Copy Link
Add to Bookmark
Report
Pig Genome Newsletter #120
From: "Christopher K. Tuggle" <cktuggle@iastate.edu>
To: angenmap@animalgenome.org
Subject: US Pig Genome Newsletter #120
Date: Wed, 15 Oct 2014 11:53:42 -0500
Pig Genome Update # 120:
- Web version is available at
http://www.animalgenome.org/pig/newsletter/No.120.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. 120 **************
* *
* October 15, 2014 *
***************************************
===========================================================================
1. Meetings Issue
- Reminder about close deadlines for PAG and other upcoming meetings
- Summer meetings highlights- ISAG and WCGALP
2. Information on NAGRP Bioinformatic tools - new and updated
3. Upcoming meetings - highlighting meetings with close deadlines
4. We want to hear from you
===========================================================================
1. Meetings Issue
o Quick reference for upcoming deadlines (see details below):
- Plant and Animal Genome XXIII (San Diego), January 10-14, 2015. Abstract
deadline is October 31, 2014. Early registration deadline is November 1, 2014
- North American PRRS Symposium (Chicago), December 5 - 6, 2014. Abstract
deadline is October 31, 2014. Registration deadline is November 15, 2014 -
- Gordon Conference (Italy) February 22 - 27, 2015. Applications for this
meeting must be submitted by January 25, 2015. GRS Speaker. Abstract deadline
is November 21, 2014.
- Midwest ASAS/ADSA meeting (Iowa) March 15-18 2015. Abstract Submission
Deadline: November 5, 2014, 11:59 PM (Central Standard Time)
o Summary of ISAG meeting July 2014
The 34th meeting of the International Society of Animal Genetics convened in
historic Xi'An China on July 27 to Aug 1, 2014. Attendance was over 1,100
scientists from 44 countries. The facilities were spacious and the scientific
sessions were well-organized. The social events were excellent, including a
trip to see the 2,000+ year old Terra Cotta warriors, part of the burial site
of Qin Shi Huang, the first emperor of China.
Many plenary talks and Workshops were of direct interest to pig genome
scientists, including workshops on Pig Genetics and Genomics, Comparative and
Functional Genomics, Genetics of Immune Response and Disease Resistance
Workshop, Domestic Animal Sequencing, and Domestic Animal Epigenetics.
Reports of many of these Workshops (current and previous Workshops) and other
Workshops can be found at the ISAG website:
http://www.isag.us/committees.asp. For the plenary talks, several stood out
and were highly relevant to pig genetics and animal agriculture. Dr. Martien
Groenen (Wageningen University, The Netherlands) presented his research on
introgression mapping, describing his whole genome re-sequencing analysis of
gene flow from Chinese to European breeds. Dr. Lusheng Huang (Jiangxi
Agricultural University, China) described substantial resources and data
documenting extensive phenotypic and genotypic diversity in Chines pig
breeds. Dr. Larry Schook (University of Illinois, USA) described the work
being done with pigs to use and further develop them as biomedical models.
Dr. Joan Lunney (USDA-ARS, USA) provided a detailed description of the highly
productive PRRSV Host Genetics Consortium, emphasizing the need for such
large collaborative projects to combat diseases such as PRRS, but
acknowledged the large effort and time needed to create and sustain such
research projects. Dr. Zhiying Zhang (Northwest Agriculture and Forestry
University, China) described his research on miRNA and miRNA binding site
variation and its role in pig and other livestock breeding, as well as his
work toward CRISPR/CAS9 gene editing of miRNA binding sites to test
functionality of such variants.
One important decision that affects future ISAG conferences was made at
the 2014 ISAG business meeting. To "frameshift" the ISAG meeting so that it
does not occur in the same year as the World Congress on Genetics Applied to
Livestock Production (see next report), the following schedule was adopted.
The next meeting of ISAG will be held in Salt Lake City, Utah on July 23-27,
2016, and the meeting after Salt Lake City will be just one year later, in
2017, in Dublin, Ireland. From then on, ISAG meetings will be held in odd
years.
o Summary of WCGALP meeting August 2014
The 10th World Congress on Genetics Applied to Livestock Production was
held at the Westin Bayshore Conference Center located on the bay in beautiful
Vancouver, British Columbia, Canada, August 17-22, 2014. A total of over
1,450 delegates representing 58 countries enjoyed a week of excellent science
and fabulous sights. Plenary lectures opened each morning including
presentations by Jerry Taylor ("Animal Breeding in the Next-Generation
Sequencing Era"), Michael Lohuis ("Bridging the Gap Between Scientific Facts
and Societal Perceptions about Agriculture"), Joseph Felsenstein
("Phylogenies Meet Quantitative Genetics: Some Attempts to Extrapolate"),
Peter Visscher ("Quantitative Genetics of Complex Traits in Human
Populations"), and Carlos Bustamante ("Population Genetics in the Personal
Genome Era"). Oral and Poster sessions kept delegates engaged throughout the
day. Proceedings papers and the virtual meeting including recordings of many
of the presentations are available at the congress website
(http://www.wcgalp.com). The joint US-Canada organizing committee is to be
commended for hosting such a successful conference. Everyone is looking
forward as plans are underway for the 11th WCGALP in Auckland, New Zealand in
February 2018.
