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Pig Genome Newsletter #121
From: "Christopher K. Tuggle" <cktuggle@iastate.edu>
To: angenmap@animalgenome.org
Subject: US Pig Genome Newsletter #121
Date: Mon, 16 Feb 2015 15:59:37 -0600
Pig Genome Update # 121:
- PDF version is available at
http://www.animalgenome.org/pig/newsletter/pdf/No.121.pdf
- Web version is available at
http://www.animalgenome.org/pig/newsletter/No.121.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. 121 **************
* *
* February 15, 2015 *
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1. PAG wrap-up including announcement of new FAANG Initiative
2. New high density SNP-Chip available
3. New RFAs for USDA-NIFA grants
4. Porcine Translational Research Database has recently been updated
5. Upcoming meetings- highlighting meetings with close deadlines
6. We want to hear from you
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1. Summary of Plant and Animal Genome 2015 January 10-14, 2015, San Diego
The 2015 Swine NRSP-8 Workshop was held January 10, 2015 in San Diego, CA in
conjunction with the 2015 Plant and Animal Genome Conference. The titles and
abstracts of all Lectures, Posters, and Workshop talks can be found at:
https://pag.confex.com/pag/xxiii/webprogram/. In addition, the winner of the
Neil A. Jorgenson Travel Award for Swine, Melanie Trenhaile, has provided a
brief summary of selected Swine-related posters. These summaries are found
here: http://www.animalgenome.org/pig/community/columns/20150125.php. Melanie
is a MS student of Daniel Ciobanu of UN-Lincoln. Thanks for your hard work on
this, Melanie!
A joint session was held with the Cattle, Sheep and Goat groups in the morning
and then each sub-commitee had separate afternoon sessions. The Swine program
had five invited international speakers representing four different European
countries. In addition, there were ten presentations from nine different NRSP-8
participating locations. The presentations were very interesting and initiated
considerable discussion among the attendees. Dr. Clutter gave an
administrator's report and Drs. Ernst and Tuggle gave their coordinators'
report as well as conducted a discussion on the use of coordinator's funds to
support collaborative research. At the morning joint session, 177 attendees
signed in representing 100 different locations. Sixty-six of these attendees
were from 19 different countries. In the afternoon, the workshop had 60 people
sign in representing 35 different locations. Thirty-four of the attendees
represented 19 different countries. During the business meeting, Dr. Kiho Lee
from Virginia Tech University was elected as the new secretary and Dr. Cathy
Ernst of Michigan State University was elected to chair the 2016 Swine
Workshop. (majority of this information was kindly provided by Gary Rohrer).
One discussion that was a bit different from previous years was a mid-afternoon
discussion on ideas for using the NRSP-8 Coordinator funds, and the development
of policies requiring matching funds to access NRSP-8 funding. One major topic
of discussion was a new high density SNP chip, and a number of Stations were
interested in this. Please see item #2 for more details.
A major event at PAG was the announcement and further organization of the
Functional Annotation of ANimal Genomes (FAANG) Consortium. The following text
is a summary of the purposes of FAANG; for further information please see the
FAANG website (www.faang.org). At the NRSP-8 Workshop on Sunday, there was an
introductory talk by Dr. Elisabetta Giuffra (INRA) and a standing-room only
crowd then participated in a roundtable discussion on implementing FAANG. A
further meeting on Monday afternoon attracted 62 persons, where a Steering
Committee was set up and discussions of a Fall meeting in Washington, DC was
started. More details as they become available.
The most significant challenge in the post-genomic era is connecting genotype
to quantitative phenotype in basic and applied biology - the genome to phenome
challenge. Significant progress has been made in associating sequence variation
with quantitative phenotypes motivated by the importance of animals as food
sources, models for human health, and key ecological actors. In domesticated
animals, the wealth of phenotypic diversity of different breeds and populations
and decades of research have been key to such progress, and coupled with
advances in sequencing the genomes of these species provides unique
opportunities to study genome-phenome relationships.
FAANG has been created as we all recognize the importance of coordinating this
effort to maximize efficiency and data quality as demonstrated by the ENCODE
project. The major goal of FAANG is to identify all functional elements in
animal genomes.
FAANG aims to deliver standardized datasets from a limited set of individuals
representing species that have reference quality draft genome assemblies and
substantial publicly available phenotypic datasets.
