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.

Animal Resources

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.

Domestic BreedsNumberContributorInstitution
AfecAssaf24Elisha GootwineThe Volcani Center
African Dorper25Mikka Tapio/Olivier HanotteILRI
African White Dorper6James Kijas / Tamesha GardnerCSIRO
Afshari41Henner SimianerUniversity of Goettingen
Altamurana24Elena CianiUniversity of Bari
Arapawa37John McEwanAgResearch
Australian Merino51James KijasCSIRO
Bangladeshi East24Faruque MdomarBangladesh Agriculture University
Bangladeshi Garole24Faruque MdomarBangladesh Agriculture University
Barbados BlackBelly24Cyril RobertsUniversity of the West Indies
Black Headed Mountain24Ottmar DistlUniversity of Veterinary Medicine Hannover
Boreray34Josephine PembertonUniversity of Edinburgh
Brazilian Creole24Samuel PaivaEmbrapa Recursos Genéticos e Biotecnologia
Bündner Oberländer Sheep24Cord Drogemuller"Institute of Genetics, University of Berne "
Castellana24JJ ArranzUniversidad de Leon
Changthangi29Jorn BenenwitzUniversity of Hohenheim
Chinese Merino23Runlin MaChinese Academy of Science
Chios24Georgios BanosAristotle University of Thessaloniki
Churra120JJ ArranzUniversidad de Leon
Comisana24Fabio PilaUniversità degli Studi del Molise
Cyprus Fat Tail30Despoina MiltiadouCyprus University of Technology
Decanni27Vidja Gupta"National Chemical Laboratory, India"
Dorset Horn21John McEwanAgResearch
East Friesian48Ottmar DistlUniversity of Veterinary Medicine Hannover
Egyptian Barki13Ahmed El Beltagy"Animal Production Research Institute, Egypt"
Engadine Red Sheep24Cord Drogemuller"Institute of Genetics, University of Berne "
Ethiopian Menz35Mikka Tapio/Olivier HanotteILRI
Finnsheep100Juha KantanenMTT Agrifood Research Finland
Galway50David MachughUniversity College Dublin
German Texel48Cord Drogemuller"Institute of Genetics, University of Berne "
Gulf Coast Native96Noelle Cockett / Jim MillerUniversity of Utah
Icelandic16Emma EythorsdottirAgricultural University of Iceland
Improved Awassi23Elisha GootwineThe Volcani Center
Indian Garole25Vidja Gupta"National Chemical Laboratory, India"
Indonesian Thin Tail Garut22Herman RaadsmaUniversity of Sydney
Irish Suffolk55David MachughUniversity College Dublin
Karakas18Ibrahim CemalAdnan Menderes University
Lacaune185Carole MorenoINRA
Leccese24Elena CianiUniversity of Bari
Local Awassi24Elisha GootwineThe Volcani Center
Macarthur Merino10James KijasCSIRO
Merinolandschaf24Georg ErhardtInstitut für Tierzucht und Haustiergenetik Justus-Liebig-Universität Gießen
Moghani35Henner SimianerUniversity of Goettingen
Morada Nova24Samuel PaivaEmbrapa Recursos Genéticos e Biotecnologia
Namaqua Afrikaner14James Kijas / Tamesha GardnerCSIRO
New Zealand Romney24John McEwanAgResearch
New Zealand Texel24John McEwanAgResearch
Norduz20Ibrahim CemalAdnan Menderes University
Norwegian spælsau50Matthew KentCiGene
Ojalada24JJ ArranzUniversidad de Leon
Qezel35Henner SimianerUniversity of Goettingen
Rambouillet104Noelle CockettUniversity of Utah
Rasa aragonesa24Jorge CalvoCITA Spain
Red Maasai48Mikka Tapio/Olivier HanotteILRI
Ronderib Afrikaner17James Kijas / Tamesha GardnerCSIRO
Sakiz22Ibrahim CemalAdnan Menderes University
Santa Inês50Samuel PaivaEmbrapa Recursos Genéticos e Biotecnologia
Sardinian Ancestral Black20Tiziana Sechi / Antonello CartaAGRIS SARDEGNA
Scottish Blackface56Lutz BungerScottish Agricultural College
Scottish Texel80Lutz BungerScottish Agricultural College
Soay566Josephine PembertonUniversity of Edinburgh
Sri Lankan1Pradeepa Silva"University of Peradeniya, Sri Lanka"
St Elizabeth24Cyril RobertsUniversity of the West Indies
Sumatran25Herman RaadsmaUniversity of Sydney
Swiss Black-Brown Mountain Sheep24Cord Drogemuller"Institute of Genetics, University of Berne "
Swiss Mirror Sheep24Cord Drogemuller"Institute of Genetics, University of Berne "
Swiss White Alpine Sheep24Cord Drogemuller"Institute of Genetics, University of Berne "
Tibetan50Han JialinILRI and CAAS
Valais Blacknose Sheep24Cord Drogemuller"Institute of Genetics, University of Berne "
Valais Red Sheep24Cord Drogemuller"Institute of Genetics, University of Berne "
Wiltshire23John McEwanAgResearch
Wild Sheep
Asiatic Mouflon3Pierre Taberlet / Francois PompanonUniversité Joseph Fourier
European Mouflon24Stefan HiendlederUniversity of Adelaide
Bighorn50Dave ColtmanUniversity of Alberta
Wyoming Bighorn3Mike HeatonUSDA
Sardinian Mouflon28Tiziana Sechi / Antonello CartaAGRIS SARDEGNA
Thinhorn3Dave ColtmanUniversity of Alberta
Argali9Stefan HiendlederUniversity of Adelaide
Urial5Stefan HiendlederUniversity of Adelaide
Out Group Species
Barbary4James KijasCSIRO
Thar5James KijasCSIRO
Chamois4John McEwanAgResearch
Cattle10Mike HeatonUSDA
Gaur2Mike HeatonUSDA
Musk ox7Mike HeatonUSDA
Pronghorn Antelope8Mike HeatonUSDA
Yak2Mike HeatonUSDA

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.

Data Analysis

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.

Analytic Objectives

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.

Selective Sweeps

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.