;
1/ determine if it is the same allele that is responsible for resistance in all cultivars
2/ identify the strongest candidate genes using bioinformatic and molecular techniques
3/ initiate the testing of candidate genes through collaboration on gene editing.

Specific objectives are:

1- Use Ren-seq technique of resistance gene sequencing (Jupe et al. 2013) to determine if the resistance genes in LD24 and KPM match Zonghau 11 which has already been tested in JHI

2- Use markers to explore segregation of resistance in crosses between resistant and susceptible cultivars to better locate the gene

3- Use available sequence data of LD24, KPM and Zhongua 11 and bioinformatic tools such as SNP-Seek and RiceVarMap to explore allelic variation in candidate genes at the sequence level.

4- Use RT-PCR to test expression of candidate genes

5- Initiate the gene editing of candidate genes to allow proof of function through collaboration with rice gene editing groups in the UK (University of Durham or NIAB) of France (CIRAD).

We also hope to use the results in a timely way to assist current nematode resistance breeding efforts with collaborators in Italy, India and Sri Lanka.

Application Procedure:

http://www.eastscotbiodtp.ac.uk/how-apply-0

Please send your completed EASTBIO application form, along with academic transcripts to Alison McLeod at [Email Address Removed]. Two references should be provided by the deadline using the EASTBIO reference form. Please advise your referees to return the reference form to [Email Address Removed].

Funding Notes

This 4 year PhD project is part of a competition funded by EASTBIO BBSRC Doctoral Training Partnership http://www.eastscotbiodtp.ac.uk/how-apply-0. This opportunity is open to UK and International students and provides funding to cover stipend and UK level tuition (limited funding is available to provide international tuition fees). Please refer to UKRI website and Annex B of the UKRI Training Grant Terms and Conditions for full eligibility criteria.

Candidates should have (or expect to achieve) a minimum of a 2:1 UK Honours degree, or the equivalent qualifications gained outside the UK, in a relevant subject.

References

Dimkpa SON, Lahari MZ, Shrestha R, Douglas A, Gheysen G, Price AH (2016) A genome-wide association study of a global rice panel reveals resistance in Oryza sativa to root-knot nematodes, J. Ex. Bot. 67: 1191-1200
Jupe F, …. Jones JDG (2013) Resistance gene enrichment sequencing (RenSeq) enables reannotation of the NB-LRR gene family from sequenced plant genomes and rapid mapping of resistance loci in segregating populations. The Plant J. 76: 530–544
Lahari Z, Ribeiro A, Talukdar P, Martin B, Heidari Z, Gheysen G, Price AH, Shrestha R (2019) QTL-seq reveals a major root-knot nematode resistance locus on chromosome 11 in rice (Oryza sativa L.). Euphytica 215:117
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