The FAANG project will establish an infrastructure capable of efficiently
analyzing genome-wide functional data for animal species. Such large-scale
analyses will contribute to our understanding of how variation in gene
sequences and functional components determine phenotypic diversity. This
understanding will inform the development and exploitation of improved models
for predicting complex phenotypes from sequence information.
Please join our initiative by signing up at the website!
o o o o o o o o o o o
2. New 650K SNP Chip- Available soon!
A high-density pig SNP array has been developed by Affymetrix with over 650,000
SNP selected by Martien Groenen and tested by Alan Archibald in collaboration
with Affymetrix. The SNP on the array are equally spaced along pig
chromosomes, and also include unassigned contigs from build 10.2. The array
includes 56K confirmed SNPs from the Illumina SNP60 chip, thus it should be
possible to input data for populations already typed using the SNP60 chip.
These SNP have high MAF, and represent a variety of European and Asian breeds.
Genotyping of a limited number of samples for US laboratories will be supported
by the NRSP8 Swine Genome Coordination Program. For more information or to
participate with samples, please contact Cathy Ernst (ernstc@msu.edu).
o o o o o o o o o o o
3. New RFAs released on USDA funding opportunities
A. Agriculture and Food Research Initiative: Food Security Challenge Area Grants
http://www.grants.gov/web/grants/view-opportunity.html?oppId=272432
Note: letters of Intent are no longer required for this opportunity.
Applications due June 4, 2015
All three different areas are relevant to animal geneticists:
1. Agricultural Production Systems
2. Breeding and Genomics of Crops and Livestock
3. National Strategy for Sustainable Crop and Livestock Production in the
United States
B. USDA Higher Education Challenge (HEC) Grants Program
http://www.nifa.usda.gov/fo/educationchallengehigheredhep.cfm
Applications are due March 19, 2015
o o o o o o o o o o o
4. Porcine Translational Research Database has recently been updated
This database currently has 7,538 gene entries including 4,813 sequences
with full 5-prime and 3-prime representation (an estimated 22.4% of the genome.
These sequences include the vast majority of genes that are commonly
studied in rodents, pigs or humans. The database also includes extensive
error annotations (2,949 gene entries) for the current NCBI and Ensembl
(build 10.2) versions of the genome including; 742 genes that have been
sequenced more than once, 904 genes that are missing from the genome and
1,046 loci that contain a partial open reading frame. The database also
contains extensive information on reagent availability for the pig
including 2,227 real-time PCR assays and 602 antibodies. The database can
be accessed at http://www.ars.usda.gov/services/docs.htm?docid=6065.
(kindly provided by Harry Dawson).
o o o o o o o o o o o
5. Upcoming meetings- highlighting meetings with close deadlines
(for meetings of relevance to the genomics community over the next 6-12 months,
see: http://www.animalgenome.org/pig/community/meetings.html)
A. Midwest ASAS/ADSA Meeting March 15-18, 2015, Des Moines, IA
The 2015 Joint ADSA-ASAS Midwest Section meeting is scheduled for March 15-18
in Des Moines, IA. See
https://www.asas.org/membership-services/asas-sections/midwest-section/meetings
for details. In addition to the regular breeding and genetics sessions, a
Functional Genomics symposium has been organized by the Breeding and Genetics
program committee. Dr. Huaijun Zhou (UC-Davis) will present a talk in this
symposium on his newly NIFA-funded project to identify functional components of
the pig, chicken and cattle genomes. This project is also being supported by
the Swine, Poultry, and Cattle Genome Coordinators and the National Pork Board.
B. The 6th International Symposium on Animal Functional Genomics (ISAFG 2015)
will be held in Piacenza, Italy from the 27th to the 29th of July, 2015.
The purpose of ISAFG 2015 is to bring together academic researchers, industry
representatives and policy makers to exchange knowledge on the leading-edge
developments in functional genomics and its applications in the livestock
sector. The symposium themes include important topics, ranging from structural
and comparative genomics to systems biology.
Conference Themes
- Comparative genomics
- Epigenetics
- Transcriptomics
- Proteomics
- Microbiome
- Systems Biology
Important Dates
- March 31st 2015: deadline for early bird registration
- June 15th 2015: deadline for abstract submission
- July 10th 2015: deadline for regular registration
(Information taken from ISAFG website; see http://www.isafg2015.it/)
o o o o o o o o o o o
6. 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. Our issues are planned for Feb 15, June 15 and October 15 each
year. Any contribution should be sent to the Coordinators one week prior to
these dates.
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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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