Cattle are essential for the global food industry through the meat and milk production. It is from an economical point of view in our best interest to make cattle as efficient as possible, whether it is milk or beef production, without negatively influencing their health and welfare. That has led to a steady increase in the interest of genetic analysis of cattle. The sequencing and identification of genomic variation has led to the association of genotypes with phenotypes of interest and the discovery of the underlaying genetic risk factors for many diseases and traits. Diseases or monogenetic traits caused by a single nucleotide polymorphism (SNP), small deletions and insertions or other small mutations are often easy to identify if the correct region is found. The diseases caused by structural variants (SVs), variants larger than 50 base pairs (bp) are still challenging. It is more challenging because they are harder to identify, especially using shortread sequencing technologies. It is therefore still a rather unexplored area for cattle and other domestic species.This thesis looks at SVs found in the Swedish Red and Brown (SRB) cattle to discover breed specific SVs. This was done by creating a pipeline with VCF files as input. The identified SVs were filtered and overlapped with externally identified SVs. The pipeline was tested with two SRB datasets. The structural variant caller, DELLY, performed poorly with low read depth data when comparing single replicate data and combined replicates data. Multiple SVs were identified in all individuals and did overlap with both functional and gene annotation. There was also overlap found with datasets in the European variant archive (EVA). This indicates that the identified SVs are shared among multiple breeds of cattle and that DELLY can be used to develop future pipelines to include long read sequencing technologies and/or data with higher read depth.
| Identifer | oai:union.ndltd.org:UPSALLA1/oai:DiVA.org:uu-448593 |
| Date | January 2021 |
| Creators | Jakobsson, Jenny |
| Publisher | Uppsala universitet, Institutionen för biologisk grundutbildning |
| Source Sets | DiVA Archive at Upsalla University |
| Language | English |
| Detected Language | English |
| Type | Student thesis, info:eu-repo/semantics/bachelorThesis, text |
| Format | application/pdf |
| Rights | info:eu-repo/semantics/openAccess |
| Relation | UPTEC X ; 21027 |
Page generated in 0.0025 seconds