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Pig Genome Newsletter #056
P I G G E N O M E U P D A T E
__________________________________________________________________
A Bimonthly Newsletter of the U.S. Pig Genome Coordination Program
************** No. 56 **************
* *
* <angenmap@db.genome.iastate.edu> *
* September. 1, 2002 *
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1. The ISAG 28th Conference met in Gottingen, Germany
2. The 7th WCGALP was held in Montpellier, France
3. Discussions on Candidate Gene Research at Montpellier, France
4. Allerton III: Beyond Livestock Genomics
5. Pig BAC Library and Filters are on the Move
6. A Pig Gene Array is on the Horizon
7. Plant, Animal & Microbe Genomes XI will be held January 11-15, 2003
8. Renewal Proposal for NRSP-8 making progress
9. A New Mirror Node for The ARKdb
10. Upcoming Meetings (4 Items)
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The 28th International Conference on Animal Genetics met in Gottingen,
Germany August 11-15 at the Georg-August University campus. The meetings
were attended by over 700 scientists, the largest attendance in the
history of ISAG, and featured many excellent workshops, presentations and
posters. Plenary presentations covered diverse topics including new
technologies (SNPs and proteomics), biodiversity in the Amazon, genomics
for healthier pigs, biotechnology in fish, and prion diseases. Of
particular note was the large number of excellent posters demonstrating
the continued progress that researchers in the Society have made since
the last meeting. For the pig, radiation hybrid maps have been expanded
and integrated with the genetic maps, high resolution BAC maps are
available, and major genomic regions including the SLA complex have been,
or will shortly be, fully sequenced. Increasing numbers of pig SNPs are
being reported, and new strategies being developed for more rapid SNP
identification and haplotyping. Major EST projects with every available
porcine tissue have been productive along with preliminary microarray
data. More detailed maps for important meat, carcass and reproductive
traits were presented. For the first time, an animal genome sequencing
workshop was held at ISAG, updating researchers on the progress made
toward sequencing chicken, cattle and pig genomes. A permanent ISAG
committee is being formed as a result of this workshop. A working group
is writing a white paper to submit to the NIH this October for a pig
genome sequencing project, following the high priority ratings given by
NIH NHGRI to chickens and, most recently, cattle. Progress was discussed
at many other workshops on pig mapping, the comparative gene mapping, and
applied pig genetics. The latter workshop will be combined with pig
mapping for future ISAG meetings. After several years of silence, an SLA
workshop was held to reformulate nomenclature based on DNA sequences
rather than serologic reagents. The Immune Response workshop discussed
immune microarray developments and data quality and control issues.
Participants were very fortunate to have an opportunity to visit
historical places in and around Gottingen during the program on a
beautiful and informative tour and the final banquet in the Town Hall.
The hosts from the Georg-August-University of Gottingen and the City of
Gottingen are to be congratulated for their efforts to make conference an
exciting and successful conference. (kindly provided by K.S. Kim, J.
Reecy and J. Lunney).
o o o o o o o o o o o
The 7th World Congress on Genetics Applied to Livestock Production was
held in Montpellier, France. Hosted by INRA and CIRAD, this was the
largest meeting of its kind with nearly 1,400 and over 300 accompanying
persons. The meeting featured an enormous program of over 1,000
presentations including plenary talks on animal breeding and society,
intellectual property rights and use of resources for developing
countries. There were over 25 separate topic areas that covered all
aspects of quantitative, statistical, molecular and applied animal
genetics in a large number of species. Of particular note was the large
number of pig papers related to new gene discovery and application.
Other sections demonstrated advances in methods to do gene discovery and
to apply those discoveries in the respective industries. The quality of
the presentations both as talks and posters was superb. Proceedings for
the conference can be obtained by visiting the web site:
http://www.wcgalp.org/. Participants were given the opportunity to take
one of many excellent tours that included historical places, the sea,
wine and olive tasting and ended the evening with a dinner in a country
chateau. As with the candidate gene meeting which preceded this meeting,
the excellent hospitality of our hosts combined with the southern French
flavor of Montpellier, the excellent organization and facilities for the
meeting and the nearness of the beach made for an unforgettable week of
science and fun. To all our hosts we say a big "Merci"!
o o o o o o o o o o o
Candidate gene research in health and immune response took center stage
at the Second International Symposium on Candidate Genes for Animal
Health held in Montpellier, France August 16-18. Hosted by INRA and
CIRAD and held at the northern CIRAD campus this meeting had over 100
participants and featured a wide range of papers covering candidate
genes, disease models, array technology and new methodologies. The
organizers did an excellent job hosting this event. The next meeting
will be hosted by Iowa State University and other US colleagues in 2-3
years time.
o o o o o o o o o o o
Allerton III: Beyond Livestock Genomics: A Roadmap for Harvesting the
Promise was held July 9th and 10th at University of Illinois in
Urbana/Champaign. This workshop was hosted by Larry Schook and Harris
Lewin, and attended by a small group of scientists and industry
representatives from several fields. Several interesting talks were
presented dealing with how genetics and genomics can and should interact
with these disciplines. In addition, the meeting was attended by several
individuals from the USDA-NRI administrative staff. Currently, the
organizers are working on drafting a white paper outlining the outcomes
from this meeting (kindly provided by James Reecy).
