- Annual meetings
- Individual members
- EU Projects
Publically available sheep genomes
The team running SheepGenomesDB is pleased to announce the completion of a significant milestone. The project has analysed publically available sheep genomes by applying a standardized read mapping and variant calling pipeline to discover sequence variants (SNP and indels). The team recently completed Run1, containing 453 sheep genomes collected from 56 globally distributed populations. The result is the production of two variant collections. First, a total of 91 M raw variants are available which represent unfiltered variant calls obtained from two independent callers (GATK-UG and SAMtools). Second, a set of 46.4 M high quality variants are available that passed filtering and were independently identified by both callers. Each variant collection (raw and high quality) is available via the European Variant Archive (EVA) and the high quality variants are being accessioned by dbSNP (links are given below). The high quality variants have been annotated using sheep genome reference OARv3.1 and are searchable using an array of filtering options via the EVA Variant Browser. We view this dataset as an essential resource for researchers performing gene variation discovery, imputation and investigations into the consequences of animal breeding and selection. Additional information were contained in a presentation to the recent ISAG meeting (Salt Lake City, July 23-27) that can be found at the project website.
The project is run under the auspices of the International Sheep Genomics Consortium (ISGC) with funding from a USDA NIFA award. Key project members include James Kijas (CSIRO), Rudiger Brauning (AgResearch), Shannon Clarke (AgResearch), Alan McCulloch (AgResearch), Noelle Cockett (Utah State University), Gary Saunders (EMBL-EBI), Marina Naval Sanchez (CSIRO), Sean McWilliam (CSIRO), Amanda Chamberlain (DEDJTR) and Hans Daetwyler (DEDJTR).
Planning is underway for Run2 which is scheduled for later in 2016, where we expect to analyse in excess of 1000 sheep genomes. If you have ovine genomes you would like included, the first step is submission of FastQ formatted sequence to the Short Read Archive. For additional information on participation please contact Rudiger (Rudiger.Brauning@agresearch.co.nz), Hans (Hans.Daetwyler@ecodev.vic.gov.au) or James (James.Kijas@csiro.au).
Data Access Links: http://sheepgenomesdb.org/home [project webpage]
Three New Council Members
During Belfast meeting, the General Assembly elected three new members of the Council. The new members are Isabel Casasùs (Spain), Veronika Maurer (Switzerland) and Mogens Vestergaard (Denmark). They will have a term of office of four years and their role is extremely important, the Council is in fact the management body of the organization. We wish them good work for all the important activities and decisions that they will be asked to perform in the next four years. They will replace Nuno Brito e Vieira (Portugal), Matthias Gauly (Germany) and Martin Scholten (the Netherlands). Our special thanks to Nuno, Matthias and Martin. In the years in which they were members, we were able to have the benefit of the expertise and the willingness that they put in managing EAAP. As everyone knows, Matthias Gauly will remain in the Council as President.
Please find below the Report from our Past President Philippe Chemineau with the activities done and results achieved by EAAP during his mandate (2012-2016)
October 26th-27th, 2016
PhenoDays in Berlin (Germany)
The phenotyping conference will be held this year in Berlin. As always, this will be an interesting and well-attended event with delegates and speakers from academia and industry across the world. The first day will focus on laboratory and greenhouse phenotyping and the second day on field phenotyping. The conference participants aim to present new science, including new research and new applications for both automated and manual phenotyping.
PhenoDays 2016 will be held at the Hotel Nhow, Berlin. To register and to see the sessions’ program now you can visit the specific website: www.phenodays.com
December 12th – 15th, 2016
International Symposium on Alternatives to Antibiotics in Paris (France)
The 2nd Symposium on Alternatives to Antibiotics will be held in Paris on December 12-15. The title of this symposium is: Challenges and Solutions in Animal Production. The locations at the World Organisation in Animal Health venue in Paris.