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Gewählte Doctoral Thesis:

Wilson Nandolo (2019): Prevalence of copy number variations and runs of homozygosity in cattle and goats.
Doctoral Thesis - Institut für Nutztierwissenschaften (NUWI), BOKU-Universität für Bodenkultur, pp 385. UB BOKU obvsg FullText

Data Source: ZID Abstracts
Abstract:
Three studies were carried out to analyse the prevalence of runs of homozygosity (ROH) and copy number variation (CNV) in goat and cattle genomes. Firstly, we investigated the possibility of some ROH islands (which are widely treated as signatures of selection) being artefacts of coverage gaps and of the presence of CNV in three Austrian cattle breeds: Brown Swiss, Tyrol Grey and Pinzgauer using Illumina BovineHD BeadChip single nucleotide polymorphism (SNP) data. The study showed that some ROH islands were due to the presence of CNVR, and it was recommended that interpretation of ROH islands should be done with caution. Secondly, we determined the extent of inbreeding in African goats using Illumina 50 K SNP data through a hidden Markov model that computes the level and age of inbreeding at both local (marker) and global levels (FG). ROH segments detected using the Viterbi algorithm based on the local inbreeding levels led to ROH-based inbreeding coefficients for all ROH (FROH) and for ROH longer than 2 Mb (FROH>2Mb). All the three inbreeding metrics varied widely across breeds, with overall means of 0.0408, 0.0370, and 0.0691 and medians of 0.0125, 0.0098, and 0.0366 for FROH, FROH>2Mb and FG, respectively. We demonstrated that the level of inbreeding in African goats is low to moderate, with some breeds having more recent inbreeding than others. Lastly, we detected CNV using whole genome sequence (WGS) data. A total of 6,231 global CNVR were found across all the animals, covering 59.2 Mb (2.4%) of the goat genome. Overall, the three studies contributed to the growing knowledge about the variation and structures of cattle and goat genomes.

Betreuer: Sölkner Johann
1. Berater: Wurzinger Maria
2. Berater: Meszaros Gabor

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