These authors contributed equally to this work.
The design and cross-population application of a genome-wide SNP chip for the great tit Parus major
Article first published online: 5 APR 2012
© 2012 Blackwell Publishing Ltd
Molecular Ecology Resources
Volume 12, Issue 4, pages 753–770, July 2012
How to Cite
Van BERS, N. E. M., SANTURE, A. W., Van OERS, K., DE CAUWER, I., DIBBITS, B. W., MATEMAN, C., CROOIJMANS, R. P. M. A., SHELDON, B. C., VISSER, M. E., GROENEN, M. A. M. and SLATE, J. (2012), The design and cross-population application of a genome-wide SNP chip for the great tit Parus major. Molecular Ecology Resources, 12: 753–770. doi: 10.1111/j.1755-0998.2012.03141.x
- Issue published online: 11 JUN 2012
- Article first published online: 5 APR 2012
- Received 22 December 2011; revision received 21 February 2012; accepted 27 February 2012
- marker development;
- next generation sequencing;
- population genetics
The vast amount of phenotypic information collected in some wild animal populations makes them extremely valuable for unravelling the genetics of ecologically important traits and understanding how populations adapt to changes in their environment. Next generation sequencing has revolutionized the development of large marker panels in species previously lacking genomic resources. In this study, a unique genomics toolkit was developed for the great tit (Parus major), a model species in ecology and behavioural biology. This toolkit consists of nearly 100 000 SNPs, over 250 million nucleotides of assembled genomic DNA and more than 80 million nucleotides of assembled expressed sequences. A SNP chip with 9193 SNP markers expected to be spaced evenly along the great tit genome was used to genotype 4702 birds from two of the most intensively studied natural vertebrate populations [Wytham Woods/Bagley Woods (United Kingdom) and de Hoge Veluwe/Westerheide (The Netherlands)]. We show that (i) SNPs identified in either of the two populations have a high genotyping success in the other population, (ii) the minor allele frequencies of the SNPs are highly correlated between the two populations and (iii) despite this high correlation, a large number of SNPs display significant differentiation (FST) between the populations, with an overrepresentation of genes involved in cardiovascular development close to these SNPs. The developed resources provide the basis for unravelling the genetics of important traits in many long-term studies of great tits. More generally, the protocols and pitfalls encountered will be of use for those developing similar resources.