[Fwd: update on rice functional genomics working group]

[Pankaj Jaiswal]

-------- Original Message --------
From: "Leung, Hei" <H.LEUNG at CGIAR.ORG>
Subject: update on rice functional genomics working group
To: "A. K. Tyagi (E-mail)" <aktpmb at hotmail.com>,"Andrzej Kilian
(E-mail)" <a.kilian at cambia.org.au>,"Andy Pereira (E-mail)"
<A.Pereira at plant.wag-ur.nl>,"Arjula Reddy (E-mail)"
<arjulsl at uohyd.ernet.in>,"Bin Han (E-mail)"
<bhan at newnetra.ncgr.ac.cn>,"Dafang Huang (E-mail)"
<dfh313 at public.bta.net.cn>,"Emmanuel Guiderdoni (E-mail)"
<guiderdoni at cirad.fr>,"Gouliang Wang (E-mail)"
<wang.620 at osu.edu>,"Gynheung An (E-mail)" <genean at postech.ac.kr>,"Hans
Bohnert (E-mail)" <bohnerth at email.arizona.edu>,"Henry Nguyen (E-mail)"
<henry.nguyen at ttu.edu>,"Hirohiko Hirochika (E-mail)"
<hirohiko at abr.affrc.go.jp>,"Jan Leach (E-mail)" <jeleach at ksu.edu>,"Joe
Tohme (E-mail)" <J.TOHME at CGIAR.ORG>,"Katsumi Sakata (E-mail)"
<ksakata at nias.affrc.gov.jp>,"Luca Comai (E-mail)"
<comai at u.washington.edu>,"Mike Gale (E-mail)"
<mike.gale at bbsrc.ac.uk>,"N. K. Singh (E-mail)"
<nagendra_singh at lycos.com>,"Narayan Upadhyaya (E-mail)"
<N.Upadhyaya at pi.csiro.au>,"Pamela Ronald (E-mail)"
<pcronald at ucdavis.edu>,"Panjak Jaiswal (E-mail)"
<pj37 at cornell.edu>,"Patrick Schnable (E-mail)"
<schnable at iastate.edu>,"Qifa Zhang (E-mail)"
<qifazh at public.wh.hb.cn>,"Robin Buell (E-mail)" <rbuell at tigr.org>,"Rod
Wing (E-mail)" <rwing at clemson.edu>,"Ronald Phillips (E-mail)"
<phill005 at tc.umn.edu>,"Shoshi Kikuchi (E-mail)"
<skikuchi at abr.affrc.go.jp>,"Steve Henikoff (E-mail)"
<steveh at muller.fhcrc.org>,"Susan McCouch (E-mail)"
<mccouch at nightshade.cit.cornell.edu>,"Tom Bureau (E-mail)"
<thomas_bureau at maclan.mcgill.ca>,"Yukiko Yamasaki (E-mail)"
<yyamazaki at lab.nig.ac.jp>

Dear Colleagues, 
I would like to briefly update you the progress towards building the
research platform since the initiation of the Working Group in October,
2000. 
 
1. Microarray resources
At the Functional Genomics workshop held at the International Rice
Genetics
Symposium at IRRI in October 2000, a small task group (Hans Bohnert,
Susan
McCouch, Andrzej Kilian, Akhilesh Tyagi, Qifa Zhang) was formed to
advise
IRRI on the feasibility and possible strategies to develop microarray
resources.  Hans Bohnert summarized an analysis of the pros and cons of
investing in such a facility at IRRI.  We have analyzed the
recommendations
and decided to set up the facility that would be of value for research
and
training in the region. 

Our initial objective is to develop a collection of stress-related EST
that
can be used for microarray analyses.  Several activities have been
initiated: 
	*	Hans Bonhert and John Bennett are applying EST microarray to
analyze gene expression in several selected lines differing in drought
response.  
	*	Several pathogen-induced subtractive libraries have been
made by Jan Leach and Guoliang Wang, and will be arrayed in Pat
Schnable's
lab.  
	*	Henry Nguyen will provide EST libraries related to drought
stress to the Working Group.  
	*	We are continuing to discuss with different groups producing
rice cDNAs induced by  different stresses and hope to bring together
these
useful resources to be shared among the Working Group members.

