Advanced Fertility Diagnostics in Livestock Improvement

In the constantly growing livestock breeding industry, optimisation of animal fertility parameters is key to economic success for animal breeders and livestock producers. Male fertility in particular in key because the use of artificial insemination (AI) means that production is highly dependent on the reproductive output of selected stud males.Achieving optimal reproductive efficiency requires understanding both the overall genetic merit of the animals to be used in the stud programme, and also the genetic and environmental factors that specifically affect semen quality and quantity. As yet, however, the technologies used to assess each of these areas are relatively simplistic and do not optimally leverage more recent advances in assay techniques.This thesis seeks to address this deficiency at multiple levels. Firstly, although FISH-based screening for chromosome structural rearrangements is gaining traction in the pig industry, it is not yet deployed in cattle. Here, I provide novel economic model analysis to demonstrate the likely positive impact of this technology. Secondly, I examine the effects of semen sexing methods on dairy cattle semen and show that at least one such technology has adverse effects on sperm DNA fragmentation that should be taken into consideration when using sexed semen. Thirdly, building on a computerised semen analysis (CASA) dataset (a routine analysis in the pig breeding industry), I provide estimates of individual animal, breed, stud environment and seasonal effects on semen quality. Finally, I have helped develop novel laboratory methods to separate sperm cells at different stages of capacitation, which in turn will enable numerous follow-up projects to understand the factors affecting this process and how these could be modulated to optimise breeding efficiency. Collectively therefore, my work showcases how different types of advanced fertility diagnostic protocol (whether examining cell biology or genetics) can be utilised to derive actionable information that can be put to use to improve fertility in livestock breeding.