“HapMap” (short for “haplotype mapping”) studies, in which a large number of members of a given species are genotyped for a large number of single nucleotide polymorphisms (SNP), have produced a great deal of genetic information. Using the information in the HapMap, researchers are able to find genes that affect health, disease, and individual responses to medications and environmental factors. For example, the goal of the International (human) HapMap Project was to compare the genetic sequences of different individuals to identify chromosomal regions where genetic variants are shared. The completion of this project has helped biomedical researchers find genes involved in disease and responses to therapeutic drugs.
A HapMap project in small ruminants (sheep and goats) is extremely important for IAEA developing Member States to enhance the ability of scientists to use genomics for improving productivity and other characteristics influenced by genetics, including adaptability and disease resistance. For this reason, a Sheep HapMap project has recently been proposed by the International Sheep Genomics Consortium, Australia, aimed to improve productivity and product quality for wool fibre and meat, improve reproduction and better host resistance to parasites. Stakeholders in global sheep production are being requested to submit samples of DNA from at least 24 sheep to undergo genotyping using a 60,000 SNP array.
It is expected to include at least 50 breeds in this study from Africa, Asia, Europe, and the Americas. The Animal Production and Health Subprogramme had particular interest in the inclusion of the African Dorper breed in the HapMap study because (i) the breed is well adapted to tropical and sub-tropical regions and is also being used in cross-breeding programmes to improve the productivity of local sheep in many Member States and (ii) this breed is one of the constituents of the reference population of animals upon which the on-going IAEA collaborative study on helminth resistance (CRP D3.10.26 - Genetic variation on the control of resistance to infectious diseases in small ruminants for improving animal productivity) is based. The IAEA in collaboration with the International Livestock Research Institute (ILRI) awarded a contract to CSIRO Livestock industries to perform genotyping of selected breed from Africa using 60,000 SNP array. ILRI provided the International Sheep Genomics Consortium with samples of sheep DNA from the African Dorper breed and data from three generation pedigrees. These sets of samples included three sets of family trios (i.e. father, mother, and offspring) as it is important for pedigree status of the animals to be known to ensure animals are not closely related except the trios.
A total of 108 DNA purified DNA samples (concentration range, 50 – 500 ng/uL) derived from whole blood have been shipped from ILRI to CSIRO, Australia representing three diverse breeds of African animals. Each sample was entered into the International Sheep Genomics Consortium DNA repository and its associated sample management system. The 108 samples were arrayed into 96 well plates and an electronic manifest prepared describing the concentration, sample identifier and the origin of breed of each animal. The 108 DNA samples received as part of a contract from the IAEA were added to other breed samples to form the International Sheep Genomics Consortium ‘Hap’Map and Breed Diversity Experiment’ making the IAEA a formalised participant in the HapMap experiment.
The DNA samples have since been shipped from the DNA repository to the Illumina ‘Fast Track’ facility in California to facilitate genotyping of each sample using the Ovine SNP50 BeadChip. This is a high-density genotyping platform which generates genetic data from approximately 50,000 SNP markers located across the sheep genome from high quality data. For each breed, the average call-rate is exceptionally high indicating that the experiment was a success. For example, only 19 SNP markers out of a total of 49,034 SNP attempted failed for the African Dorper DNA samples i.e. 99.96% of SNP markers tested returned high quality data. The success rate for the other breeds was as high or higher.
The full set of genotypic data obtained under this contract was released for public analysis in March 2009 via the International Sheep Genomics Consortium website (www.sheephapmap.org) including the genotypic data from the 100 African animals as part of the HapMap Breedv1 data release. The full dataset contains information from over 2800 animals implying it is a large dataset and consists of > 140 million genotypic data points. To allow researchers world-wide access, the data was formatted and released as .PED and .MAP files which can be analysed using the program PLINK (http://pngu.mgh.harvard.edu/~purcell/plink/index.shtml) which is designed specifically for large SNP datasets and is freely available.
To date, over 40 research groups have downloaded the dataset. In general, the process of receiving and genotyping the animals was very successful. Dr James Kijas and the International Sheep Genomics Consortium are in the process of preparing a manuscript which describes global sheep genetic diversity. This project yield information on the genetic biodiversity of sheep globally, the evolution of breeds with respect to global distribution, and genetic relationships among breeds. In addition, information regarding the genomic location of genes affecting important traits is expected to be obtained. On the other hand, the Bovine HapMap Consortium published a paper entitled ‘Genome-Wide Survey of SNP Variation Uncovers the Genetic Structure of Cattle Breeds’ in Science (Science 324: 528-532, 2009). More details about this are available here http://www-naweb.iaea.org/nafa/aph/stories/2009-bovine-genome.html