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Pig Genome Newsletter #096
From: "Rothschild, Max F [AN S]" <mfrothsc@iastate.edu>
To: angenmap@animalgenome.org
Subject: US Pig Genome Newsletter #96
Date: Wed, 29 Apr 2009 15:44:51 -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. 96 **************
* *
* <angenmap@animalgenome.org> *
* May 1, 2009 *
**************************************
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1. The Swine Genome Sequencing Project is entering the final stages of
clone selections
2. Community feedback is needed
3. Pig Breeders Roundtable was held in Canterbury, UK
4. The Swine Genome Sequencing Consortium (SGSC) will co-host with The
Wellcome Trust Sanger Institute a workshop from November 2 to 3, 2009
in Hinxton, UK
5. The NRSP-8 Bioinformatics Coordination team has released an update for
pig QTLdb, which includes a number of new improvements
6. USDA Grant update
7. Illumina and the International Porcine SNP Chip Consortium are pleased
to announce that the porcine 50K+ SNP panel is available
8. PAG XVII, January 10-14, 2009 was a great success
9. Please provide your input
10. Upcoming meetings ( 5 items )
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The Swine Genome Sequencing Project is entering the final stages of clone
selection. Every effort is being made to identify clones that will
contribute new sequence data. Radiation hybridizations are planned to
identify new extending clones from each map contig. So far, clones selected
and sent for sequencing cover 96.26% of the physical map and clones
sequenced cover 89.18%. Currently, 16,707 clones are in the sequencing
pipeline. Of these, 15,485 have sequence (4x) with 10,381 having been
improved (>6x). Sequence data have reached a total of 2,635Mb with 72.39Mb
at finished quality. The completion date is December 31, 2009. We are on
track to have achieved >98% sequence coverage at ~6X coverage.
Community feedback is needed: 1) The Ensembl team has taken the Pig
assembly and plans to run the automated Genebuild. The timeframe is
expected to be 5 months as it is not an easy process. This will add Pig
to the list of species found on the Ensembl website. The best QC for
the analysis will be feedback from the community and we would like lots
of it! Guidance to problematic areas means they can then be corrected
in time for a second Genebuild upon completion of the project; 2) Manual
annotation for some clones is a possibility, but resources are limited.
Therefore, it would be hugely beneficial for the community to identify
any sequenced clone that would benefit from increased annotation provided
by manual intervention and 3) One advantage of opting for the BAC by BAC
sequencing approach was to allow targeted sequencing of important regions
first. These regions identified by the swine community are sequenced as
"Top Priorities" and allow rapid sequence feedback to the community long
before completion of the project. So far, 28 regions of interest have
been prioritized spanning 518 clones or ~3% of the genome. If you know
of a region that would benefit from prioritized sequencing, please email
pig-help@sanger.ac.uk. The deadline is 31st June to send a request
carol@sanger.ac.uk (kindly provided by Richard Clark and Carol Churcher).
o o o o o o o o o o o
Pig Breeders Roundtable was held in Canterbury, UK. Over 50 researchers
and industry personnel discussed advances in swine breeding and the role
genomics has played in those advances. Advice and input from the
community was also sought to help with the final stages of the
sequencing effort. Early results from multiple SNP experiments on boar
tant, genetic abnormalities and other traits were presented.
o o o o o o o o o o o
The Swine Genome Sequencing Consortium (SGSC) will co-host with The
Wellcome Trust Sanger Institute a workshop from November 2 to 3, 2009 in
Hinxton, UK. In anticipation of the completion of the pig genome
sequencing project, this workshop will focus on "Pig Genome Assembly and
Annotation". The SGSC workshop will be held in conjunction with the EU
PigNet Genome Meeting that will be held at the same location from
November 3 to 4 and will focus on strategies for full utilization of the
pig genome sequence information. All investigators are encouraged to
attend and fully participate in these two workshops. Registration and
Program details will be released soon. Interested parties should
contact either Larry Schook (schook@illinois.edu), Alan Archibald
(alan.archibald@roslin.ed.ac.uk, or Martien Groenen
(Martien.Groenen@wur.nl).
