Genomic variation across European cattle: contribution of gene flow

Abstract

European cattle display vast phenotypic diversity which can be attributed to genomic variations such as single nucleotide polymorphisms (SNPs) and structural variations (SVs). The distribution of these genomic variations in a population is heavily influenced by different population genomic forces. In this thesis, I used genome-wide SNPs to characterize genomic variation and admixture across different European cattle populations. Broadly, I show the difference in the domestication histories for north-western and southern European cattle. I argue that this difference can be attributed to a differential pattern of genomic admixture involving wild local aurochs and zebu cattle. Genomic admixture analysis revealed share ancestry between Balkan and Italian cattle (BAI) breeds, and zebu cattle. Moreover, I also show that southern European cattle breeds displayed shared ancestry with African taurine cattle. Using linked SNP based approaches, I inferred a common origin of the African taurine and zebu cattle ancestry in BAI cattle breeds. Furthermore, I also characterized the genomic diversity and structure in European cattle populations. I show that, on average, nucleotide diversity is higher in southern European cattle than western European (British and commercial) cattle. However, some of these southern European cattle breeds such as Romagnola and Maltese appeared to have undergone a recent bottleneck. On the other hand, Swedish native cattle breeds like Swedish Mountain cattle, despite recorded bottleneck in the past, still display significant genomic diversity. However, southern Swedish cattle breeds like Vaneko and Ringamalako requires attention for conservation management as these breeds display lowest genetic diversity among all the Swedish cattle breeds. To understand the patterns of genomic variations comprehensively, I also characterized the structural variations (SVs) in the genome of European cattle. I inferred the influence of demographic changes in the distribution of SVs in the cattle genome. In addition, I also identified an SV CNV overlapping the KIT gene in English Longhorn cattle which has previously been associated with color-sidedness. Finally, using whole genome sequencing data, I identified various protein-coding genes and regulatory elements encompassing SVs which represents valuable resources for future studies aimed at finding the association between physiological processes and SVs in cattle.