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The test case applies state-of-art tools of modern genomic research, animal feeding experiment and animal physiology studies to unfold the genetics and genomic architecture of prolific sheep breeds as well as the environmental and nutritional effect on the prolificacy of sheep. The final goal of the project is to promote sustainable use of genetic resources of prolific sheep breeds through the use of genomic data.
The highly prolific breeds of domestic sheep (Ovis aries) are valuable genetic resources for global sheep industry. E.g. the native Finnsheep is well-known for its prolific traits and has been imported into 40 countries to develop new breeds and to improve fertility of local sheep breeds. Female prolificacy traits of sheep are critical factors controlling biological and financial performance of sheep production systems. In our study we are interested in the high ovulation rate and litter size. An access of modern high-throughput genomic tools has led to an increased understanding of the genetic architecture and nature of these complex traits in domestic animals, including sheep.
In domestic sheep, a large range in litter size (1-8 offspring) has been observed among- and within- breeds. This is contrast to several other domestic species whose females have generally either 1-2 (e.g. cattle and goat) or ≥ 4 offspring (e.g. dog and pig). Studies have indicated that the ovulation rate and litter size can be genetically regulated either by a set of different genes with each having a small effect or alternatively, by the action of single genes with major effect, namely the fecundity genes. In addition, nutrition is one of the environmental factors that affect reproduction in sheep.
Our aim is to investigate genetic basis of the highly prolific domestic sheep breeds and their utilisation. By using genome-wide SNP genotyping, candidate gene (e.g. FecB, GDF9, BMP-15, BMPR-1B) sequencing, transcriptome sequencing, animal nutrition experimentation, animal physiology studies, bioinformatics, and population genetics tools, the project will elucidate the specific contributions of genetic and nutritional factors in shaping the phenotypic variability in prolific sheep. In practise, information will enable breeding plans to be developed that maximize the benefits of increased prolificacy in the sheep breeds and their crosses.
The sheep breeds under our focus are also globally important genetic resources being worthy of genetic and genomic characterization.
PhD, Professor Meng-Hua Li, MTT, Jokioinen, Finland and Chinese Academy of Sciences, Beijing, PR of China PhD, Professor Juha Kantanen, MTT, Jokioinen, Finland PhD, Pricipal Research Scientist Jaana Peippo, MTT, Jokioinen, Finland MSc, Bioinformatics Scientist Kisun Pokharel, MTT, Jokioinen, Finland PhD, Bioinformatics Scientist Daniel Fischer, MTT, Jokioinen, Finland PhD, Researcher Mervi Honkatukia, MTT, Jokioinen, Finland Vet Med Johanna Rautiainen, ProAgria Pirkanmaa, Tampere, Finland International Sheep Genomics Consortium (http://www.sheephapmap.org)
In addition, there are available Sheep HapMap (http://www.sheephapmap.org) whole-genome sequence data. In total, 75 genomes of sheep have been sequenced (Illumina and Roche 454 approach). Currently the sheep genome assembly v3.1 has been released by NCBI and the ISGC (International Sheep Genomics Consortium).
The objectives of the SOMICS-project are: