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FINE-SCALE RECOMBINATION MAPS OF THE CATTLE GENOME INFERRED BY LINKAGE DISEQUILIBRIUM
MOHAMMADI, Fardokhtsadat
Recombination is a genetic event that occurs during meiosis and leads to the exchange of genetic material between paternal and maternal homologous chromosomes. The intensity of recombination is shown to vary across genomes between and within species, yet the determinants of recombination patterns among populations of the same species are not fully understood. In this thesis, we estimated fine-scale, breed-specific recombination maps of a subset of chromosome 25 of Braunvieh and Fleckvieh cattle for different populations with respect to inbreeding coefficients using the R package LDJump under two assumptions, neutrality and demography. Moreover, we studied the association between recombination rates and genomic features such as SNP count, GC content, and the density and nature of genes. We observed a statistically-significant, weak negative correlation between recombination rates and SNP count, where low recombination rates are accompanied by higher SNP count, and vice versa. More complex demographic scenarios as well as the level of inbreeding should be incorporated in further research using LDJump to address this possible association between SNP count and recombination rates. On the contrary, we observed no such relationship between recombination rates and GC content. We detected a substantial difference in gene density between the lowest and highest SNP-count regions of chromosome 25.
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