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From: "John Liu" [liuzhan@auburn.edu]
To: "aquaculturegenomics" [aquaculturegenomics@newcastle.auburn.edu]
Subject: [aquaculturegenomics] Aquaculture genomics Newsletter 31
Date: Fri 8/6/2012 10:28 PM
Thanks and best wishes to Dr. Muquarrab Qureshi: It is with mixed feelings that
we report the promotion of Dr. Muquarrab Qureshi to the position of Assistant
Director, Institute of Youth, Family, and Community in the National Institute
of Food and Agriculture (NIFA). As many of us know, Dr. Qureshi previously
served as Director of the Division of Animal Systems and the National Animal
Genome Research Program. He provided great leadership to the animal systems
research. We will miss him in the animal genome community, and wish him well
in this larger capacity of the Institute. Leadership of the national animal
genome research program has transferred to Dr. Lakshmi Matukumalli who was
appointed as National Program Leader of Animal Breeding, Genetics and Genomics
in NIFA last year.
High density SNP chip for rainbow trout: High Density SNP Chip for Rainbow
Trout: A large data set of SNPs from RAD-tags sequencing of doubled haploids has
been collected and a design for a high density chip is expected by the end of 2012
with production of a chip in early 2013. If you are interested in using the chip
for your research, please contact Yniv Palti (yniv.palti@ars.usda.gov) with the
following information: 1) Do you have SNPs sequence data that you would like to
contribute to the SNP chip design? 2) How many SNPs that would likely be
informative for your research population do you want to see on the chip? 3)
Assuming a chip of 90K SNPs of which at least 50K SNPs are informative for your
population of choice at a cost of $150 per sample (you need to provide good
quality DNA); How many animals would you be interested in genotyping? Can you
fund the genotyping right now, or would you need to submit grant proposals to
fund the research? 4) Comments, suggestions, questions and any other information
that you would like to share on this issue.
High density SNP chip for catfish: The design of a high density SNP chip for
channel catfish and blue catfish is underway. This chip will include 250K SNPs,
using Affymetrix technology. At this stage, the entire aquaculture genome
community is encouraged to join the consortium to contribute to the construction
cost to make this happen. The cost is approximately $120 per sample. Interested
scientists please contact Dr. John Liu (liuzhan@auburn.edu) at Auburn University.
This offer is open till September 2012.
ISGA XI Conference: Thanks are given to Dr. Rex Dunham for his great effort in
organizing the International Symposium on Genetics in Aquaculture. The 11th
International Symposium on Genetics in Aquaculture was held at Auburn University,
Alabama, USA from June 22-30, 2012. Approximately, 150 attendees from 30
countries attended the conference. One of the themes of the conference was
applying genomics for genetic enhancement in aquaculture. Jerry Taylor from the
University of Missouri delivered the keynote address on this topic illustrating
how this was being accomplished in the cattle industry. This was followed by a
lively and informative roundtable discussion on this topic. A variety of papers
were delivered scanning the spectrum of aquacultured species on the topics of
quantitative genetics, genetic biotechnology, environmental risks of genetic
enhancement and genomics. An overview of bioinformatics advancements and programs
available from iPlant was covered by a special workshop. Farm tours highlighted
applications of practical genetic enhancement on farms in Alabama. The 12th
conference will be held in Spain in 2015 so make plans to attend as we continue
to improve integration of genetics and genomics for the betterment of aquaculture.
The first International Conference on Integrative Salmonid Biology: The first
International Conference on Integrative Salmonid Biology (www.icisb.org) sponsored
by the International Cooperation to Sequence the Atlantic Salmon Genome was held
in Oslo June 17-20, 2012. This meeting attracted more than 170 people from eleven
countries, and covered every aspect of salmonid biology. The structure of the
meeting, which featured eight sessions interspersed with poster sessions and lots of
opportunities to chat during the coffee breaks, was designed for researchers with
different backgrounds to gain an appreciation of the full range of salmonid biology
and develop partnerships using their complementary skills. Tom Quinn (University of
Washington) gave the opening keynote address, in which he reviewed a dozen of the
most important publications showing what makes salmon so worthy of study. This
set the stage by posing specific questions about life history, population
dynamics, conservation strategies and the interactions between wild and cultured
salmonids. Session 1 paid tribute to the Atlantic salmon sequencing project,
reviewed the current genomic resources and discussed what these are telling us
about the complexity and evolution of salmonid genomes. An underlying theme of
the conference was the interplay between genomics and salmonid biology. This
theme was admirably illustrated in Session 2 in the presentation by Louis
Bernatchez (Laval University), in which he showed how genomics is being applied to
the conservation of salmonids. Sex determination in salmonids has been a hot topic
for many years, with two competing hypotheses: the first suggesting that there is a
common salmonid sex-determining gene (SEX) that can "jump" around genomes such
that different species appear to have SEX on different linkage groups, and the
second that there are multiple SEX loci. In Session 3, Yann Guigen ((INRA) revealed
the nature of SEX in rainbow trout and presented convincing evidence that this gene
is responsible for sex determination in most, if not all, salmonids. How this
relates to the report of three SEX loci in Tasmanian salmon (Will Eisbrenner,
