Genome-wide SNP detection in the great tit Parus major using high throughput sequencing


  • This paper is part of an ongoing project on SNP discovery to map QTLs for timing of breeding and personality in great tits. Nikkie van Bers is a postdoctoral fellow working on this project. Knees van Oers is at the Netherlands Institute of Ecology and its interested in the evolutionary genetics of animal personality. Hindrik Kerstens is a PhD at Animal Breeding and Genomics Centre, Wageningen University and has a strong interest in bioinformatics. Bert Dibbits is technical assistant in molecular biology at Animal Breeding and Genomics Centre, Wageningen University. Richard Crooijmans is assistant professor at Animal Breeding and Genomics Centre, Wageningen University, Dand is interested in genome research of farm animals. Marcel Visser is professor at the Department of Animal Ecology at the Netherlands institute of Ecology and is interested in great tit lay date plasticity and its micro-evolution in response to climate change. Martien Groenen is Professor in Animal Genomics at Animal Breeding and Genomics Centre, Wageningen University, Project and has a broad interest in comparative and population genomics of animals.

Kees van Oers, Fax: 31 26 4723227; E-mail:


Identifying genes that underlie ecological traits will open exiting possibilities to study gene–environment interactions in shaping phenotypes and in measuring natural selection on genes. Evolutionary ecology has been pursuing these objectives for decades, but they come into reach now that next generation sequencing technologies have dramatically lowered the costs to obtain the genomic sequence information that is currently lacking for most ecologically important species. Here we describe how we generated over 2 billion basepairs of novel sequence information for an ecological model species, the great tit Parus major. We used over 16 million short sequence reads for the de novo assembly of a reference sequence consisting of 550 000 contigs, covering 2.5% of the genome of the great tit. This reference sequence was used as the scaffold for mapping of the sequence reads, which allowed for the detection of over 20 000 novel single nucleotide polymorphisms. Contigs harbouring 4272 of the single nucleotide polymorphisms could be mapped to a unique location on the recently sequenced zebra finch genome. Of all the great tit contigs, significantly more were mapped to the microchromosomes than to the intermediate and the macrochromosomes of the zebra finch, indicating a higher overall level of sequence conservation on the microchromosomes than on the other types of chromosomes. The large number of great tit contigs that can be aligned to the zebra finch genome shows that this genome provides a valuable framework for large scale genetics, e.g. QTL mapping or whole genome association studies, in passerines.