Sheep HapMap and Animal Resources The International Sheep Genomics Consortium has been very active in the area of SNP discovery over the last 12 months and a 60k Illumina SNP array will be ready in mid 2008. It is therefore time to collect the breed samples and associated information for the HapMap and Breed Diversity project. The opportunity to participate is still open, as delays in the SNP discovery component of the work have resulted in a delayed timeline. This means the opportunity to become a Breed Champion for your favourite sheep breed still exists. A Breed Champion is responsible for coordinating the selection and sampling of suitably unrelated sheep and for meeting the DNA submission and financial deadlines. The current list of confirmed participants and breed champions is:   Sheep breed Number of sheep Breed Champion, Organisation   New Zealand Romney 24   John McEwan, AgResearch   New Zealand Texel 24   John McEwan, AgResearch   International Mapping Flock 127   John McEwan, AgResearch   Australian Poll Dorset 200   James Kijas, sheepGENOMICS   Australian Merino 200   James Kijas, sheepGENOMICS   Australian White Suffolk 200   James Kijas, sheepGENOMICS   Australian Texel 100   James Kijas, sheepGENOMICS   Australian Border Leicester 100   James Kijas, sheepGENOMICS   Rambouillet 100   Noelle Cockett, Utah State University   Louisiana (Gulf Coast) Native 100   Noelle Cockett, Utah State University   Red Maasai 50   Olivier Hanotte, ILRI   Soay 50   Josephine Pemberton, University of Edinburgh   Bighorn 50   David Coltman, University of Alberta   Thinhorn 50   David Coltman, University of Alberta   Santa Ines 50   Samuel Paiva, Embrapa Recursos Genéticos e Biotecnologia   Morada Nova 24   Samuel Paiva, Embrapa Recursos Genéticos e Biotecnologia   East Friesian 24   Ottmar Distl, University of Veterinary Medicine Hannover   Norsk Spaelsua 50   Matthew Kent, CIGENE   Galway 24   David MacHugh, University College Dublin   Suffolk (UK)   David MacHugh, University College Dublin   Improved Awassi 24   Elisha Gootwine, The Volcani Center   Assaf 24   Elisha Gootwine, The Volcani Center   Asian breed(s) 24   Massoud Malek and Paul Boettcher, IAEA   Rasa aragonesa 24   Jorge Calvo, CITA Spain   Finnsheep 24   Juha Kantanen, MTT Finland   Churra 100   Juan Jose Arranz, University of Léon   Castellana 24   Juan Jose Arranz, University of Léon   Ojalada 24   Juan Jose Arranz, University of Léon   Swiss White Alpine 24   Cord Drögemüller, University of Berne, Institute of Genetics   Swiss Black-Brown Mountain 24   Cord Drögemüller, University of Berne, Institute of Genetics   Valais Blacknosee 24   Cord Drögemüller, University of Berne, Institute of Genetics   Valais Red 24   Cord Drögemüller, University of Berne, Institute of Genetics   Spiegel 24   Cord Drögemüller, University of Berne, Institute of Genetics   Engadine Red 24   Cord Drögemüller, University of Berne, Institute of Genetics   Bündner Oberländer 24   Cord Drögemüller, University of Berne, Institute of Genetics   Texel   Cord Drögemüller, University of Berne, Institute of Genetics   Altamurana   Elena Ciani, University of Bari   Leccese   Elena Ciani, University of Bari   Lacaune   Carole Moreno, INRA   INRA sheep RH panel   Carole Moreno, INRA   MerinoLand   Georg Erhardt, Justus-Liebig University of Giessen   Sarda   Paolo Ajmone Marsan, Università Cattolica del S. Cuore   Comisana   Fabio Pilla, Università degli Studi del Molise   Texel (UK)   Lutz Bunger, Scottish Agricultural College   Scottish Blackface   Lutz Bunger, Scottish Agricultural College   Chios   Georgios Banos, Aristotle University of Thessaloniki   Turkish breeds   Ozden Cobanoglu, Namik Kemal University   Iranian breeds   Mohammad Shariflou, University of Sydney and Mohammad Moradi, University of Tehran