Simon Fraser University) remains a mystery at this time. There is clearly a lot
of work to be done in this area. The salmonid immune system was the topic for
Session 4, and Chris Secombes (University of Aberdeen) elegantly described how
the first assembly of the Atlantic salmon genome is enabling the characterization
of the cytokine repertoire in salmonid fish. Environmental physiological genomics
is a grand title for a growing field of research that examines how wild
populations respond to changes in climate and man's impacts. In Session 5, Tony
Farrell (University of British Columbia) gave a spirited talk about how his team
is following Fraser River sockeye salmon during their homeward migration and
using expression profiling to predict which fish would make it to the spawning
grounds and of these which would contribute to the next generation. The use of
marine-based feed for salmonid aquaculture is of concern to many groups. Using
genomics to understand salmonid physiology and nutrition, especially with respect
to the introduction of even more plant-based feed in salmonid aquaculture, was
covered in Session 6, with a thought-provoking keynote talk by Ron Hardy
(University of Idaho). An important point of the conference was to enable salmon
conservation biologists and representatives of the aquaculture industry to
interact with one another. Session 7 on breeding, QTL detection and selection
illustrated that the techniques developed for animal and food production are
equally relevant for our understanding of how individuals and populations of
salmonids change in response to different pressure, be they natural or imposed by
man. The final Session (8) returned to life history biology of salmonids. Jeff
Hutchings (Dalhousie University) gave the closing keynote presentation, and
brought together many of the points raised during this wonderful meeting. All
attendees have reported that this first International Conference on Integrative
Salmonid Biology should definitely not be the last. As the genome of Atlantic
salmon is completed as a reference for all salmonids and as the genomes of
rainbow trout and other salmonids become available, there will be benefits to be
reaped by all branches of salmonid biology. Stig Omholt's inspired idea for the
format and content of conference is already paying dividends for those who were
fortunate enough to attend. The future is indeed bright for salmonid genomics
and its integration into all aspects of salmonid biological research.
NRSP-8 Renewal: The National Research Support Project NRSP-8 is up for
renewal this year. The re-write team for NRSP-8 is led by Tom Porter and Milt
Thomas, along with the various species coordinators and other "voluntees". A
draft version of the new proposal was submitted to Administrative Advisors and
NIFA Representatives for their input on June 30.
NIFA to release 2012-2013 AFRI Foundational Grant RFA: 2012-2013 AFRI
Foundational RFAs will be released around Mid-August. For other specific NIFA
program announcements such as mitigation strategies for antimicrobial resistance
and deadlines please visit
http://nifa.usda.gov/funding/afri/afri_program_deadline_dates.html.
The International Plant & Animal Genome XXI meeting is on the horizon once
more, scheduled for January 12-16, 2013, in San Diego, CA, USA (see
http://www.intlpag.org/). As usual, the aquaculture genomics community will gather
for a 1.5 day workshop currently under planning with anticipated plenary speakers
addressing topics including epigenomics and whole-genome selection strategies. In
addition to invited plenary speakers, additional workshop speakers will be chosen
by the committee from abstracts submitted directly via e-mail to the Aquaculture
Workshop Chair, Dr. Eric Peatman (peatmer@auburn.edu). In order to be selected for
an oral presentation, you must meet the abstract submission deadline of September
30, 2012. Please note that all abstracts (for both oral and poster presentations)
must ALSO be submitted directly to PAG using the PAG website
http://www.intl-pag.org/ (deadline: TBD). Abstracts being considered for an oral
presentation will be reviewed by committee after the September 30, 2012 internal
deadline, and those selected for oral presentations will be notified in October 2012.
Abstracts will be judged on both the scientific quality of the abstract, and interest
to USDA National Animal Genome Project (National Research Support Project NRSP-8)
aquaculture species stakeholders.
NRSP-8 AquacultureTravel Award Applications: The Aquaculture Genomics
group of the NRSP-8 is pleased to announce the availability of a limited number of
travel awards, of up to $1000, to support the attendance of graduate students and
postdoctoral fellows at PAG XXI. All full-time graduate students and postdoctoral
fellows who submit an abstract to the Aquaculture Workshop are eligible for
consideration with the following restrictions: a) travel award recipients from 2012
are not eligible in 2013; b) a maximum of two travel awards will be granted to a
single PI'’s group. Applicants should submit all the required items as listed
below by the deadline, through e-mail to Eric Peatman (peatmer@auburn.edu): 1)
the abstract to be submitted to the PAG conference website, including the title
and authors; 2) a statement of the anticipated costs for the applicant to attend
the PAG meeting, including information on additional resources (if any) that will
be available to support their attendance; and 3) Travel award applicants MUST
also arrange for their supervisor to send an e-mail to Eric Peatman confirming
their status as a current graduate student or postdoctoral fellow. Note: Please
use the official PAG travel award form provided at http://www.intlpag.org/ under
the Travel menu. Award selections will be made and awardees will be notified soon
after the deadline. Awards will be paid after the meeting as a travel stipend.
Deadline: Applications must be received by October 8th, 2012.
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