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From: "John Liu" []
To: "aquaculturegenomics" []
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 ( 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 ( 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 ( 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

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 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 ( 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 (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'ís group. Applicants should submit all the required items as listed below by the deadline, through e-mail to Eric Peatman ( 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 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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