Universitą degli studi di Pavia


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Bonfiglio research activity

Analysis of mitochondrial DNA (mtDNA) variability in modern cattle
The analysis of complete bovine mitochondrial genomes (Achilli et al. 2008) revealed that, although the gene pool of modern taurine cattle mostly derives from the Near East (Neolithic domestication), there was also a minor genetic contribution from European aurochs (Bos primigenius).
The aim of my research was to further clarify the nature and extent of gene flow from European B. primigenius to modern taurine cattle, by analyzing mtDNAs of numerous subjects belonging to cattle breeds mainly from Europe. At a first level of analysis, mitochondrial control regions of the samples were sequenced to classify them into haplogroups. The mtDNAs that turned out to carry putative aurochs haplotypes were then completely sequenced and added to the existing phylogenetic tree to clarify their phylogenetic relationships.
Another aim of the research was to enrich the still poor detailed phylogeny of haplogroup T1 by the analysis of numerous complete mitochondrial genomes from both European and African subjects.
During the realization of my research, I spent a brief period at the Istituto di Genomica Applicata (IGA) in Udine to collaborate on the development of a multiplexing protocol to sequence complete mitochondrial genomes with Illumina Genome Analyzer IIx.

Analysis of Y-chromosome variability in modern cattle
The studies of cattle Y-chromosome variability performed so far have been based on a few biallelic markers (SNPs) covering just about 3.5 kb of some Y-specific genes due to the absence of an annotated sequence of bovine Y-chromosome.
The aim of my research was to increase the number of bovine Y- specific biallelic markers as a means to identify novel paternal lineages in modern cattle populations, in order to build a more informative phylogeny of the bovine Y-chromosome and to also gain a better knowledge on domestication issues, which have been investigated so far by mainly taking into account mtDNA. To the purpose, a bioinformatic approach was employed to mine Y- chromosome sequence data retrieved from GenBank for potential Y-specific markers, which were then analyzed for polymorphisms using Denaturing High-Performance Liquid Chromatography (DHPLC) and sequencing. In addition, DNA samples from male cattle available in the laboratory were tested for known polymorphisms in order to classify them into the currently available taurine Y1 /Y2 or zebuine Y3 haplogroups.
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