Ms. A. (Andreia) de Jesus Amaral Gomes Barbosa Fonseca: Nucleotide variation and footprints of selection in the porcine and chicken genomes

Study of genetic variation and detection of selection events in pig and chicken

The aim of the research presented in this thesis was the characterization of genetic diversity of the porcine and chicken genomes and to infer footprints of artificial selection.  To this purpose, the extent of linkage disequilibrium (LD) was evaluated in ten European pig breeds, in ten Chinese pig breeds and in the European wild boar. Results showed a contrasting difference between European and Chinese breeds. Chinese breeds showed levels of extent of LD similar to human populations whereas European pig breeds and the European wild boar showed levels of LD similar to other domesticated species.  These results showed  minimum of 30,000 informative SNPs (molecular markers – single nucleotide polymorphisms) would be required to characterize genetic diversity of European pig breeds. A cost-effective assay was performed to make genome-wide identification of SNPs in the porcine genome using pooled DNA and massive parallel sequencing. A total of ~17,000 informative SNPs with a success rate of 96% were identified. Second, it showed that this strategy could also be used to characterize nucleotide variation along whole genomes and identify phenomena of artificial selection.  The variation of nucleotide diversity and the identification of footprints of selection were assessed in the porcine and chicken genomes respectively. Results show that selection has most affected different genes related with similar biological pathways. As expected, results suggest that these domesticated species have been mostly positively selected for growth and muscle development.