From: "Rothschild, Max F [AN S]" <mfrothsc@iastate.edu>
To: angenmap@animalgenome.org
Subject: US Pig Genome Newsletter #93
Date: Fri, 31 Oct 2008 35:13:09 -0500
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. 93 **************
* *
* <angenmap@animalgenome.org> *
* November 1, 2008 *
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1. Progress on the sequencing project continues to be excellent
2. Illumina and International Porcine SNP Chip Consortium announcement
3. NRSP-8 was renewed and the Genome Coordinators named
4. USDA Grant update
5. The 4th Allerton conference on "Phenotypes" was recently held
6. PAG XVII, January 10-15, 2009, is already underway
7. Upcoming meetings ( 7 items )
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Progress on the sequencing project continues to be excellent, with 93%
of the physical map having been selected from 15,424 BAC clones for
sequencing. Some 78% of the map has sequence available which gives
2,207Mb from 12,884 clones. A further 7,453 of these clones have been
"improved". More information on specific BAC clones and updates can be
found at www.sanger.ac.uk/Projects/S_scrofa/. The aim is to complete
the project with approximately 1,500 further clones which will be
selected over the next 6-7 months, bringing the total number of
sequenced clones for the entire project to 17,000. The average overlap
between BAC tile path clones stands at about 40kb. Notoriously, the
final stage of sequencing projects can prove more difficult, leading to
an increase in redundancy. They are hoping to avoid this by selecting
the remaining clones using sequence alignments rather than fingerprint
overlaps alone. (kindly provided Lucy Matthew, Sanger)
o o o o o o o o o o o
Illumina and the International Porcine SNP Chip Consortium are pleased
to announce that the porcine 60K SNP panel is under production. Thanks
to considerable cooperation and work among researchers and Illumina
chips were ordered for $99.99 as product. Considerable effort is now
underway to organize breed samples and family material for the initial
testing of the product. This work will be ongoing and chips should be
available by December 1 to those who previously ordered. If you did
not place an order please do not hesitate to contact Illumina for
further information or questions at
http://www.illumina.com/contactMe.ilmn?CS=1.
o o o o o o o o o o o
NRSP- 8 was renewed and the Genome Coordinators named. NRSP-8 was
renewed for another 5 years beginning October 1, 2008 with a FY 2009
total budget of $500,000. A modest increase in budget was obtained
despite the fact that competition for multi-state research funding has
become increasingly intense, reflective of the past success of the
NAGRP. Special thanks go to Mary Delany for leading the renewal
proposal writing team and Muquarrab Qureshi, who continues as Director,
as well as all our CSREES administrative team. Genome coordinators have
been reappointed by the USDA-CSREES. These now include John Liu and
Caird Rexroad III, aquaculture; Juan Medrano who replaces Jim Womack
for cattle, Jerry Dodgson and Hans Cheng, poultry; Noelle Cockett,
sheep; Ernie Bailey; Horse; Jim Reecy and a team of ISU researchers
(Sue Lamont, Chris Tuggle and Max Rothschild and Shane Burgess),
bioinformatics. A special thanks to Jim Womack for his help and
cooperation. Many of you were very kind to submit my name for the next
five years and I have been reappointed also. The confidence which you
have shown in the work we have accomplished together is much
appreciated and there are so many people whose help I have appreciated.
I hope the next five years will be as much fun and productive as
before. Please do not hesitate to suggest ideas, improvements or
concerns. Thank you again for your continued strong support.
o o o o o o o o o o o
USDA Grant update. Due to the establishment of the National Institute
for Food & Agriculture (NIFA) that consolidates USDA competitive
research, education and extension programs, a new competitive grant
program will replace the National Research Initiative for FY 2009. An
initial alert to include projected program application deadlines is
expected to be released in November, 2008. The actual 2009 RFA is
expected next January. This means that the earliest application
deadlines (e.g., Animal Protection & Biosecurity) likely will not be
prior to March, 2009. The Animal Genome deadline is uncertain but will
most likely remain in June. The exact amount of funding available also
is uncertain, since it is unclear when a FY 2009 budget bill will be
passed by Congress.
o o o o o o o o o o o
The 4th Allerton conference on "Phenotypes" was recently held at the
University of Illinois. Great talks and a beautiful venue all
contributed to an excellent meeting. Eighteen speakers from six
countries presented talks centered around the need to collect, analyze
and warehouse animal phenotypes. Attendees were provided insights into
the use of the latest high density SNP chips based on real data (e.g.
Drs. Jerry Taylor, Theo Meuwissen). Dr. John McEwan illustrated the
real value to be gained from a central genetic hub or "information
nucleus" as a way of linking research to industry populations. Dr.
Sussman talked about technology after SNP chips with an exhilarating
gallop through 25,000 bp reads from single molecule sequencing to
real-time metabolomics of the (mouse) brain. On the swine side, Dr.
Martien Groenen presented an update on the Swine SNPchip and Dr. Ming
Che (Jay) Wu talked about Taiwan's efforts to conserve swine germplasm.
Drs. Larry Schook, Harris Lewin and Jon Beever plan to develop a white
paper summarizing the conference. (kindly provided by G. Plastow and J.
Reecy.)
o o o o o o o o o o o
PAG XVII, January 10-15, 2009, is already underway. The new chairs of
the swine genome section are Melissa Ashwell and Cathy Ernst and the
program is now posted on the web. Ideas for speakers are gladly being
taken by Max Rothschild or Hans Cheng for plenary talks in 2010. Some
reorganization of the species workshops on Saturday and Sunday has
taken place to avoid overlap and increase attendance to the NRSP8
meeting which is all Sunday afternoon. The main PAG meeting runs
Sunday night through Wednesday. See http://www.intl-pag.org/ for more
information and to register. Register prior to Nov. 1 for lower rates.
Some funds to assist travelers for the swine workshop may be available
on request.
o o o o o o o o o o o
Upcoming meetings (see:
http://www.animalgenome.org/pigs/community/meetings.html)
Ninth International Long-Oligonucleotide Microarray Workshop, Jan. 4-9,
2009. The University of Arizona, Tucson, AZ. Further details at
http://ag.arizona.edu/microarray/workshopJan2009.html
Plant & Animal Genome Conference, PAG XVII, Jan. 10-14, 2009, Town &
Country Hotel, San Diego, CA. More info. will be available at
http://www.intl-pag.org/ .
Advances in Genome Biology & Technology Conference, Feb. 4-7, 2009.
Marco Island, FL. Information at www.agbt.org
Genomic Impact of Eukaryotic Transposable Elements, Feb. 6-10, 2009.
Asilomar Conference Center, Pacific Grove, CA. Information at
http://www.girinst.org/conference/Asilomar-2009/index.html
Gordon Conference on Quantitative Genetics and Genomics, Feb. 22-26,
2009.
Hotel Galvez, Galveston Island, TX. Register at
https://www.grc.org/application.aspx?id=3D8785
Midwest ASAS, ADSA regional meetings. March 16-19 in Des Moines IA.
Details at http://adsa.asas.org/midwest/2009/
Statistical Genetics of Livestock for the Post-Genomic Era, May 4-6,
2009. University of Wisconsin, Madison, WI. Additional information to
be sent out soon.
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Items for Pig Genome Update 94 can be sent to me by no later than December 15
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
http://www.animalgenome.org/pigs/
cc: Muquarrab Qureshi, 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.animalgenome.org/pig
| USDA/CSREES sponsored Pig Genome | Mail: angenmap@animalgenome.org
| Coordination Program |
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