Bioinformatics approaches to the analysis of complex traits in domestic animals

Eva Čeh (2013) Bioinformatics approaches to the analysis of complex traits in domestic animals. PhD thesis.

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Abstract

In this thesis, we focus on the characterization of the genetic mechanisms responsible for the complex traits in domestic animals using a variety of bioinformatics approaches. Complex traits are usually considered to be affected by a number of interacting genes, as well as by environmental factors. In contrast to simple Mendelian traits, inheritance patterns of complex traits are more difficult to study and understand, but are in reality more common. Thanks to the rapid progress of the development of high-throughput sequencing and genotyping technologies, huge amounts of genomic data can be quickly gathered. Therefore we are now faced with a new challenge of interpreting huge collections of genomic data and dissection of biologically relevant information. This dissertation consists of three case studies: population genetics study, analysis of a genetic disease and a transcriptomic analysis of a laboratory model of an infectious disease. In all three studies we attempt to identify the underlying genetic factors and interpret the complex genetic patterns that affect the studied traits. We address biologically relevant problems using different computational approaches. The population genetics study of livestock guard dog breeds from the Western Balkans reveals a surprisingly strong influence of genetic drift on the resolution of genetic relationships of studied breeds. In the next section we take advantage of a limited gene pool of the Karst Shepherd breed for the purpose of a genome-wide scan and homozygosity mapping of ureteral ectopia. We further present suggestive genomic loci for susceptibility to ureteral ectopia in this breed. In the third case study we investigate the experimental model of contagious agalactia based on RNA sequencing data and show temporal transcriptomic profiles of the pathogen and host organisms during the first 24 hours of infection. We identify possible causal genetic factors in all three study cases, offer insight into the specific population characteristics or phenotypic traits as well as complex traits in general, and also lay foundation for future research and implementation of the acquired knowledge in breeding practices.

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