The great tit (Parus major) is a well-studied wild bird which has been used as a model species to document the effects of global warming on nature. The recent completion of a reference genome sequence of the great tit and the availability of a high density (HD) 500K SNP-chip, have enabled detailed genomic studies in this species. These genomic tools allowed precise and scalable measures of genetic and non-genetic (i.e. epigenetic marks) variation as well the identification of SNP variants under selection. Here we present an initial copy number variation (CNV) analysis in great tit genomes using the HD SNP-chip intensities and allele frequencies from over 2000 females. We found regions of CNVs (CNVRs) significantly enriched for neuronal related pathways as ‘neuroactive ligant-receptor interaction’ and ‘Gap junction’. Interestingly, genes related to neuronal functions were previously identified at regions under positive selection and prone to be methylated in great tits. This suggests that complex variation (CNV + SNP + methylation) plays an important role in great tit microevolution. A representative example is the gene CD200 which is associated with Parkinson´s disease, neuroimmunity, and is under positive selection in the Dutch great tit population and overlaps a highly frequent CNVR. The CNV analysis is at an early stage and the next steps include strategies to improve the SNP-chip overall signal quality, SNP-CNV haplotype reconstruction, a selection analysis as well as a genome-wide association study for seasonal phenotypes (e.g. timing of breeding) changing as a result of global warming.
|Publication status||Published - 4 Feb 2016|
|Event||WIAS Science Day 2016 - Wageningen, Netherlands|
Duration: 2 Feb 2016 → 2 Feb 2016
|Conference||WIAS Science Day 2016|
|Period||2/02/16 → 2/02/16|