Test Case Title

Genetics, Genomics and Evolution of prolific breeds of domestic sheep (Ovis aries)

Test Case Acronyme

SOMICS

Test Case Class

Livestock

Contact person

Juha Kantanen

Contact

juha.kantanen@mtt.fi

Test Case Description

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.

Background knowledge

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.

Actors

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)

Initial state of the Test case
  1. RNA sequencing and micro-RNA profiling (Illumina HiSeq2000); approximately 18 individuals in 2013
  2. Whole-genome SNP genotyping (Illumina ovine 700K SNP BeadChip); >1,000 individuals for population genomics analysis and GWAS in 2013
  3. Whole-genome sequences (Illumina HiSeq2000); “few individuals” selected from the feeding experiment in 2014

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).

Desired final state of the Test Case

The objectives of the SOMICS-project are:

  1. By applying genome-wide association studies, we aim to identify the SNP variations and the candidate genes associated with different fertility phenotypes of sheep and to detect signatures of selective sweeps.
  2. By further sequencing candidate regions and whole-genome sequencing of few sheep samples with different phenotypes, we aim to get a detailed and whole picture of functionally relevant candidate regions and the whole genomic profile of few sheep.
  3. By using the statistical and bioinformatics methods in conducting the global analyses of the multiple data sets including the molecular, nutritional and environmental data for the sheep breeds, we aim to uncover accurate gene interaction networks and pathways. We further compare the genomics of sheep with other mammals such as mice and human.
  4. By designing a feeding experiment for diffrent sheep breeds and by investigating transcriptome and micro-RNA sequences of the breeds, we aim to evaluate the effect of nutrition on gene expression patterns and to infer putative candidate genes for the prolificacy of sheep.
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