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Pig Genome Newsletter #119
From: "Christopher K. Tuggle" <cktuggle@iastate.edu>
To: angenmap@animalgenome.org
Subject: US Pig Genome Newsletter #119
Date: Thu, 19 Jun 2014 14:38:00 -0500
Pig Genome Update # 119:
- PDF version is available at
http://www.animalgenome.org/pig/newsletter/pdf/No.119.pdf
- Web version is available at
http://www.animalgenome.org/pig/newsletter/No.119.html
- Plain text version is appended below:
P I G G E N O M E U P D A T E
_________________________________________________________________
A Periodic Newsletter of the U.S. Pig Genome Coordination Program
************** No. 119 **************
* *
* June 20, 2014 *
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1. Out with the Old, In with the New
2. Role of Species Coordinators
3. NIFA Update
4. Pig SNP Arrays Available from GeneSeek
5. We want to hear from you
6. Upcoming meetings
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1. Out with the Old, In with the New
Many of you know that there has been a change in the leadership of the USDA
Swine Genome Coordination effort, but many scientists probably have not, and
we want to also take this opportunity to describe in detail the changes and
new policies for this important effort.
a) Many thanks to Max for a job well-done. Chris Tuggle (IA) and Cathy Ernst
(MI) were approved late September 2013 to become the new Joint Coordinators,
replacing Max Rothschild, the long-time Coordinator. Max has been the
Coordinator for 20 years, and ably led the Swine Sub-committee from the
beginning of the NRSP-8 project where we were focused on generating linkage
maps and physical maps, until October 2013 to a position where we have a
very large number of useful tools for genome analysis. Thanks for your
leadership, Max!
b) New goals and policies moving forward. Cathy and Chris will be splitting
the duties of the Coordinator, and we have developed some goals for the next
5 years. Some past policies we will be continuing, such as the Newsletter
and multi-station criteria for funding projects, which was shared with Swine
Subcommittee members earlier this year. We are also introducing some new
policies. A significant one is the creation of an Advisory Committee, who
will provide guidance on policy as well as help evaluate requests for
funding. The members of this Advisory Board represent the swine industry,
swine genomics and biotechnology researchers, NRSP-8 Stations and
participating USDA labs. The members are: Joan Lunney (USDA-BARC), Chris
Hostetler (National Pork Board), Randy Prather (U. Missouri), Jack Dekkers
(ISU), and Juan P. Steibel (MSU).
An important goal of the Coordinators is increasing the number of Stations
and ARS laboratories participating in the Swine Sub-committee. To facilitate
this, we offered to pay half of the PAG 2014 registration fees for anyone
willing to join the Swine Sub-committee. We welcome one new member, Melissa
Merrill, North Carolina State University. If you know of a suitable
researcher who should be encouraged to consider joining our group, please
let us know and we will follow up. The partial travel support for new
members will be provided again next year.
Another goal is to further encourage collaborations within the group and
support such group genomics research. What are your needs and how can we help
you accomplish collaborative research? We plan to work with the organizers of
the next Swine Sub-committee meeting to maximize group discussions on this
topic.
c) Communication is important. We plan to produce the Pig Genome Update
approximately 3 times per year, timed for our major Genome activities. These
will include a February issue, with a PAG summary, a June issue describing
summer meetings and research opportunities, and an October issue with PAG
meeting announcements and reminders. If there are other methods we can use
to facilitate discussion and communication, please don't hesitate to contact
us.
Role of Species Coordinators
Individual investigator or a team of investigators pursue a research hypothesis
or develop an idea into a proposal and can be successful in implementation.
However community resources such as databases, big ideas and large projects
such as genome sequencing and genotyping assay development require community
mobilization and funding coordination with federal agencies, private
industries and international partners. NRSP8 genome coordinators provide
leadership not only to its members but also for the species community as a
whole and will help implement big projects. Hence, I encourage all
researchers to stay in close contact with their species coordinators and let
them know when you have a big idea or a large project. Chris Tuggle and
Cathy Ernst are both great leaders and are committed to serve the swine
genomics community (Kindly provided by Lakshmi Matukumalli).
o o o o o o o o o o o
3. NIFA Update
a) NIFA is looking for a National program leader in Aquaculture.
(https://www.usajobs.gov/GetJob/ViewDetails/371716700)
b) In response to stakeholder comments NIFA is streamlining its business
practices for timely release of RFAs annually for AFRI foundational program
and challenge areas. Projects supporting animal sciences research can be
found in AFRI foundational program and most Challenge areas (Water is a new
challenge area introduced this year and is expected to continue). The
priorities in the foundational program do not significantly change each
year, but the challenge area RFAs are different each year. So please make
sure to read the challenge area RFA priorities closely
http://www.nifa.usda.gov/funding/afri/afri.html. For easily tracking new
NIFA RFAs released on www.grants.gov for automatic email notification:
Register at http://www.grants.gov/search/subscribeAdvanced.do and provide
CFDA Numbers; AFRI="10.310"; SBIR="10.212"; Higher Education Challenge
Grants="10.217"; Ecology & Evolution of Infectious Diseases ="47.074" (CFDA
numbers for other programs are on the NIFA website)
c) NIFA introduced two new programs in the AFRI Foundational RFA this year
and are expected to be continued. (See the AFRI foundational RFA for more
details)
(i) Exploratory Research Program: For projects that require $100,000 or
less with the following criteria: new and emerging problems with high
potential impact;(2) applications of new knowledge or new approaches to
unsolved challenges that have high potential impact;(3) develop tools
required tools required to have a paradigm shift in the field; and or,(4)
provide a rapid response to natural disasters or similar unanticipated
events should consider the Exploratory Program in this solicitation.
Applications are accepted year-round. **Letters of intent for FY 2014 are
accepted through September 30, 2014; it is required that a researcher
contact the Program Area Priority Contact - Dr. Michel Bowers (202) 401-4510
or mbowers@nifa.usda.gov BEFORE a Letter of Intent is submitted. See the
AFRI Foundational pdf (page 31-33;
http://www.nifa.usda.gov/funding/rfas/pdfs/14_afri_foundation_mod.pdf).
(ii) Critical Agricultural Research and Extension (CARE) To address critical
problems that impede the efficient production and protection of
agriculturally-important plants and animals. These problems may be local,
regional, or national, and may call for work focused on one or more
scientific disciplines. However, all need immediate attention to meet
producer needs. Finding and implementing solutions to these critical
problems require partnership and close coordination among researchers,
extension experts, and producers. Funded projects will quickly yield
solutions or practices that can be rapidly implemented by producers.
Proposal budget up to $150,000 (Kindly provided by Lakshmi Matukumalli).
o o o o o o o o o o o
4. Pig SNP Arrays Available from GeneSeek
GeneSeek, a Neogen Company, currently offers two custom Illumina Infinium
BeadChips for genomic profiling of pigs. The GeneSeek Genomic Profiler for
Porcine LD features approximately 8,500 SNPs for high density chip
imputation. This chip also includes several genetic markers that may
directly impact disease and performance traits. The Genomic Profiler for
Porcine HD is the most comprehensive commercial genome-wide BeadChip for the
porcine genome, and it features nearly 70,000 SNPs specifically chosen for
high minor allele frequency that uniformly span the porcine genome. This
BeadChip also includes several genetic markers that may directly impact
disease and performance traits. For more information:
geneseekinfo@neogen.com, www.neogenagrigenomics.com. The annotation
information is available from the NAGRP Data Repository
(http://www.animalgenome.org/repository/pig/Pig70K_SNP_annotations.csv.gz)
thanks to Jeremy Walker (JWalker@neogen.com) for providing the information.
o o o o o o o o o o o
5. We want to hear from you!
The swine genome coordinators are always glad to hear from NRSP-8 members
and other readers about ways that the coordination effort can be improved or
provide resources that are needed. If you have items of general interest to
the swine genetics and genomics communities that can be included in this
newsletter please share.
o o o o o o o o o o o
6. Upcoming meetings
(for meetings of relevance to the genomics community over the next 6-12
months, see: http://www.animalgenome.org/pigs/community/meetings)
Because of its importance, a special highlight for the quadrennial World
Congress is provided below.
World Congress 2014
The 10th World Congress on Genetics Applied to Livestock Production (WCGALP)
is being held from 17-22 August 2014 at the Westin Bayshore Conference
Center in Vancouver, British Columbia, Canada. The WCGALP takes place every
four years, and researchers and professionals involved in livestock genetic
improvement from around the world gather to attend the scientific program
and network with colleagues. This year's conference will have a strong
swine section with approximately 60 talks and posters being presented by
scientists from around the world. Genomics will feature strongly in the
oral sessions on Monday, Tuesday and Thursday (2 sessions), and there will
be sessions on swine genetics on Wednesday and Friday. Swine symposia
include "Omics and Swine: From GWAS to Small Panels and QTN" with invited
speakers LuSheng Huang, John Bastiaansen and Brian Kinghorn; "Genomics of
Disease in Swine" with invited speakers Daniel Ciobanu, Larry Schaeffer and
Ning Li; and "Utilizing Whole Genome Sequence Information in Swine Breeding"
with invited speakers Max Rothschild, Robert Kemp and John Hickey.
Information provided by Graham Plastow and Filippo Miglior; More
information: http://www.wcgalp.com/.
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Joint Coordinators:
Christopher Tuggle Catherine Ernst
2255 Kildee Hall Anthony Hall, 474 S. Shaw Lane, Room 1205
Department of Animal Science Department of Animal Science
Iowa State University Michigan State University
Ames, IA 50011 East Lansing, MI 48824
Phone: 515-294-4252 Phone: 517-432-1941
Fax: 515-294-2401 Fax: 517-353-1699
Email: cktuggle@iastate.edu Email: ernstc@msu.edu
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Supported by Multi-State Research Funds to the National Research Service
Program (NRSP-8). National Animal Genome Research Program (NAGRP),
Lakshmi Matukumalli, NAGRP Director, NIFA, USDA
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Web: http://www.animalgenome.org/pig | Mail: angenmap@animalgenome.org
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