The following is a list of individuals and groups who have expressed interest in participating but who have not yet found a source of funding:   Urial, Argali, Mouflon   Stefan Hiendlander, University of Adelaide   Chinese breed   Han Jianlin, ILRI CAAS   UK breeds   Alan Archibald and Steve Bishop, Roslin Institute   French breeds   Carole Moreno and Andre Eggen, INRA   Garole   Chanda Nimbkar, NARI

The list of breeds is not complete and additional breeds are being sought from Asia, Europe, the Middle East and South America. The revised key dates are given below, along with information about the process for participation. If you have an interest in joining the sheep HapMap project, the minimum number of animals for participation is 24 individuals per breed. This number of individuals will enable estimates of genetic diversity for a breed, but based on the bovine HapMap data 24 individuals will be insufficient for accurate analysis of linkage disequilibrium within populations or haplotype sharing between populations. Similarly, the ability to detect selection signatures between/within populations will also be markedly enhanced with larger numbers of animals. If investigation of these latter aspects are an important reason for the participation of your breed in the study, then we suggest that you should provide at least 50 individuals for LD analysis (note: better LD decay results will be obtained with 100 animals), or at least 100 individuals if you want to detect selection signatures. Cost The following costs are current best-guess estimates and include both array construction and custom genotyping of the 60K SNP array. There are three tiers at which participation can be arranged. 24 individuals USD $7,200 50 individuals USD $15,000 100 individuals USD $30,000 Please note that there is no upper limit on the number of animals that can participate per breed other than what can be paid for. Each additional animal will cost USD$300. Note also that the above costs do not include the cost of shipping the DNA samples (shipping costs are the responsibility of the organisation that submits the samples), and that the costs apply to the number of individuals submitted rather than to the number that can be successfully genotyped (it is the responsibility of the submitting organisation to ensure that the DNA quality is suitable for genotyping using a 60K SNP array). Timeline There are two key dates - a financial commitment date and a DNA submission date. The financial date is Thursday 31st June 2008 and is the date by which firm commitments to support the inclusion of breed sets are required. The commitment itself will take the form of a purchase order (PO) with Illumina. Illumina has agreed to arrange a separate PO for each participant. This will be an invoice for payment to be arranged between each Institution and Illumina, and will describe the total financial commitment payable by that Institution. All of the POs will be attached to a single quote, meaning everyone benefits from cost savings associated with managing the process collectively (more details will be provided soon). After this time, participation will not be possible in the initial ISGC Sheep HapMap project and it should be noted that the price per animal in subsequent experiments is likely to be significantly higher. It is therefore essential that participants very quickly determine their level of available funding. Note: the previous financial date has been adjusted to 31st July to allow for delays in the Solexa ovine SNP discovery project. The second key date is also Thursday 31st July 2008 which is the deadline for submission of DNA samples into the ISGC DNA Repository. The updated requirements for participation are: a minimum of 24 individuals per breed. This may include 3 sets of family trios (e.g. father, mother, offspring). a minimum of 100 μg of high quality DNA per individual submitted to the ISGC DNA Repository. a commitment on the number of animals to be funded (at $300 USD / animal) by 31st July 2008 three generation pedigrees for each individual. Known pedigree status is required to ensure individuals (with the exception of trios) are not closely related. anonymous animal identifiers which shows only breed and pedigree position. No phenotypic data will be collected or used by the project for genotyped sheep. a completed Breed Information Datasheet, click for template pdf or word file. a signed Material Transfer Agreement (MTA) needs to be provided with the samples, click for template pdf or word file. submission of DNA, pedigree information and MTA to the ISGC DNA repository by 31st July 2008 and notification of firm financial commitment to ISGC and purchase order to Illumina by the same date. The samples will be genotyped with the 60K Illumina SNP array and the genotyping results will be deposited into dbSNP. Interested parties are encouraged to participate during the analytical phase of the project. The results will be presented to the public via a consortium member's GBrowse website. Please contact the secretary to register expressions of interest and for further information concerning participation. The consortium is an open forum and will consider reasonable modifications to any of the requirements listed above.

Last modified: 12^th July 2008
Maintainers: John McEwan, AgResearch, Jill Maddox, University of Melbourne
Email: jillm@rubens.its.unimelb.edu.au