Archived Post

From  Mon Dec 20 09:25:26 2004
Message-ID: <>
From: Max F Rothschild <>
Date: Mon, 20 Dec 2004 11:18:18 -0600
Postmaster: processed by
Subject: US Pig Genome Newsletter #70
To: Multiple Recipients of <>

                  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. 70  **************
                  *                                    *
                  *  <>  *
                  *          January 1, 2005           *
 1. The Lauren Christian Symposium held on December 9-10 in Ames, Iowa
 2. PAG-XIII will be January 15-19, 2005 in warm, beautiful San Diego
 3. The 2005 NRI competitive grants program has been announced
 4. A small number of pig oligo arrays remain to be printed and released
 5. A pig quantitative trait loci database has been created at ISU
 6. Swine Genome Sequencing Project (SGSP) makes significant progress
 7. The 3rd International Symposium on Genetics of Animal Health
     will convene on July 13-15, 2005, in Ames, Iowa
 8. Upcoming meetings (7 items)

Iowa State University and National Swine Improvement Federation (NSIF)
sponsored The Lauren Christian Symposium in honor of the deceased ISU
scientist.  Former students presented updates on developments in the seed
stock and swine industry both in the US and in other countries during the
2-day workshop on December 9-10 in Ames, Iowa.  The meeting was well
attended by over 90 producers, swine industry personnel, researchers and
students.  Thanks go to Dr. Ken Stalder, ISU, and Steve Moeller, OSU for
all their efforts.  Program papers can be found in the near future at

           o    o    o    o    o    o    o    o    o    o    o

PAG-XIII will be January 15-19, 2005 in warm, beautiful San Diego at the
Town and Country Hotel.  See for a schedule and
registration information.  Registration is $575 for those from non-
profit organizations and $750 for industry participants, with fees going
up by $100 on-site. Student registration is $325 now and $375 on site.  A
weekend rate (Fri.-Sun. only) is available at $300 now or $350 on site.
Among others, Nobel Laureate Rich Roberts from New England Biolabs and
Bill Haseltine from Human Genome Sciences are scheduled to give plenary
lectures.  The NRSP-8 Swine genome committee will meet. Joan Lunney is
chairing the meeting and plans for an excellent program are underway.  The
meeting is scheduled to start at 8 am on Saturday, January 15. In
addition, the Swine Genome Sequencing Committee will meet on Sunday from
12 noon - 2 pm.  Both meetings are open to all interested participants.
Limited partial travel assistance will be available for NRSP-8 swine
committee members or members of their labs.  Please contact the
Coordinator, Max Rothschild, as soon as possible if interested.

           o    o    o    o    o    o    o    o    o    o    o

The 2005 NRI competitive grants program has been announced
(  Deadline dates are now May 17, 2005, for
Animal Growth and Nutrient Utilization; and June 15, 2005, for Animal
Genomics, Animal Genome Reagent & Tool Development and Functional Genomics
of Agriculturally Important Organisms.  Total 2005 NRI funding remains was
set at $181M in the recently passed Consolidated Appropriations Act.  As
previously reported, the Animal Genome Reagent & Tool Development program
that has been very successful is now scheduled to end after the 2005 year.
In response to concerns expressed, Dr. Anna Palmisano, Deputy CSREES
Administrator for Competitive Programs (
responded at length on Oct. 1, including the following: "We have just
begun the planning process for the FY2006 RFA. If the NRI Animal Genome
Reagents and Tools program continues beyond FY 2005, we feel that the
emphasis of the program will need to change considerably. Therefore, we
would like to challenge the NRSP-8 committee, including all of the species
subcommittees, to address priority areas for the NRI Animal Genome
Reagents and Tools program at the NRSP-8 business meeting at the Plant &
Animal Genome meetings in San Diego, CA. We request that the members of
NRSP-8 present the NRI National Program Leaders with a list of 4 to 5
prioritized areas for possible inclusion in an FY 2006 NRI Animal Genome
Reagents and Tools RFA, should the program be continued." Thanks to Dr.
Palmisano for her prompt and thoughtful reply (kindly provided by Jerry

           o    o    o    o    o    o    o    o    o    o    o

A small number of pig oligo arrays still remain to be printed and released.
Some individuals have failed to request a shipping date and need to do so.
Cost is $20/slide plus shipping.  Slide orders will be on a first come
first serve basis.  Please immediately contact Max Rothschild at

           o    o    o    o    o    o    o    o    o    o    o

A pig quantitative trait loci (QTL) database (PigQTLdb) has been created
at the Iowa State University.  The database has gathered all pig QTL data
published during the past 10+ years.  The database and its peripheral
tools were made to compare, confirm, and locate on pig chromosomes the
most feasible location for a candidate gene responsible for quantitative
trait(s) important to pig production.  To date, 791 QTL from 73
publications have been curated into the database.  Those QTL represent 219
different traits. The database can be reached at .  The database content has also been
submitted to the NCBI Gene and Map Viewer resources, where the information
about markers are matched to marker records in NCBI's UniSTS database.
Support from NAGRP and NCBI have made this possible.

