Minutes of Multistate Research Activity

PROJECT NUMBER: NRSP-8

PROJECT TITLE: NRSP-8: Swine Species Genome Committee

PERIOD COVERED: January 1 to December 31, 2002

DATE OF THIS REPORT: January 21, 2003

ANNUAL MEETING DATE(S): January 11, 2003

PARTICIPANTS: see page 3

ADOPTED AGENDA: Include everything added during the meeting.

Invited Speakers

"Molecular dissection of an imprinted QTL on SSC2 with major effect on muscle

mass"

"Using cDNA microarrays to study ovarian follicle development in pigs selected for

increased ovulation rate"

"Bioinformatics update"

"Use of Real-time assays of immune gene expression to assess genetic basis of disease resistance"

Experiment Station Reports

Indiana – Diane Moody

Iowa – Max Rothschild, Chris Tuggle

Michigan – Cathy Ernst

Minnesota – Lee Alexander, Mike Murtaugh

Nebraska – Daniel Pomp

Nevada – Craig Beattie

USDA/ARS BARC – Joan Lunney

USDA/ARS MARC – Gary Rohrer

Washington – Zhihua Jiang

Illinois

Kansas

North Carolina

Swine Genome Coordinator’s report – Max Rothschild

Administrative Advisors’ report

Discussion Items

NRSP-8 Swine Committee Business Meeting, Max Rothschild, chair

BRIEF SUMMARY OF MINUTES OF ANNUAL MEETING:

New Business Items:

1) Location of NRSP-8 Swine Species Genome Committee for 2004

Daniel Pomp moved that the 2004 meeting be held at the Plant and Animal Genome Conference in San Diego, CA, as a joint meeting with NC-1004.

Joan Lunney seconded the motion.

Motion passed.

2) Industry Representative

Dr. Tom Rathje, Danbred North America, was introduced as the official industry representative to the NRSP-8 Swine Species Genome Committee.

3) Electronic reports

Max Rothschild reminded participants that electronic copies of station reports are needed by the end of the week.

4) Officers

Diane Moody will serve as the committee chair for the upcoming year.

Joan Lunney volunteered to serve as secretary.

KEY DISCUSSIONS: For example, elaborate information by objective or by state

1) NC1004 Update. Daniel Pomp announced that the first NC-1004 meeting will be held May 29-31 in Hastings and Clay Center, Nebraska. Brad Freking will serve as the local host.

2) Development of Pig Microarrays. Max Rothschild reported that he has begun investigating options of using Swine Genome Coordinator funds to develop and purchase a general pig microarray. He reported initial discussions with Agilent and Affymetrix had not led to feasible agreements because of intellectual property and cost issues, respectively. Additional options, including spotting cDNA collections at Michigan State University, or synthesis of long oligonucleotides through a commercial source such as Qiagen, were presented. Considerable concerns regarding quality control issues with the cDNA spotting approach were expressed. It was suggested that validation and curation of cDNA clones from multiple sources would be highly problematic. However, Michigan State has experience with quality control issues and is willing to make individual clones available to researchers for validation of specific array elements. Concerns relating to the synthesis of oligos included the ability to design suitable oligos for 10,000 sequences given the current publicly available sequences. Questions regarding the bioinformatics that would be used to select sequences and design oligos were also raised. Representatives from Qiagen addressed many of these questions and provided information describing their bioinformatics tools. It was decided that a committee would make a final recommendation to the Genome Coordinator regarding which approach to pursue, and that plans to make an initial pig microarray would move forward in the coming months.

ASSIGNED RESPONSIBILITIES/DEADLINES/TARGET DATES:

A committee was established to review options for making a pig microarray and provide a recommendation to Max Rothschild by February 1, 2003. Committee members include:

Chris Tuggle, co-chair Cathy Ernst

Daniel Pomp, co-chair Diane Moody

Mike Murtaugh

Participant

Institution

Participant

Institution

Aaron Singsey

Biogenetic Services, Inc.

Shuhong Zhao

Iowa State Univ.

Akiko Takasuga

Sirakawa Inst. Of Animal Genetics

Stacey Meyers

Univ. of Illinois

Ana-Maria Gaseneau

Iowa State Univ.

Tim Smith

USDA/ARS MARC

Archie Clutter

Monsanto

Tom Rathje

Danbred North America

Atabak Royaee

USDA/ARS BARC

Tun-Ping Yu

Sygen International

Audra Kazlauskas

Univ. of Illinois

Udaya Desilva

Oklahoma State Univ.

Bart Tungerius

Wageningen University

Ulaus Olek

Univ. Bonn Biopsytisc

Brandy Marron

Univ. of Illinois

Zhihua Jiang

Washington State Univ.

Cathy Ernst

Michigan State Univ.

Zhiliang Hu

Iowa State Univ.

Chad Bierman

Babcock Genetics Inc.

Charles Otieno

Iowa State Univ.

Chris Bidwell

Purdue Univ.

Chris Tuggle

Iowa State Univ.

Christian Looft

Univ. of Kiel

Craig Beattie

Univ. of Nevada

Dan Nonneman

USDA/ARS MARC

Daniel Pomp

Univ. of Nebraska

Dave Burt

Roslin Institute

Deb Hamernik

USDA-CSREES

Diane Moody

Purdue University

Gary Rohrer

USDA/ARS MARC

Glenn Zhang

Oklahoma State Univ.

Honghe Coi

Univ. of Guelph

Jack Dekkers

Iowa State Univ.

Joan Lunney

USDA/ARS BARC

John Byatt

Monsanto

John McEwan

AgResearch

Jun Heon Lee

Chingnam Nat’l Univ., Korea

Kelly Swanson

Univ. of Illinois

Larry Schook

Univ. of Illinois

Lauree Rind

Univ. of Illinois

Lee Alexander

Univ. of Minnesota

Margaret OKomo-Adhiambo

Univ. of Nevada

Mark Thallman

USDA/ARS MARC

Matt Ehrhardt

Univ. of Illinois

Max Rothschild

Iowa State Univ.

Michael Grosz

Monsanto

Micheal Murtaugh

Univ. of Minnesota

Rick Van Wyle

Inst. Of Pig Genetics, Netherlands

Serguei Golovan

Univ. Guelph