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UNIVERSITY OF LIVERPOOL

School of Biological Sciences


BBSRC funded Studentship


Identifying useful SNP in UK breeding varieties of Wheat

Dr. A.J.W. Hall
Anthony.hall@liv.ac.uk
, Professor N. Hall
neil.hall@liv.ac.uk

and Dr. O.
Vasieva
o.vasieva@liv.ac.uk



Wheat is a major UK food crop with an annual value of approximately £1.2 bn. In order to meet increasing
worldw
ide demand for wheat a step change in breeding methods is required. As part of our BBSRC wheat
genomics grant, funded at the start of 2009, we aim to sequence the genic regions of four UK breeding lines
Avalon, Cadenza, Rialto and Savannah, identifying sin
gle nucleotide polymorphisms (SNPs) between these
varieties. Although, with recent technology advances, this number may increase to 30.


In this PhD project we propose to take a first step in interpreting the biological relevance of some of the varietal
SN
Ps identified.


The project will have two components, one bioinformatics and one lab based RNAseq component. The
bioinformatics component will aim to develop a pipe
-
line for scoring the significance of non
-
synonymous SNPs
based on sequence conservation acr
oss monocot species. Similar genome wide approaches have already been
used in other species (Burke
et al.

2007). Here, we will specifically focus on key pathways associated with
yield, fitness and stress. Secondly, an RNAseq experiment will investigate dif
ferential gene expression between
the four varieties. This will provide data on whether a SNP containing variant is expressed, a key factor in an
allohexaploid genome such as wheat. It will also allow us to identify potential pathways to target for
identif
ication of useful SNPs. We will use loci alignment methods to identify true isofunctional orthologs of
genes with promising SNPs and use gene proximity data along with pathway mapping for gene functional
characterization.


The output of this project would
be a set of valuable candidate SNPs, the exploitation of which we would
ensure, via ongoing collaboration with the UK wheat breeding community and NIAB.


Training:

The project will provide training in the areas of:

Next generation sequencing:
The student
will be trained in next
-
generation DNA sequencing, in particular in the
bioinformatics analysis associated with handling the massive amounts of data that the 454 and SOLiD
sequencing systems generate

(
Schuster 2008)


Programming:

Training will be provided in basic script writing to develop pipelines for dealing with large data
sets, they will also attend specific modules from the Bioinformatics MSc run at Liverpool.

Transferring knowledge between model and crop species:

The proje
ct will involve identifying wheat homologs
of Arabidopsis/rice genes in key pathways. Thus, giving training in how to transfer knowledge and
understanding between models and crops.

The project will provide training in plant genomics and crop g
enetics. The
student will also
attend UK crop
science workshops and networking meetings.

For more information please contact Dr Anthony Hall or visit the centre website
(
http://www.liv.ac.uk/cgr/index.htm
)


References:

Burke, D.F., Worth, C.L., Priego, E.M., Cheng, T., Smink, L.J., Todd, J.A. and Blundell, T.L.
(2007)
Genome bioinformatic analysis of nonsynonymous SNPs.
BMC Bioinformatics
,
8
, 301.


Schuster S.C. (2008).

Next
-
generation sequencing transforms t
oday's biology
.
Nature Methods

5
,
16
-

18


Applications are invited from students who either hold or expect to obtain, a First or Upper Second class
Honours degree in a relevant subject
. Application by email, indicating the project(s) of interest (and
su
pervisors) in priority order, giving the reasons for this, together with a c.v. including the names and contact
details of two academic referees, should be sent as soon as possible to: Mrs. Linda J. Marsh, Research Support
Office, School of Biological Scie
nces, The Life Sciences Building, Crown Street, Liverpool L69 7ZB (email:
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biolres@liverpool.ac.uk
, Fax: 0151 795 5122). Review of applicati
ons begins from mid February 2010
. Please
indicate where you first
saw the project(s) advertised.