Pig genome sequencing progress continues to move along. Recent
progress is shown on the graph. A total of 13,296 clones have been
selected and sent for sequencing. The coverage is now 82.5% of the
map. The total sequence now equals 1421 Mb of which 60.1 Mb is
finished quality from 8,999 sequenced clones with 4,741 clones at an
improved status. Sequencing appears on schedule but it is clear more
funding is desired.
GO TO TOP
Registration for the Pig Annotation Workshop July 16-18 at the.
Wellcome Trust Sanger Institute is needed. The Sanger institute is
organizing an annotation workshop to bring together researchers from
the pig genome community to participate in the manual annotation of
the genome sequence. The even is sponsored by EADGENE and SABRE. The
resulting annotation from the participants will be eventually
displayed in the Ensemble browser. The aim of the three day workshop
is to teach participants how to use annotation software so they can
begin to annotate regions of interest to them. The organizers will
provide support during and after the workshop to enable participants
to work remotely to finish their annotation using the experience
gained at the workshop. Registration is free and there are a number
of grants available to pay for the cost of accommodations.
Registration is limited to 40 participants and the last day of
registration is May 31, 2008. For details see
http://www.sanger.ac.uk/Projects/S_scrofa/workshop_Hinxton08/index.shtml
GO TO TOP
Dense SNP chip development continues. International efforts to
develop the first large scale (50K) dense SNP chip continue. Several
groups in Europe and the US have been busy making libraries and doing
sequencing to produce SNPs. The overall plan is to attempt to get 30X
coverage on about 10% of the genome and to produce about 1 Million
SNPs. These will then be tested using bioinformatics and other tools
to come up with a set that are wide spread across the genome and which
work with the technology provider's platform. The plan also is to
have those with validated SNPs to deposit them in dbSNP. The plan is
for ALL SNPs to be deposited by June 1 to be considered. Members of
the consortium from the USDA (ARS, CSREES), University of Illinois,
Iowa State University and the National Pork Board have met with two
technology providers and discussed the technologies and the possible
costs to produce chips. It appears that Illumina will fit the needs
of the community best. To work with them it will be necessary to have
all the sequencing, validation, and bioinformatics completed by August
22. In addition, all contracts for initial purchase will need to be
executed by August 22, 2008. All interested parties should prepare to
consider how much funding they have available. Cost per chip will
depend on numbers of chips contacted at the date the contract period
ends. We suspect that value could be in the $125 range if sufficient
numbers are sold.
GO TO TOP
USDA-NRI Grant RFA for FY 2008 is now available at
http://www.csrees.usda.gov/ or
http://www.grants.gov. Program 43.0, Animal
Genome, contains Translational Animal Genomics, Tools and Resources,
Bioinformatics, and Functional Genomics. The deadline for these is
June 5, 2008. However, integrated proposals only for Translational
Animal Genomics and all proposals for Functional Genomics require
submission of a letter of intent by March 14, 2008. Please see the
RFA for deadlines for other animal-related programs. Letters of
intent are required for some programs/elements to insure that proposal
aims meet the goals of the program and to minimize wasted effort in
the application process.
GO TO TOP
Planning for PAG XVII, January 10-15, 2009, is already underway. The
new chairs of the swine genome section are Melissa Ashwell and Cathy
Ernst. Ideas for speakers are gladly being taken by Max Rothschild or
Hans Cheng for plenary talks. Some reorganization of the species
workshops on Saturday and Sunday is likely to take place to avoid
overlap and increase attendance to the NRSP8 meetings. Stay tuned for
developments.
GO TO TOP
The pig oligo arrays can be ordered. Swine oligo arrays can now be
ordered at http://www.pigoligoarray.org/. A validation experiment,
funded in part by the participants and the USDA Pig Genome
Coordinator, was reported on at PAG 2008.
GO TO TOP
Upcoming meetings (see:
http://www.animalgenome.org/pigs/community/meetings.html)
-
NC-1037 Genetic and functional genomic approaches to improve
production and quality of pork May 14-15, USDA Beltsville, MD. For
information please contact Joan Lunney at
Joan.Lunney@ARS.USDA.GOV
- Pig Genome II, The Second European Conference on Pig, June 4-5, 2008
in Ljubljana, Slovenia. For details see
http://www.piggenomeii.si/
- ASAS 2008 Centennial meeting, July 7-11, 2008, Indianapolis, Indiana,
USA. See
http://www.asas.org/100years/.
- XXXI conference of the International Society of Animal Genetics (ISAG)
July 20-24, 2008 Amsterdam, The Netherlands. See
www.isag2008.nl.
- Kennedy Conference on Quantitative Genetics and Animal Breeding,
August 11-12, 2008 Guelph, Ontario Canada. For details please contact
Larry Schaeffer at
lrs@uoguelph.ca.
Items for Pig Genome Update 91 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
© US Pig Genome Coordination Program