University of Natural Resources and Life Sciences, Vienna (BOKU) - Research portal
Gewählte Master / Diploma Thesis:
Chang Xu
(2022):
Predicting effective population size based on linkage disequilibrium in African chicken.
Master / Diploma Thesis - Institut für Nutztierwissenschaften (NUWI),
BOKU-Universität für Bodenkultur,
pp 54.
UB BOKU
obvsg
- Abstract:
- African chicken is an important livestock asset and is kept around the whole continent, while it has a convoluted demographic history, with multiple introductions across and within the continent. The main goal of this thesis was to predict the trends in effective population size of Ethiopian and Nigerian chickens. Materials include whole-genome sequence data of 234 Ethiopian and 119 Nigerian chicken samples. SNPs were filtered based on 50K density. SNPs with minor allele frequency below 0.01 and missing call rate above 0.1 were filtered out. The SNeP software and a manual script were used to estimate effective population size. Principal component analysis and Fst analysis by PLINK and admixture analysis by ADMIXTURE1.3 were performed to understand population structure. Migration events were predicted using TreeMix v1.1. The predicted effective population sizes follow an increasing trend for both populations when looking into the more distant past, as expected. The effective population size increase from 946 (19 generations ago) to 5325 (700 generations ago) in Ethiopian chicken population and from 668 to 4162 in Nigerian chicken population. The effective population sizes are generally lower in the Nigerian chicken population compared to the Ethiopian chicken population but the difference decreases as looking into the more recent past. The subpopulation Hugub was found separated from the Ethiopian chicken while Nigerian chicken was found unstratified. Four migration events were predicted for Ethiopian chicken and one for Nigerian chicken. This study can further provide evidence for unveiling African chicken population history and potentially contribute to local chicken breeding and conservation programs.
- Beurteilende*r: Meszaros Gabor
- 1.Mitwirkender: Sölkner Johann