           o    o    o    o    o    o    o    o    o    o    o

Swine Genome Sequencing Project (SGSP) makes significant progress. During
2004, multiple planning sessions occurred between researchers, the USDA,
swine industry representatives, and the Alliance for Animal Genome
Research.  These activities have provided an important context for
developing and implementing a plan to sequence the swine genome. Several
prevailing themes emerged.  These included the need: (1) to focus on an
integrated and universally accepted (high priority) scientific plan; (2)
to capture cost savings associated with technological advances in DNA
sequencing; (3) to garner industry support to ensure full utility of the
sequence information; and (4) to demonstrate matching funds towards a USDA
led initiative.  Additional collaborative research efforts have led to the
identification of an animal to sequence, creation of swine BAC libraries
(funded by USDA-NRI), completion of a physical map, identification of a
minimal tiling path (consisting of ~20,000 BAC contigs) for sequencing,
and creation and distribution of small insert libraries for whole genome
shotgun sequencing. Thus the necessary reagents are available to begin
sequencing the swine genome in 2005.  The cost of DNA sequencing has
decreased significantly.  These costs have been captured in the proposed
SGSP.  The cost of the cattle sequencing project (6X coverage, cDNAs, and
SNPs) was approximately $53M.  As a result of on-going collaborations
between the Sanger Institute, INRA and UIUC researchers, an effective
hybrid for launching the SGSP has been developed. Currently, we estimate
that approximately $30M will be needed to conduct this hybrid sequencing
approach that includes a BAC contig skim (3X) and whole genome shotgun
(3X) sequencing to generate an approximate 6X working draft.  During 2004,
SGSP representatives met with the National Pork Board (NPB) and industry
representatives from Iowa and North Carolina.  The scope of the plan and
the need to develop a global network (including the potential to conduct
sequencing outside the USA) was discussed.  The SGSP was reviewed in the
respective research committees and has been recommended for approval by
these associations. To date, the NPB has approved $750,000 (available in
2005 and 2006) and the Iowa Pork Producers have also agreed to provide
$100,000. Additional support from Iowa State University, University of
Illinois and other state pork agencies is likely to exceed $300,000 to
provide a total of approximately $1.2M in matching funds (beginning in
2005). Equally important, is the recommendation of the research committees
to provide future funding to support utilization of the sequencing
information.  Recently, as a result of discussions with the Alliance, the
Wellcome Trust Sanger Institute has expressed their willingness to provide
matching funds towards completion of the proposed 6X hybrid pig genome
sequencing model.  Our success in securing industry support, reducing the
cost of sequencing by over 40% and the identification of matching funds
address the issues expressed by the USDA leadership during our
discussions.    In mid-December, USDA Under Secretary Jen met with
Alliance executive director, Eversole, and with the Interagency Working
Group secretary, Green, to discuss the consortium's request for USDA to
provide $15 million over the next 2-3 years to support the SGSP.   Under
Secretary Jen confirmed that USDA will continue its leadership role and
that, at a minimum, there would be $10 million provided from the NRI ($5
million per year for FY 05 and 06) and that $5 million could be available
for FY 07 if that were necessary.  In addition, we discussed the
possibility of getting $1 million from ARS (equivalent to the amount that
was committed by ARS for both the swine and chicken projects).  It is
hoped that the USDA will announce the RFA at the beginning of the new year
so that sequencing could start by June 1, 2005. (kindly provided by Larry
Schook, Jon Beever, Joe Cassady, Kellye Eversole, Gary Rohrer, Jane Rogers
and Max Rothschild).

           o    o    o    o    o    o    o    o    o    o    o

The 3rd International Symposium on Genetics of Animal Health (formerly,
Candidate Genes for Animal Health) will convene on July 13-15, 2005, in
Ames, Iowa, USA.  The meeting will feature several invited speakers,
contributed presentations and poster sessions and should be an exciting
continuation of past meetings.  Please note the dates on your calendar,
and bookmark the GAH2005 web home page:  More information will follow!

           o    o    o    o    o    o    o    o    o    o    o

Upcoming meetings (see:

. Plant, Animal and Microbial Genome XIII, joint with the NAGRP annual
  meetings, Jan. 15-19, 2005, Town & Country Convention Center, San Diego,
  CA.  Please see for information.

. Swine in Biomedical Research Conference, January 27-29, 2005, Chicago
  Illinois; Please see or
  contact Larry Schook for details.

. Advances in Genome Biology & Technology and Automation in Mapping & DNA
  Sequencing, Feb. 9-12, 2005, Marco Island, Florida.  See

. Gordon Conference on Quantitative Genetics and Genomics, Feb. 20-25, 2005,
  Ventura Beach Marriott, Ventura, California.  See

. The Biology of Genomes, May 11-15, 2005, Cold Spring Harbor Laboratory,
  Cold Spring Harbor, NY.  See for more information.

. 3rd International Symposium on Genetics of Animal Health, July 13- 15,
  2005, in Ames, Iowa, USA, Please see:

. Symposium on Integration of Structural and Functional Genomics (14th
  Annual Growth Factor and Signal Transduction Conference), September 22-25,
  2005, Iowa State University, Ames, Iowa.  See

           o    o    o    o    o    o    o    o    o    o    o

A special thanks to all of you who have helped to make my job a bit easier
and move our efforts forward.  Please take some time and enjoy this
holiday season and may the new year bring good health, happiness and
success.  Happy Holidays.

           <>   <>   <>   <>   <>   <>   <>   <>   <>   <>   <>

Items for Pig Genome Update 71 can be sent to me by no later than February 15

                    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

cc: Muquarrab Qureshi, CSREES and Caird Rexroad II, ARS

| Paid for by funds from the NRSP-8 |  Web:
| USDA/CSREES sponsored Pig Genome  | Mail:
| Coordination Program              |



© 2003-2024: USA · USDA · NRPSP8 · Program to Accelerate Animal Genomics Applications. Contact: Bioinformatics Team