The Genomic and Transcriptomic Landscape of the Indian Water Buffalo (Bubalus bubalis)
The water buffalo (Bubalus bubalis) is one of the most important domesticated species in India providing milk, meat, hide and draft power. At over 100 million animals, India has the highest number of water buffalo in the world, however, the species is found across the globe, including Europe where the Mediterranean subspecies is farmed. Despite the importance of this domesticated bovid, there are limited high-resolution genomic and transcriptomic analyses across these animals. The aim of this thesis was to use whole genome and RNA sequencing data to characterise regulatory variation and genome evolution in the water buffalo. Specifically, I explored the presence of regulatory variation in macrophages of water buffalo in the form of allele-specific expression (ASE) and investigated signatures of selection and breed divergence across water buffalo breeds. Water buffalo are exposed to a range of important pathogens, many of which that are zoonotic in nature. Differences in regulatory variation between animals have been shown to underlie some of the diversity in response to these pathogens. Macrophages are among the first cells of the innate immune system to act against a pathogen through its recognition, phagocytosis and destruction playing an important role in host disease susceptibility. Regulatory variants acting in macrophages are thus important candidates for explaining differences in disease susceptibility to infectious diseases among water buffalo. To detect the presence of regulatory variation, I used whole genome sequencing and RNA-seq data in 4 Mediterranean water buffalo to identify ASE in macrophage expressed genes. The analysis revealed that regulatory variation does exist in macrophage expressed genes which could be reliably detected as ASE signature. To understand the impact of domestication and how water buffalo have evolved I used whole genome sequencing data from 81 animals spanning seven distinct breeds. I identified the population structure of these breeds and explored how gene flow has shaped their genomes. I also characterised the signatures of putative selection between breeds. Sites identified included genes linked to milk production, coat colour and body size and interestingly a number of these overlapped those found to be under selection in other domesticated species suggesting some extent of convergent domestication. In this thesis, I consequently undertook one of the first high-resolution evolutionary and regulatory variation analyses of an important domesticated species, Bubalus bubalis. The results from this study are likely to be invaluable to inform future studies of how regulatory variants may confer tolerance to water buffalo pathogens as well as the impact of domestication on its genome.