Association mapping to identify and clone matching avirulent

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20 Φεβ 2013 (πριν από 4 χρόνια και 7 μήνες)

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PhD project proposal template

2011
-
12


Please submit completed proposal forms to
pgbio@warwick.ac.uk



This PhD project is suitable for:

BBSRC remit

Yes



Food Security

NERC remit

No

MRC
Imaging DTG

No


Note: All projects will

also be advertised as available for students who have a
scholarship, plan to apply for a scholarship or who can self
-
fund.


Principal Supervisor name and department
:

Professor Jim Beynon, School of
Life Sciences


Second Supervisor name and department:

Dr
Mary Coates, School of Life
Sciences


PhD project title:

A
ssociation map
p
ing to identi
fy and clone matching avirulent

effector genes in the downy mildew pathogen, Hyaloperonospora ar
abidopsidis
and resistance genes

in the host plant, Arabidopsis thaliana.


Project description

(max 500 words)
:


Background

The group works on understanding how pathogens suppress host immune systems.
We work on a group of pathogens called oomycetes

which deliver proteins (effectors)
into their host to alter the host immune system to favour pathogen growth and
development. This group of pathogens infect humans, animals and cause major crop
diseases (for example causing the death of millions of peopl
e

in the Irish Potato
Famine).


We wish to understand the depth of the pathogen’s effector arsenal. Some effectors
actually trigger host defence mechanisms. Whether a particular strain of the pathogen
causes a resistance response in the host will depend on

the allelic form of the effector
protein responsible for triggering that response. This allows us to use genetic mapping
approaches to identify the effectors responsible.


Although several effector (avirulence) and resistance gene pairs have been cloned
in
reality these only represent a tiny proportion of the number of such interacting gene
pairs in a plant. Our picture of this interaction between pathogen and host proteins is
extremely limited. Considering that this is the basis of most plant breeding to

prevent
pathogen invasion this is remarkable.



Proposed Experiments

We have an amazing opportunity here to completely change this picture by
identifying a whole range of novel defence triggering effectors and their
complementing host resistance genes.


In order to map and clone genes it is necessary to have segregating genetic
populations resulting from crosses. We already have several crosses between isolates
PhD project proposal template

2011
-
12


of the pathogen in which we know many avirulence loci segregate. However, the
matching resista
nce genes are in accessions of Arabidopsis for which similar
segregating populations do not exist, making it hard to identify the underlying
resistance genes. However, there now exist many recombinant inbred lines (RILs) of
Arabidopsis that are available
,
which make

cloning host genes easy.


Therefore, we will:

1.

Screen the parents of the RILs with a range isolates to determine which
identify resistance genes in the plant lines.

2.

Determine the most informative pathogen cross to carry out to identify the
most e
ffectors that trigger resistance.

3.

Carry out one or more crosses between pathogen isolates and generate F2
populations

4.

Carry out restriction
-
site associated DNA tags (RAD) mapping of these crosses
to clone the effectors.

5.

Use the RILs to map and clone the ma
tching host resistance genes.



Key
experimental skill
s

involved
:

1.

Pathogenicity. Carrying out pathogen screening assays, crosses and
segregation analysis.

2.

Genetics. Segregation analyses and gene mapping.

3.

Bioinformatics. Analyses of the genomes in the
region of the mapped genes to
determine final cloning strategies.

4.

Molecular Biology. You will use a range of modern techniques including
GATEWAY cloning, PCR, RAD mapping and potentially genome
sequencing.


References:


Coates, M. E. and Beynon, J. L. (20
10) 'Hyaloperonospora arabidopsidis as a
pathogen model',
Annual Review of Phytopathology,
48
329
-

345


Baxter, L., Tripathy, S., Ishaque, N., Boot, N., Cabral, A., Kemen, E

et al
. (2010)
'Signatures of adaptatio
n to obligate biotrophy in the H
yaloperonos
pora arabidopsidis
genome',
Science,
330
(6010), 1549


1551



Keywords

(these will help your project to show in search listings on
e.g.
FindAPhD
.com
)
:

effector, avirulence, resistance gene, Hyaloperonospora
arabidopsidis, association mapping


Contact
details for application enquiries
:
jim.beynon@warwick.ac.uk


PhD project proposal template

2011
-
12


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