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Pig Genome Newsletter #083
From: "Rothschild, Max F [AN S]" <mfrothsc@iastate.edu>
To: angenmap@animalgenome.org
Subject: US Pig Genome Newsletter #83
Date: Wed, 28 Feb 2007 12:15:17 -0600
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. 83 **************
* *
* <angenmap@animalgenome.org> *
* March 1, 2007 *
**************************************
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1. Chinese New Year, the Year of the Pig recently celebrated
2. PAG-XV was held January 13-17, 2007 in San Diego
3. The Swine Genome Sequencing Workshop will next meet in St Croix
4. SNP chip under discussion
5. The new pig oligo arrays are here and can be ordered
6. Pig Genome Update has gone electronic only beginning January 1
7. The CSREES FY 2006 National Research Initiative
8. Upcoming meetings ( 6 items )
===========================================================================
Chinese New Year, the Year of the Pig recently celebrated. For those that may
not know the Chinese New Year is the longest and most important celebration
in the Chinese calendar. The Chinese year 4705 began on February 18, 2007. In
honor of the Year of the Pig, the International Journal of Biological
Sciences (http://biolsci.org/) has launched a special issue on Swine Genome
Science; edited by Dr. Zhihua Jiang, Washington State University and Dr. Max
Rothschild, Iowa State University. Several leading scientists in the field of
swine genomics have contributed six reviews to this special edition, which
cover swine genome sequencing, mapping and evolution (Chen et al., IJBS 2007
3:153-165), swine trancriptomics (Tuggle et al., IJBS 2007 3:132- 152), swine
and mammalian concordant QTL maps (Rothschild et al., IJBS 2007 3:192-197),
swine whole genome linkage disequilibrium (Du et al., IJBS 2007 3:166-178),
swine biomedical model genomics (Lunney, IJBS 2007 3:179-184) and the USDA
efforts in agricultural animal genomics (Green et al., IJBS 2007 3:185-191).
This series of papers offers the opportunity to all interested researchers to
see the big picture of porcine genomics.
o o o o o o o o o o o
PAG-XV was held January 13-17, 2007 in San Diego and included some
outstanding plenary talks and workshops. The new format included an evening
plenary talk Sunday night by Martina Newell- McGloughlin on public
perceptions of agricultural biotechnology. Other topics included micro-RNA
diversity and its role in shaping genome evolution (e.g., plenary talks by
David Bartel and Isidore Rigoutsos). Ian Baldwin and Detlef Weigel extended
the reach of genomics "into the field" and "around the world", looking at
questions of ecology and speciation. Jerry Tuskan and Kirsten Lindblad-Toh
described novel insights obtained from the sequences of the poplar, dog,
horse and oppossum genomes. The swine genome workshop was held Saturday and
reviewed progress over the past years (see special ITBS addition discussed
above). Finally the swine genome sequencing workshop highlighted the
sequencing results obtained in the last year. Next year PAG-XVI will be held
Jan. 12-18, 2008, at the same location. NRSP-8 will meet jointly with PAG.
Ideas for speakers should be shared with Max Rothschild at
mfroths@iastate.edu.
o o o o o o o o o o o
The Swine Genome Sequencing Workshop will next meet in St. Croix. The meeting
will be held on Thursday, Friday and Saturday, March 15 to 17, 2007. The
program will address specific issues of the sequencing project, identifying
approaches to resolving issues, identifying approaches to ensure broad and
rapid utilization of the sequence information, developing educational
programs, and discussions on companion manuscripts for the sequencing paper.