o o o o o o o o o o o
2. Information on NAGRP Bioinformatic tools - new and updated
The NAGRP Bioinformatics Team has been working on new and updated tools and
resources that impact pig genome scientists. See their recent updates at
http://www.animalgenome.org/community/mail/view.php?f=db/6492. Of direct
interest:
- Animal QTLdb updates: Announcing Release 24 of the Animal QTLdb: A sum of
3,876 new QTL have been added to the database since last release. This brings
the current total number of QTL in the database to 28,624, including 11,610
in Pig.
- Data repository: The pig 70K SNP chip annotations are now available from
the NAGRP data repository. Thanks to Jeremy Walker (JWalker neogen.com) for
this resource.
- Announcement since the September Update #3: The state of art online
alignment tool - Jbrowse - has been setup for QTL/association data alignment
with annotated genes among other genome features. The advantage of Jbrowse is
that it allows easy user quantitative data - XYPlot, Density, in BAM or VCF
format - to be loaded for comparisons directly to user's browser in a local
environment. See: http://i.animalgenome.org/jbrowse/
o o o o o o o o o o o
3. 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)
Highlighted meetings:
o Plant and Animal Genome 2015 January 10-14, 2015, San Diego
The PAG meeting will be held in San Diego at the Town & Country Hotel. The
preliminary program can be found at:
https://pag.confex.com/pag/xxiii/webprogram/. The Swine Workshop will be held
on Saturday January 10 (all day). As in previous years, in the morning, the
Swine group will meet with the Cattle Subcommittee to hear several invited
lectures. In the afternoon, the Swine group will meet separately and hear
Station reports from members, Administrative Advisors and NRSP-8
Coordinators, and hold a business meeting. Important
o North American Porcine Reproductive and Respiratory Syndrome Symposium
December 5-6, 2014, at Intercontinental Hotel, Magnificent Mile in Chicago
(see https://ksvma.site-ym.com/?NAPRRS):
Dates to Remember:
- October 31st: Abstract submission deadline
- November 3rd: Hotel reservation deadline
- November 5th: Travel fellowship applications due
- November 15th: Registration deadline
Porcine reproductive and respiratory syndrome (PRRS) is the most economically
significant disease of pigs in the world. A new coronavirus, porcine epidemic
diarrhea virus (PEDV), is seriously impacting the industry. In addition to
PRRS, this year's meeting features a special session devoted to PED. Abstract
submission is invited for all three diseases: PRRS, PED and PCVAD. Travel
fellowships will be available for students and post-docs. Friday evening will
feature a poster session and short talks selected from the abstracts.
Registration is $150 for regular attendees and $100 for students, and
includes proceedings, lunch on Saturday and all refreshment breaks. A special
room rate of $189/night is available from Wednesday, December 3 through
Tuesday, December 9. Attendees requiring visas are encouraged to register
early.
o Gordon Conference on Quantitative Genetics and Genomics February 22-27,
2015, Lucca (Italy)
The Gordon Conference on Quantitative Genetics and Genomics entitled
"Deciphering the Genetic Basis of Complex Phenotypes for the Benefit of
Mankind" will be held at the Renaissance Tuscany Il Ciocco Resort in Lucca
(Barga), Italy, February 22-27, 2015. See
http://www.grc.org/GRC/programs.aspx?id=12072 for details and the preliminary
program. Applications for this meeting must be submitted by January 25, 2015.
GRS Speaker Abstract Deadline is November 21, 2014. There is also a Gordon
Research Seminar entitled "Consequences and Evolution of Genomic Variation"
associated with this Conference that will be held February 21-22; see
http://www.grc.org/GRC/programs.aspx?id=15733 for details.
o 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, there are preliminary plans for a Functional Genomics
symposium being organized by the Breeding and Genetics and Physiology program
committees; details on that Symposium will be provided at a later date.
Abstract Submission Deadline: November 5, 2014, 11:59 PM (Central Standard
Time).
o o o o o o o o o o o
4. 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.
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
===========================================================================
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
---------------------------------------------------------------------------
Web: http://www.animalgenome.org/pig | Mail: angenmap@animalgenome.org
===========================================================================
