From: "Christopher K. Tuggle" <cktuggle@iastate.edu>
To: angenmap@animalgenome.org
Subject: US Pig Genome Newsletter #123
Date: Wed, 23 Mar 2016 22:47:56 -0500
Pig Genome Update # 123:
- PDF version is available at
http://www.animalgenome.org/pig/newsletter/pdf/No.123.pdf
- Web version is available at
http://www.animalgenome.org/pig/newsletter/No.123.html
- Plain text version is appended below:
P I G G E N O M E U P D A T E
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A Periodic Newsletter of the U.S. Pig Genome Coordination Program
************** No. 123 **************
* *
* April 1, 2016 *
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1. Recent meetings summary- GO-FAANG and PAG 2016
2. Update on new functional genomics project FAANG activities
3. Update on USDA-NIFA-AFRI
4. Reminder on Joint Annual Meeting (ASAS, ADSA, CSAS) and ISAG registration
deadlines
5. Upcoming additional meetings information
6. pdate on projects supported by NRSP-8 funds- We want to hear from you!
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1. Recent meetings summary
a. Gathering On FAANG Workshop (GO-FAANG)
The FAANG (Functional Annotation of ANimal Genomes) Consortium held the
GO-FAANG Workshop in Washington, DC on October 7-8, 2015. The Workshop
gathered together from around the world a group of 100-plus genome
scientists, administrators, representatives of funding agencies and
commodity groups to discuss the latest advancements of the Consortium, new
perspectives, next steps and implementation plans The Workshop was streamed
live and recorded, and all talks, along with speaker slide presentations,
are available at www.faang.org.
The GO-FAANG Workshop objectives included establishing priorities for
research efforts; planning the management structures required for efficient
use and sharing of samples, data and computational tools; and identifying
resources needed to accomplish these goals. Three plenary talks and
presentations by funding agency representatives set the stage for what is
possible in functional annotation of genomes. An emphasis was then placed
on small group discussions; these were designed to develop policies and
approaches to maximize the success of this crucial next phase in animal
genomics. Reference datasets are being established under pilot projects;
plans for tissue sets, morphological classification, and methods of sample
collection for different tissues were organized; and core assays and data
and meta-data analysis standards were established. For more information,
please visit the FAANG website (http://www.faang.org).
b. Plant and Animal Genome (PAG):
The 2016 NRSP-8 Swine Workshop was held January 9, 2016 in San Diego, CA in
conjunction with the Plant and Animal Genome XXIV Conference. A joint
session was held with the Cattle, Sheep and Goat Workshop in the morning
focused on the theme of Genome Editing. The afternoon Swine Workshop
program (see https://pag.confex.com/pag/xxiv/webprogram/Session3175.html)
included invited presentations by four young scientists from Konkuk
University in South Korea, the University of Barcelona, the Roslin
Institute, and the University of Florida, who spoke about their work in
emerging areas of pig genomics. The Jorgensen Pig Travel Award winner,
Jeremy Howard, from NSCU was introduced and he gave a lightening talk on
his area of research. There were also ten presentations from nine
different NRSP-8 participating locations. The presentations covered a
range of topics from functional genomics to SNP analysis, as well as a
broad range of important phenotypes, and sparked discussion among attendees
throughout the workshop. Drs. Clutter and Matukumalli gave administrator's
reports and Drs. Tuggle and Ernst gave their coordinators' report, as well
as conducted a discussion on community needs and resources. At the morning
joint session, 176 attendees signed in, including 80 (45%) from 20
different countries outside the US. Attendees from the US represented 21
universities, 14 industry companies and 2 government agencies. In the
afternoon, the Swine Workshop had 33 people sign in, although it is
estimated that at least 75 were present for the invited talks. Among those
signing in, 12 attendees represented 7 countries outside the US, and the 21
US attendees were from 10 universities, 3 industry companies and 2
government agencies. During the business meeting, Dr. Tuggle was elected as
the new chair-elect, and Dr. Kiho Lee (Virginia Tech) will chair the 2017
Swine Workshop.
o o o o o o o o o o o
2. Update on new functional genomics project FAANG activities - Special
Symposium on FAANG to be held during JAM (Joint Annual Meetings of ASAS,
ADSA, CSAS)-ISAG overlap day
As described in prior PG Updates, the FAANG Consortium has been organized
and held meetings. The following text is a summary of the activities of
FAANG since the last PG Update; for further information please see the
FAANG website (www.faang.org).
a) A meeting report of the GO-FAANG Workshop described above was written by
a small group representing the FAANG Subcommittees and attendees. This has
been submitted to Animal Genetics for publication, pending peer review.
b) A full day FAANG Symposium has been organized for July 23, 2016, which
can be attended by registrants of either the Joint Annual Meeting of Animal
Science Societies (https://asas.org/meetings/jam-2016/home) or the
International Society of Animal Genetics (ISAG;
https://asas.org/meetings/isag2016/home). Seven world-class speakers will
provide up-to-the-date information on the use of functional annotation to
explore human and model species genomes, early results on the use of such
data for understanding results from Genome-wide Association studies, as
well as new methods to assemble animal genomes. This Symposium promises to
be excellent, and a very good reason to attend one or both of these great
meetings!
