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From: "John Liu" []
To: "aquaculturegenomics" []
Cc: "Grant Burgess" []
Subject: [aquaculturegenomics] Aquaculture genomics Newsletter 34
Date: Fri, 20 Dec 2013 14:14:55 -0600

 Aquaculture Genomics Workshop at PAGXXII: The Aquaculture Genomics
Workshop will be held on January 11th of 2014 as part of the International 
Plant & Animal Genome XXII meeting ( in San Diego, 
CA, USA. In addition to an array of presentations on current research efforts, 
there will be three invited presentations which will provide a fresh 
perspective on genomics and aquaculture. The invited speakers include Chris 
Amemiya (Benaroya Research Institute), Chris Ashwell (North Carolina State 
University), and John Rawls (Duke University). More information including a 
complete schedule can be found at (

 ENCODE Workshop: Prior to PAG, a one day meeting on 10 January 2014
dedicated to the deployment of ENCODE-like strategies for animal genomics will
take place. The morning sessions are open to all interested parties and will
feature presentations by Elise Feingold (National Institutes of Health, ENCODE
Program Director), Bing Ren (UC San Diego, Institute for Genomic Medicine and
ENCODE researcher) and Ewan Birney (Associate Director of EMBL-EBI and lead 
analysis coordinator of ENCODE). The afternoon is organized around smaller, 
closed session breakout workshops, one of which will focus on Aquaculture.

 Aquaculture Species Coordinators: Dr. Dina Proestou, an ARS scientist
located at the University of Rhode Island, has agreed to serve as the NRSP8
Species Leader representing oysters, we look forward to working with her on the
project objectives. We are still seeking a Species Leader for shrimp, please
contact John Liu and Caird Rexroad if you are interested.

 Annual Report: We are currently working on the Aquaculture Genome Annual
Report, Species Leaders have been asked to document progress under NRSP8
objectives. If you would like to contribute to this report, please send a 
brief description of progress for each objective and 2013 publications with 
full citations to your Species Leader (Salmonids: Dr. Yniv Palti; Catfish: 
Dr. Sylvie Quiniou; Striped bass: Dr. Craig Sullivan, and Oysters: Dr. Dina 
Proestou). This report must be submitted prior to PAG, please send your 
updates at your earliest convenience. The NRSP8 Objectives are: 1) Advance 
the status of reference genomes for all species, including basic annotation 
of worldwide genetic variation, by broad sequencing among different lines 
and breeds of animals; 2) Develop strategies to identify and exploit genes 
and allelic variation that contribute to economically relevant phenotypes and 
traits, in part through improving functional annotation of the genomes of our 
species; 3) Facilitate analysis, curation, storage, distribution and 
application of the enormous datasets now being generated by next-generation 
sequencing and related "omics" technologies with regard to animal species of 
agricultural interest.

 Rainbow trout SNP chip: The rainbow trout 57K SNP chip (O_my_50K) is now
commercially available from Affymetrix (P/N 550468).For questions on pricing
and ordering information, please contact LuAnn Glaser from Affymetrix
( If you want to coordinate your order with the
SNP chip consortium, please contact Dr. Yniv Palti ( A
manuscript describing the SNP discovery effort and the SNP database resource
that was generated to facilitate the development of the SNP chip was accepted
for publication in Molecular Ecology Resources, and another manuscript on the
SNP chip validation is in progress.

 NRSP-8 Aquaculture Travel Awards: The Aquaculture Genomics group of the
NRSP-8 is pleased to announce the travel award winners:

 Miyako Kodama, University of Washington
 A Genome Map for a Species with Male Tetrasomic Inheritance, Coho Salmon,
 and Location of Quantitative Trait Loci 

 Ali Ali Middle, Tennessee State University
 Characterization of Rainbow Trout Spleen Transcriptome and Identification of
 Immune-Related Genes
 Xi Xue, Memorial University of Newfoundland
 Atlantic Salmon Liver Transcriptome Response to Diets Containing Camelina

 Lisui Bao, Auburn University
 Bulk Segregant RNA-Seq Reveals Expression and Positional Candidate Genes and 
 Allele-Specific Expression for Disease Resistance Against Enteric Septicemia 
 of Catfish

Congratulations to these winners!

Happy Holidays!

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