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]
http://www.ebi.ac.uk/eva/?Home [European Variation Archive] http://www.ncbi.nlm.nih.gov/SNP/ [dbSNP]
We are please to announce the new members of the Study Commissions:
We wish to all members of the EAAP Commissions to have success and to work at their best for constantly improving the services that EAAP offers to the animal science community!
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)
EU-PLF project: Bright Farm by Precision Livestock Farming
29 September 2016
The final conference of the EU funded project EU-PLF will be held in Brussels. Registration is now open! For more information on programme, venue and cost of registration, take a look at the project website: http://www.eu-plf.eu/index.php/registration-now-open/
4th International Conference on Responsible use of Antibiotics in Animals
26-28 September 2016
THE HAGUE, THE NETHERLANDS
Key themes of the conference include:
– integration of animal, human and environmental health
– approaches at global and national levels
– engagement of stakeholders
– innovations in disease prevention and detection, including
gut health, alternatives to antibiotics, rapid diagnostics, etc.
– new areas to explore