Meeting Registration and Hotel Reservation materials can be obtained at
www.piggenome.org. Please register immediately so we can ensure proper hotel
and meeting materials.
o o o o o o o o o o o
SNP chip under discussion. One of the issues discussed at the swine genome
workshop was the need for a SNP chip in pigs. There has been some development
in this area and a "private" chip of about 7.5K SNPs is under manufacture by
Illumina for a group of European scientists. Max Rothschild and Gary Rohrer
and some of the European research group met with Illumina personnel. We
discussed the possibility of using these SNPs and others to produce a 10K
chip. Gary has agreed to head a committee to work on this and the committee
includes several other swine researchers. Look for developments to be
reported in the future.
o o o o o o o o o o o
The new pig oligo arrays are here and can be ordered. Thanks to efforts of a
number of groups and individuals we have developed a novel 70-mer
oligonucleotide microarray for profiling expression of the pig (Sus scrofa)
genome. The Swine Protein-Annotated Oligonucleotide Microarray has been
developed as an OPEN SOURCE collaboration between investigators and
institutions with an interest in pig physiology. The sequences of the
oligonucleotides, the consensus sequences they represent, and the annotation
of the consensus sequences are provided at no cost to the entire research
community. New swine oligo arrays ordering can now be ordered
(http://www.pigoligoarray.org/). Please note ordering depends on the source
of your funding. Labs associated with agriculture (at US Colleges or
Universities, US government laboratories, or foreign Universities or
governments) please order using the "Arrays for USDA NAGRP-8 supported
activities" button. If you are a PRRS researcher please order using the
"Arrays for PRRS CAP supported activities" button. Commercial concerns
(domestic or foreign) or any biomedical researchers (domestic or foreign)
please order using the "Array for Biomedical and Commercial Applications"
resource button. Validation of arrays will take place. Thanks to efforts of a
number of the swine genome community a validation experiment, funded in part
by the participants and the USDA Pig Genome Coordinator will take place over
the next few months. The plan is to report the information to the community
at the earliest possible date.
o o o o o o o o o o o
Pig Genome Update has gone electronic only beginning January 1. For those who
used to get the hard copy version of this newsletter, it now will be
distributed by email format only though Angenmap
(http://www.animalgenome.org/community/discuss). Acrobat .pdf versions
(with graphics) are also posted on our website at
http://www.animalgenome.org/pigs/newsletter/index.html.
o o o o o o o o o o o
The CSREES FY 2006 National Research Initiative (competitive grant program)
request for proposals can be found at
http://www.csrees.usda.gov/funding/rfas/nri_rfa.html. Total FY 2006 NRI
funding was $181.7M. The House FY 2007 budget and the Senate Appropriations
Committee allocated about $190M for next year's NRI, but almost all
appropriations bills failed to get through by the Oct. 1 deadline and it
seems likely that another Omnibus Appropriations Act will be required, and
one can never tell what that may contain. Note: next year's FY 2007 NRI
applications will require electronic submission through http://grants.gov/
(provided by Jerry Dodgson).
o o o o o o o o o o o
Upcoming meetings (see:
http://www.animalgenome.org/pigs/community/meetings.html)
Swine Genome Sequencing Workshop, March 15-17, 2007 in St. Croix. Details can
be seen at www.piggenome.org.
Chicken Development and Genomics, April 12-15, 2007, Barcelona, Spain. See
www.lists.bbsrc.ac.uk/mailman/listinfo/chicken-genome
3rd International Conference on Quantitative Genetics, August 18-24, 2007,
Zheijiang University, Hangzhou, China. Conference Organizers: Jun Zhu
(jzhu@zju.edu.cn) and Zhao-Bang Zeng (zeng@stat.ncsu.edu)
Advances in Applied and Comparative Genomics, April 26,27 2007 in College
Station, Texas to celebrate the impact James Womack has had on the field of
comparative genomics Further information, program and registration are
available at http://www.cvm.tamu.edu/womacklab/index.htm
Convergence of Genomics and the Land Grant Mission: Emerging Trends in the
Application of Genomics in Agricultural Research, September 10-12, 2007,
Purdue U., West Lafayette, Indiana. See= www.entm.purdue.edu/conference.
International Symposium on Animal Genomics for Animal Health, October 23-25,
2007, OIE Headquarters, World Organization for Animal Health, Paris, France.
For information contact Cyril Gay, cyril.gay@ars.usda.gov, or Marie-Héne
Pinard, pinard@dga2.jouy.inra.fr
<> <> <> <> <> <> <> <> <> <> <>
Items for Pig Genome Update 84 can be sent to me by no later than April 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
===========================================================================
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 |
+-----------------------------------+--------------------------------------