o o o o o o o o o o o
The NRSP-8 Bioinformatics Coordination team has released an update for
Pig QTLdb, which includes a number of new improvements. Within this
update, there are 569 newly curated QTL and data download functions
that allow users to download pig QTL data by either their linkage
location ("cM") or genome location ("bp", for chromosomes that have
preliminary genome assemblies are available). The QTL genome location
data are available in GFF format so that users can directly import it
for analyses in external programs such UCSC for genome feature
alignments. Please see http://www.animalgenome.org/QTLdb/pig.html for
details. Data can be downloaded for the entire Pig genome, for specific
chromosomes, or for a refined chromosomal view. In addition, GBrowse
has been installed so that pig QTL can be visualized in combination with
pig transcripts, mRNA, annotated genes, etc. Currently, this option is
only available for pig chromosomes 1, 4, 5, 7, 11, 13, 14, 15, 17, and
X. As the pig genome assembly is updated, the GBrowse display will be
updated as well. Users can find links to GBrowse either at the Pig
QTLdb web site, or use this link
http://www.animalgenome.org/cgi-bin/gbrowse/pig/ (kindly provided by
Zhi-Liang Hu).
o o o o o o o o o o o
USDA Grant update. The 2008 Farm Bill authorized the creation of the
Agriculture and Food Research Initiative (AFRI), which replaces the
National Research Initiative (NRI). AFRI offers research, education,
extension project opportunities that focus on six key areas of
importance to agriculture, nutrition, food safety, environment, and
rural communities. CSREES released the AFRI program announcement on the
agency's Web site
http://www.csrees.usda.gov/funding/afri/pdfs/program_announcement.pdf
and on http://grants.gov/ . The program announcement provides an
overview of the legislation that created the AFRI program and describes
programs being offered in Fiscal Year 2009. The program descriptions
contain the program priorities, deadline dates, budget limitations, and
contact information. The program announcement does not contain all
information needed to submit an application. That information will be
contained in the AFRI Request for Applications (RFA). The AFRI RFA is
anticipated in January 2009. Important information regarding the Animal
Genome, Genetics, and Breeding Program: The program name for the Animal
Genome program has been changed to "Animal Genome, Genetics, and
Breeding" Letters of Intent are required for research priorities 1
through 4 and the letter of intent deadline is March 5, 2009. The
proposal deadline for research priorities 1 through 4 is May 14, 2009
(kindly provided by D. Hamernik and P. Burfening).
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 50K+ SNP panel is available and being
shipped. 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
PAG XVII, January 10-14, 2009 was a great success. The swine workshop
and the swine sequencing workshop both had excellent presentations
including one on the usefulness of the new 60K SNP chip. The abstracts
are now posted on the web. See http://www.intl-pag.org/ for more
information. Planning is well underway for next year and your
involvement is encouraged.
o o o o o o o o o o o
Please provide your input The Pig Genome Coordinator is always glad to
hear from NRSP-8 members and other readers about ways to improve the
coordination effort or provide resources that are needed and with which
the coordination program can help
o o o o o o o o o o o
Upcoming meetings (see:
http://www.animalgenome.org/pigs/community/meetings.html)
Statistical Genetics of Livestock for the Post-Genomic Era, May 4-6,
2009. University of Wisconsin, Madison, WI. Additional information can
be found by contacting grosa@wisc.edu.
Systems Biology: Integrative, Comparative, and Multi-Scale Modeling: The
18th Annual Growth Factor and Signal Transduction Conference, June
11-14, 2009, Iowa State U., Ames, Iowa. See
http://www.bb.iastate.edu/~gfst/phomepg.html
7th U.C. Davis Transgenic Animal Research Conf., Aug. 17-22, 2009,
Granlibakken Resort and Conference Center, Tahoe City, CA. See
http://conferences.ucdavis.edu/transgenic
Next generation sequencing: challenges and opportunities. October 1-3,
2009, Casa Convalescencia, Barcelona, Spain http://ngs2009.uab.es
Plant & Animal Genome Conference, PAG XVIII, Jan. 9-13, 2010, Town &
Country Hotel, San Diego, CA. Information available at http://www.intl-
pag.org/ .
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Items for Pig Genome Update 97 can be sent to me by no later than June 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 |
+-----------------------------------+--------------------------------------
