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Title: Genome-wide analysis of goat genetic diversity and production systems in Uganda

Date Published: 2019
Author/s: Robert Boyle Onzima
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Affiliation: Wageningen University


The need to promote sustainable utilization and conservation of indigenous livestock
genetic resources has increased over the last century. Genetic diversity is a
prerequisite for adaptation in the face of future challenges, therefore highlighting
the need to ensure that animal genetic resources remain available to promote food
security for future generations. The advances in genotyping technology provide
unique opportunities for in-depth assessment of genetic diversity and to prioritize
breeds for conservation and sustainable use. The aim of the research described in
this thesis was therefore to characterize production systems and goat genetic
resources in Uganda. First, using participatory approaches in defining breeding goal
traits, smallholder farmers identified adaptation traits to be critical in an ideal goat
breed for smallholder production systems. Subsequently, three indigenous goat
breeds were assessed for their variation in resistance/resilience to the
gastrointestinal nematode Haemonchus contortus. A weakly significant difference
among breeds in faecal egg count (FEC) and packed cell volume (PCV) was observed
suggesting potential differences in resistance to Haemonchus contortus. Secondly,
using the caprine SNP50 BeadChip, the genetic diversity, population structure and
admixture in Ugandan goat breeds was assessed. Moderate to high genetic
variability was observed among the Ugandan indigenous goat breeds. The breeds
exhibit a weak population structure and limited admixture with the exotic breed Boer