o o o o o o o o o o o
Pig BAC library and filters are on the move. Thanks to some real
partnering with Dr. Pieter de Jong, Children's Hospital Oakland Research
Institute and interested labs the new porcine BAC library and filters
will be shared among 12 swine genomics labs in the US. The library and
filters were prepared with funding from a USDA grant (USDA#
99-35205-8537). The library has been designated as "CHORI-242". The
library has received some provisional characterization. Once completed,
the data will be posted on a web page
(www.chori.org/bacpac/porcine242.htm) and also linked by the US Pig
Genome Web page (www.genome.iastate). High-density colony filter sets
are available for library screening. Each filter contains 18,432 clones
from 48 microtiter dishes from the library (36,864 colonies due to
duplicate stamping). A total of 11 filters is required for screening the
entire library. In July a request went out for interested parties to
request filters and libraries. The USDA grant will be paying for 5
libraries to be shared and the US Pig Genome Coordinator will be paying
for an additional 3 library copies and 10 filter sets to be shared at
this time. The receiving labs will pay the shipping charges.
Unfortunately this offer could not be extended to foreign colleagues and
industry groups at this time. If you are interested and missed the first
call, contact the US Pig Genome Coordinator to see if the offer will be
extended in 2003.
o o o o o o o o o o o
A pig gene array is on the horizon. One project the US Pig Genome
Coordinator is now working on is to make pig gene microarray materials
available to each lab at a reduced cost. To date several parties have
suggested considerable interest. At present the Pig Genome Coordinator
with assistance from others is working to design a general pig gene chip
with 8,000 genes on it for expression work. If you have interest,
please contact the US Pig Genome Coordinator at mfrothsc@iastate.edu.
o o o o o o o o o o o
Plant, Animal & Microbe Genomes XI will again be at the Town & Country
Convention Center in San Diego, CA, from Saturday, January 11 through
Wednesday, January 15, 2003. The pig workshop meeting will likely begin
on the afternoon of Saturday, January 11. Max Rothschild is the
organizer and is looking for the names of 1-2 good speakers for the
session. Speakers will receive free registration for the meeting.
Please provide names if you have good suggestions.
o o o o o o o o o o o
Renewal proposal for NRSP-8 making progress! The new objectives will
focus on: 1. Mapping and comparative genomics as they lead to the
development and use of full genome sequences; 2. Functional genomics;
and 3. Informatics. Cathy Ernst is coordinating the overall writing
team. Draft proposals are already being circulated and will be revised
soon with E-1 (effort) forms collected from Ag Experiment Stations by
October. The final and complete proposal is due to Area Administrators
by Dec. 1, 2002.
o o o o o o o o o o o
The Roslin Bioinformatics Group (http://bioinformatics.roslin.ac.uk) is
pleased to announce the availability of a new mirror node for their
ARKdb series of databases. The site is hosted at the Australian National
Genomic Information Service and is intended to provide a more accessible
service for users in the Southern hemisphere. It can be found at the URL
http://angis.thearkdb.org and carries the full complement of ARK-based
species, namely pig, chicken, cattle, sheep, salmon, turkey, tilapia,
deer, horse and cat. The new Australian site joins the three existing
nodes at Roslin (http://www.thearkdb.org), Iowa
(http://iowa.thearkdb.org) and Texas (http://texas.thearkdb.org). Users
of the ARKdb databases are encouraged to cite the databases as follows -
ARKdb-<insert species name> <insert date database accessed for
information cited> http://www.thearkdb.org Hu, J., Mungall, C., Law, A.,
Papworth, R., Nelson, J.P., Brown, A., Simpson, I., Leckie, S., Burt,
D.W., Hillyard, A.L. and Archibald, A.L. 2001. The ARKdb - genome
databases for farmed and other animals. Nucleic Acids Research 29,
106-110.
o o o o o o o o o o o
Upcoming meetings (for more details see:
http://www.genome.iastate.edu/community/meetings.html).
2nd UK Farm Animal Functional Genomics Workshop (ARK-Genomics Workshop),
September 12, 2002, Pentlands Science Park, Bush Loan, Penicuik,
Midlothian EH26 0PZ. For more information please email
info@arkgenomics.org for details and a registration form.
TIGR's 14th International Genome Sequencing and Analysis Conference,
October 2-5, 2002, Boston, MA. Please see www.tigr.org/conf/gsac/.
Plant, Animal and Microbial Genome XI, joint with NC-168 and NAGRP
annual meetings, Jan. 11-15, 2003, Town & Country Convention Center,
San Diego, CA. For more information see information on the web at
www.intl-pag.org/.
The John M. Airy Beef Cattle Symposium 2003: Visions for Genetics and
Breeding May 15-17, 2003 in Des Moines, Iowa will be hosted by Iowa
State University. For more information contact James Reecy at
jreecy@iastate.edu.
Additional items can be found at:
http://www.agbiotechnet.com/calendar/index.asp.
<> <> <> <> <> <> <> <> <> <> <>
Items for Pig Genome Update 57 can be sent to me by no later than October
20 please.
Max Rothschild
U.S. Pig Genome Coordinator
2255 Kildee Hall, Department of Animal Science
Iowa State University
Ames, Iowa 50011
Phone: 515-294-6202, Fax: 515-294-2401
mfrothsc@iastate.edu
cc: Dick Frahm, CSREES and Caird Rexroad II, ARS
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U.S. PIG GENOME COORDINATION PROJECT
+-----------------------------------+
| Paid for by funds from the NRSP-8 | Web: http://www.genome.iastate.edu
| USDA/CSREES sponsored Pig Genome | Mailing list:
| Coordination Program | angenmap@db.genome.iastate.edu
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