Sheep HapMap and Animal Resources
The International Sheep Genomics Consortium is conducting a large experiment into the variable component of the ovine genome. Progress to March 2009 has seen the development of the ovine SNP50 BeadChip and its application to genotype a wide range of breeds, wild sheep and out-group species.
A total of 3004 domestic sheep from 71 breeds were recruited into the experiment which likely represents the most comprehensive sampling of any livestock species achieved to date. Breeds were collected from Africa, Asia, South America, Europe, the Middle East, Australasia, the USA and Caribbean. The data was made available in two releases, with the first being made available in early 2009. The coordinator responsible for inclusion of each breed is listed below.
|AfecAssaf||24||Elisha Gootwine||The Volcani Center|
|African Dorper||25||Mikka Tapio/Olivier Hanotte||ILRI|
|African White Dorper||6||James Kijas / Tamesha Gardner||CSIRO|
|Afshari||41||Henner Simianer||University of Goettingen|
|Altamurana||24||Elena Ciani||University of Bari|
|Australian Merino||51||James Kijas||CSIRO|
|Bangladeshi East||24||Faruque Mdomar||Bangladesh Agriculture University|
|Bangladeshi Garole||24||Faruque Mdomar||Bangladesh Agriculture University|
|Barbados BlackBelly||24||Cyril Roberts||University of the West Indies|
|Black Headed Mountain||24||Ottmar Distl||University of Veterinary Medicine Hannover|
|Boreray||34||Josephine Pemberton||University of Edinburgh|
|Brazilian Creole||24||Samuel Paiva||Embrapa Recursos Genéticos e Biotecnologia|
|Bündner Oberländer Sheep||24||Cord Drogemuller||"Institute of Genetics, University of Berne "|
|Castellana||24||JJ Arranz||Universidad de Leon|
|Changthangi||29||Jorn Benenwitz||University of Hohenheim|
|Chinese Merino||23||Runlin Ma||Chinese Academy of Science|
|Chios||24||Georgios Banos||Aristotle University of Thessaloniki|
|Churra||120||JJ Arranz||Universidad de Leon|
|Comisana||24||Fabio Pila||Università degli Studi del Molise|
|Cyprus Fat Tail||30||Despoina Miltiadou||Cyprus University of Technology|
|Decanni||27||Vidja Gupta||"National Chemical Laboratory, India"|
|Dorset Horn||21||John McEwan||AgResearch|
|East Friesian||48||Ottmar Distl||University of Veterinary Medicine Hannover|
|Egyptian Barki||13||Ahmed El Beltagy||"Animal Production Research Institute, Egypt"|
|Engadine Red Sheep||24||Cord Drogemuller||"Institute of Genetics, University of Berne "|
|Ethiopian Menz||35||Mikka Tapio/Olivier Hanotte||ILRI|
|Finnsheep||100||Juha Kantanen||MTT Agrifood Research Finland|
|Galway||50||David Machugh||University College Dublin|
|German Texel||48||Cord Drogemuller||"Institute of Genetics, University of Berne "|
|Gulf Coast Native||96||Noelle Cockett / Jim Miller||University of Utah|
|Icelandic||16||Emma Eythorsdottir||Agricultural University of Iceland|
|Improved Awassi||23||Elisha Gootwine||The Volcani Center|
|Indian Garole||25||Vidja Gupta||"National Chemical Laboratory, India"|
|Indonesian Thin Tail Garut||22||Herman Raadsma||University of Sydney|
|Irish Suffolk||55||David Machugh||University College Dublin|
|Karakas||18||Ibrahim Cemal||Adnan Menderes University|
|Leccese||24||Elena Ciani||University of Bari|
|Local Awassi||24||Elisha Gootwine||The Volcani Center|
|Macarthur Merino||10||James Kijas||CSIRO|
|Merinolandschaf||24||Georg Erhardt||Institut für Tierzucht und Haustiergenetik Justus-Liebig-Universität Gießen|
|Moghani||35||Henner Simianer||University of Goettingen|
|Morada Nova||24||Samuel Paiva||Embrapa Recursos Genéticos e Biotecnologia|
|Namaqua Afrikaner||14||James Kijas / Tamesha Gardner||CSIRO|
|New Zealand Romney||24||John McEwan||AgResearch|
|New Zealand Texel||24||John McEwan||AgResearch|
|Norduz||20||Ibrahim Cemal||Adnan Menderes University|
|Norwegian spælsau||50||Matthew Kent||CiGene|
|Ojalada||24||JJ Arranz||Universidad de Leon|
|Qezel||35||Henner Simianer||University of Goettingen|
|Rambouillet||104||Noelle Cockett||University of Utah|
|Rasa aragonesa||24||Jorge Calvo||CITA Spain|
|Red Maasai||48||Mikka Tapio/Olivier Hanotte||ILRI|
|Ronderib Afrikaner||17||James Kijas / Tamesha Gardner||CSIRO|
|Sakiz||22||Ibrahim Cemal||Adnan Menderes University|
|Santa Inês||50||Samuel Paiva||Embrapa Recursos Genéticos e Biotecnologia|
|Sardinian Ancestral Black||20||Tiziana Sechi / Antonello Carta||AGRIS SARDEGNA|
|Scottish Blackface||56||Lutz Bunger||Scottish Agricultural College|
|Scottish Texel||80||Lutz Bunger||Scottish Agricultural College|
|Soay||566||Josephine Pemberton||University of Edinburgh|
|Sri Lankan||1||Pradeepa Silva||"University of Peradeniya, Sri Lanka"|
|St Elizabeth||24||Cyril Roberts||University of the West Indies|
|Sumatran||25||Herman Raadsma||University of Sydney|
|Swiss Black-Brown Mountain Sheep||24||Cord Drogemuller||"Institute of Genetics, University of Berne "|
|Swiss Mirror Sheep||24||Cord Drogemuller||"Institute of Genetics, University of Berne "|
|Swiss White Alpine Sheep||24||Cord Drogemuller||"Institute of Genetics, University of Berne "|
|Tibetan||50||Han Jialin||ILRI and CAAS|