To make use of these EST resources, IRRI has formed a collaboration with
Perkin Elmer to set up the microarray facility as a reference site for
the
company.  IRRI will acquire both the arrayer and a scanner and Perkin
Elmer
will donate a slide hybridization processor.  The reference site
arrangement
provides technical and training support from Perkin Elmer for the next
two
years.  We expect the equipment to be installed in August.  We hope the
available instrumentations at IRRI will facilitate the sharing and use
of
EST clones generated by different laboratories.  

We have tentatively planned to conduct a training workshop on microarray
and
bioinformatics as part of the Asian Rice Biotechnology Network (ARBN)
training program near the end of November or early December 2001.  The
intended audience is our research partners in the ARBN and researchers
at
IRRI.  We will invite researchers and trainers with experience in
microarray
technologies to conduct this workshop.  Several members of the Working
Group
have tentatively agreed to help with the training. We will keep the
Working
Group posted on the planning of this workshop. 

2. Mutant resources
A number of Working Group members have been successful in winning public
grants to produce mutants as a public resource.  The European consortium
led
by Andy Pereira has renewed support from the European Union to continue
their work on transposon insertional mutagenesis in rice. The consortium
involves research laboratories in five European countries (Plant
Research
International and Leiden University, the Netherlands; CIRAD, France;
John
Innes Center, UK; University of Milan, Italy; and Centro de
Investigacion y
Desarrollo, Spain).  In the United States, a consortium to produce
mutant
resources (Jan Leach, Pat Schnable, Pam Ronald, Guoliang Wang and IRRI)
will
be supported by the US National Science Foundation.  The two consortia
have
agreed to work together to produce activation lines by sharing
constructs,
starter lines, databases and trait analyses.  

IRRI continues to expand the production and characterization of the
deletion
lines in the indica rice IR64.  Currently, there are about 17,000
independent lines at M4 stage. These are being distributed to different
groups for phenotyping.  A prototype database that describes the
phenotypes
of about 200 mutants has been posted at the Working Group website.  In
addition to producing the chemical and irradiation induced deletion
stocks,
IRRI has produced point mutation stocks with EMS to collaborate with
research groups at Fred Hutchinson Cancer Center (Steve Henikoff) and
University of Washington (Luca Comai) to explore TILLING in rice.  The
technology has good potential to be a robust reverse genetics system for
chemical-induced rice mutants (see their recent publication: Colbert et
al.
2001 Plant Physiology 126:480-484).  

These new collaborations together with the on-going efforts by different
groups (Gynn An, Narayan Upadhyaya) will make it possible to develop a
comprehensive rice mutant library for use by the research community.    

3. Databases 
Richard Bruskiewich, bioinformatics specialist at IRRI, has been active
in
initiating international collaborations to facilitate the linking of
databases.  Through this effort, we have: 
	*	Initiated discussion on database integration with different
institutions and projects, such as RGP/INE, USDA/Gramene, NIG/OryzaBase
and
others. 
	*	Collaborated with the National Center for Genome Resources
(NCGR) in Santa Fe, USA, and other international agricultural centers
(CIP,
CIMMYT, ICRISAT) to develop a comparative mapping tool integrated into
plant
genetic databases  
	*	Collaborated on functional annotation with the Canadian NRC
Plant Biotechnology Institute in Saskatoon and McGill University in
Montreal. 
	*	Continued to improve the IR64 mutant database through
linkage with OryzaBase at National Institute of Genetics, Japan. 
	*	Developed a prototype 'StressGenesDb' (Ken McNally and
Richard Bruskiewich) to curate abiotic (mostly drought) plant stress
response related sequences and annotation.  StressGenesDb is intended
for
future trait-specific functional genomic databases at IRRI and will
likely
be extended to cover biotic stress response genes.

In summary, we have achieved in part some of the modest goals planned
for
2001.  We are happy to see an increasing number of research groups
expressing interest in joining the Working Group.  We now have a nucleus
of
laboratories working together to produce mutants, several labs donating
ESTs
to the Working Group, and active discussion in linking databases
together.
We will continue to expand on these activities in the second half of
2001.
In particular, we will try to expand IRRI's capacity to propagate the
transgenic insertion lines.  I wish to continue to request your
contributions of any sorts--summary of your lab activities, news, people
comings and goings etc.--to post on the Working Group Website.  

Thank you all for your continuing support to the Working Group. 

Sincerely, 

Hei Leung   

Distribution list (Working Group members plus colleagues with interest
in
the Working Group).