Towards sustainable agriculture: Utilising genetics to sustainably improve the efficiency and longevity of cattle agriculture on both large-scale and localised level farming, in view of climate change effects

Livestock products have high densities of critical nutrients. As the world population increases, so too does the demand for animal products (such as milk), whilst climate change induced stressors are expected to intensify competition for resources, indicating that livestock systems must increase climatic resilience, alongside productivity and efficiency. The genetic diversity of livestock breeds is shaped by evolutionary forces such as genetic drift, migration, selection and geographical separation. Modern livestock genetics have also been influenced by human-mediated selection. As a result, many highly specialized breeds are adapted to localised environments as well as having evolved to meet a variety of human needs. Both processes have left traces in the genome of domestic livestock species as genome-wide variants such as short-nucleotide polymorphisms, 'SNPs'. The growing availability of computationally efficient genomic tools means that selection signatures can be readily analysed to assess the genetic diversity and population structure in cattle breeds and among cattle populations. This research utilised genetics in consideration of the growing need to safeguard livestock populations, by considering the need to increase efficiency as well as climate-change induced resilience, with a focus on cattle. We investigated and analysed the population structure and diversity of South-Asian cattle populations, with a focus on the understudied Thailand cattle, as a potential novel genetic resource for resilience and adaptability to climate change. A combination of medium and high-density Illumina Bovine SNP arrays was used, alongside a combination of genomic tools- the PLINK toolkit, STRUCTURE and TreeMix. These results revealed the population history and genetic structure of Asian breeds, validating previous research efforts which identify Thailand cattle as unique among other Indicine breeds, presenting an understudied genetic resource potential, requiring greater genetic management and further research.

We also investigated methods to increase efficiency of European dairy-cattle farms by reducing losses incurred by the prevalent parasite infection cryptosporidiosis. High-density Bovine SNP arrays was used for an association study with the aim of identifying selection signatures associated with Cryptosporidium infection. Using a combination of the PLINK toolkit, various R Packages and PANTHER Gene Ontology assessment, putative candidate genes associated with Cryptosporidium infection are discussed, and future research options are suggested. Putative genes include FMN2, TPM2 and TLN1 (novel), and CA9 and FGD4 (previously found to be directly/indirectly associated with Cryptosporidium infection).