|Valais Blacknose Sheep||24||Cord Drogemuller||"Institute of Genetics, University of Berne "|
|Valais Red Sheep||24||Cord Drogemuller||"Institute of Genetics, University of Berne "|
|Asiatic Mouflon||3||Pierre Taberlet / Francois Pompanon||Université Joseph Fourier|
|European Mouflon||24||Stefan Hiendleder||University of Adelaide|
|Bighorn||50||Dave Coltman||University of Alberta|
|Wyoming Bighorn||3||Mike Heaton||USDA|
|Sardinian Mouflon||28||Tiziana Sechi / Antonello Carta||AGRIS SARDEGNA|
|Thinhorn||3||Dave Coltman||University of Alberta|
|Argali||9||Stefan Hiendleder||University of Adelaide|
|Urial||5||Stefan Hiendleder||University of Adelaide|
|Out Group Species|
|Musk ox||7||Mike Heaton||USDA|
|Pronghorn Antelope||8||Mike Heaton||USDA|
In addition to domestic sheep a selection of wild sheep and out group species have also been genotyped. The coordinators of these extra animal resources are also listed.
The ISGC has appointed project leaders to take responsibility for each of the major analytical objectives. Project leaders will liaise with any scientist interested to contribute and coordinate each aspect of the analysis. As a result, if you would like to get involved please contact the project leaders or coordinator (James Kijas) as a start point. Project leaders will also report into the consortium wide conference calls on behalf of the group and form a higher level team to handle overlap between objectives and the requirement for sequential ordering for some analysis.
Validation and Performance of the Ovine SNP50BeadChip
Project Leaders: Brian Dalrymple and John McEwan
Description: Summary statistics describing the performance of the BeadChip. The outcome will be information concerning the success of the three SNP discovery approaches and BeadChip design.
Analytical Approaches: Analysis of call rate, locus success rate and minor allele frequency profiles when compared between SNP discovered using Sanger, Illumina or 454 sequencing.
Genetic Diversity Within Breeds, Relationship Between Breeds and Population Structure.
Project Leaders: James Kijas and Hans Lenstra
Description: Analysis of genetic diversity will be made for each breed and compared between breeds. The relationship between breeds will be examined in an effort to reconstruct aspects of the population history of domestic sheep. The presence of stratification within breeds, identification of closely related breed groups and the strength of phylogeographic structure will be examined.
Analytical Approaches: Estimation of gene diversity (He), allelic richness (AR), the proportion of polymorphic loci (Pn) and minor allele frequency profile for each breed. Analysis of mtDNA SNP to assess the composition of known mitochondrial lineages. Model based cluster analysis (STRUCTURE), network diagrams, principal component analysis based on D, population divergence measured as FST. Partitioning of genetic variation based on breed, geographic origin or shared phenotypic characteristics.
Linkage Disequilibrium and Past Effective Population Size
Project Leaders: Ben Hayes and Herman Raadsma
Description: The decay of LD and past effective population size is highly informative about this breed development and the population history of a species.
Analytical Approaches: Decline of r2 as a function of increasing genetic distance, estimation of Ne within and between populations, haplotype sharing between populations.
Project Leaders: Bill Barendse, Ben Hayes and John McEwan
Description: Domestication and subsequent selection is predicted to have left detectable signatures across the genome. Multiple breeds were recruited which have been independently selected for the production of wool, meat and milk. Genomic regions showing evidence for selection will be compared with those in cattle and other domestic species.
Analytical Approaches: Extended haplotype homozygosity (EHH and iHS), analysis of population divergence using FST or tests using a composite likelihood ratio.
Relatedness Between Wild and Domestic Sheep
Project Leaders: James Kijas and Dave Coltman
Description: Analysis of the genetic variation observed in domestic sheep when compared to that present within Mouflon, Argali, Urial, Thinhorn and Bighorn sheep. Outcomes will may include conclusions about the domestication process and identity of the ancestor of modern sheep.
Analytical Approaches: Testing for the presence of shared haplotypes between wild and domestic sheep. Cluster based analysis. Consideration of ascertainment bias.
Project Leaders: Jill Maddox and Mike Heaton
Description: Information from the polymorphic component of the genome will be used to develop resources such as a parentage panel, a high density linkage map and information which will ground the construction of a de novo assembly of the sheep genome.
Analytical Approaches: Meiotic map construction using data from the International Mapping Flock. LODE map construction from the HapMap data. Identification of marker subsets for parentage.
For further information, please contact the coordinator of the HapMap project, Dr. James Kijas.