c) Two FAANG pilot projects coordinated by Institut National de la
Recherche Agronomique (INRA) in France and University of California-Davis
(UC Davis) in USA were started in 2015. The Davis project has been
supported by NRSP-8 funding from the Swine, Bovine, and Chicken
Coordinators, as well as the National Pork Board. These projects aim at
identifying regulatory elements within domesticated animal genomes by
refined functional annotation of biologically important representative
tissues. For both projects, the first phase consisted of sampling of a wide
variety of tissues from reference animals in four species: chicken, pig and
cattle (both UC Davis and INRA) and goats (INRA only). Different protocols
were used to perform multiple assays (histology, chromatin assays, gene
expression, DNA conformation and accessibility). Specific representative
tissues were selected (cerebellum, cortex, hypothalamus, liver, lung,
adipose tissue, muscle and spleen for UC Davis; liver and immune cells
(CD4+ and CD8+) for INRA for core molecular assays development and data
production (beginning in 2016). In addition to RNA-seq, UC Davis focused on
ChIP-seq (histone marks and CTCF) and chromatin accessibility assays
(DNase-seq) while INRA focused on small RNA-seq sequencing, chromatin
accessibility assays (ATAC-seq), and genome-wide Chromosome Conformation
Capture (Hi-C). Preliminary results for ChIP-seq, ATAC-seq and Hi-C assay
development were presented at the Plant and Animal Genome XXIV Conference
during the FAANG workshop (see http://www.faang.org/bbs?s=PAG2016_workshop..txt).
d) During 2015-2016, new projects joined the FAANG community. Several of
these projects aim at identifying the impact of genetic variation on the
functional features of the pig and cattle genomes, with the ultimate goal
to identify causative variations affecting complex traits. In one, the
"WUR-pigENCODE" project, led by Wageningen University (NL) in collaboration
with the University of Illinois (US), is adding new functional annotations
to previous methylome studies. In another, a complete range of FAANG
annotation is being generated in parallel to eQTL and allele specific
expression approaches in dairy cattle. This project is being led by
scientists in Australia. Finally, two projects recently funded by the
Genome Canada Competition "Genomics and Feeding the Future" are linked
to FAANG. These projects focus on dairy cattle and feed efficiency and pigs
and disease resilience.
e) Responding to FAANG member requests, a new webpage has been developed to
provide information on new funding opportunities for FAANG related
proposals (available on FAANG website, member's area page).
o o o o o o o o o o o
3. Update on USDA-NIFA-AFRI
In case you missed it: A Dear Colleague Letter was emailed to Angenmap from
Dr. Matukumalli in March on the following opportunity:
NSF-USDA Joint Funding Opportunity - Early Concept Grants for Exploratory
Research (EAGERs) to Develop and Enable Breakthrough Technologies for
Animal and Plant Phenomics and Microbiomes�. Up to $300,000 over 2 years
can be requested. Interested PIs are required to email a two-page
pre-proposal summary to papm@nsf.gov by May 12, 2016, 5:00 PM proposer's
local time. More information can be found at the website:
http://www.nsf.gov/pubs/2016/nsf16058/nsf16058.jsp, or by contacting
Lakshmi Matukumalli,lmatukumalli@nifa.usda.gov or 202-401-1766.
The AFRI request for applications for the yearly genome-oriented
opportunities is anticipated to be released approximately early to
mid-April, with deadlines approximately 6 weeks later. Be sure to read and
consider applying for these opportunities! If a letter of support,
including matching funds from NRSP-8, would be useful, please let the
Co-coordinators know early in the process.
o o o o o o o o o o o
4. Reminder on Joint Annual Meeting (ASAS, ADSA, CSAS) and ISAG
registration deadlines
A reminder that the Joint Annual Meeting of ASAS, ADSA and several other
groups is being held July 17 - 23 in Salt Lake City. As well, the
International Society of Animal Genetics (ISAG) meeting is being held in
the same city, from Jul 23 - 27. As discussed above, there is one day
overlapping with the JAM (Joint Annual Meetings of ASAS, ADSA, CSAS) and
ISAG meetings, where the FAANG Symposium discussed above will be held.
The next early registration deadline for JAM is June 3, 2016, while the
deadline for full registration for the ISAG meeting is prior to the start
of the meeting, at which time only the higher on-site registration will be
available. Importantly, registration for either meeting allows you to
attend the FAANG Symposium on July 23!
o o o o o o o o o o o
5. Upcoming additional meetings information
Besides the JAM and ISAG meetings discussed above, there are many other
meetings of relevance to the genomics community over the next 6-12 months,
see: http://www.animalgenome.org/pig/community/meetings)
6. Update on projects supported by NRSP-8 funds - We want to hear from you!
Update on PEDV Resistance Genetics project: Dr. F. Bertolini presented a
poster on the first results from a collaborative project headed by M.
Rothschild et al. See the poster abstract at:
https://pag.confex.com/pag/xxiv/webprogram/Paper20373.html. Dr. Bertolini
also gave a summary at the Swine Workshop.
Update on FAANG project: Dr. H. Zhou presented a poster summarizing the
FAANG project; see the poster abstract at:
https://pag.confex.com/pag/xxiv/webprogram/Paper20545.html. There were also
several reports given at the FAANG Workshop covering the Davis project that
have NRSP-8 support: see
https://pag.confex.com/pag/xxiv/webprogram/Session3544.html.
o o o o o o o o o o o
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 now planned for February 1 and
October 1 each year. Any contribution should be sent to the Coordinators
one week prior to these dates.
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Items for Pig Genome Update 124 can be sent to me by no later than July 15
please.
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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