Abstract
Migratory birds are of particular interest for population genetics because of the high connectivity between habitats and populations. A high degree of connectivity requires using many genetic markers to achieve the required statistical power, and a genome wide SNP set can fit this purpose. Here we present the development of a genome wide SNP set for the Barnacle Goose Branta leucopsis, a model species for the study of bird migration. We used the genome of a different waterfowl species, Mallard Anas platyrhynchos, as a reference to align Barnacle Goose second generation sequence reads from an RRL library and detected 2188 SNPs genome wide. Furthermore, we used chimeric flanking sequences, merged from both Mallard and Barnacle Goose DNA sequence information, to create primers for validation by genotyping. Validation with a 384 SNP genotyping set resulted in 374 (97%) successfully typed SNPs in the assay, of which 358 (96%) were polymorphic. Additionally, we validated our SNPs on relatively old (30 years) museum samples, which resulted in a success rate of at least 80%. This shows that museum samples could be used in standard SNP genotyping assays. Our study also shows that the genome of a related species can be used as reference to detect genome wide SNPs in birds, because genomes of birds are highly conserved. This is illustrated by the use of chimeric flanking sequences, which showed that the incorporation of flanking nucleotides from Mallard into Barnacle Goose sequences lead to equal genotyping performance when compared to flanking sequences solely composed of Barnacle Goose sequence.
Highlights
Migration of animals is one of the most visible natural phenomena and as such has attracted much scientific attention
Previous genetic marker sets for goose species only included a small number of microsatellites [5,6,31,32,33], which have considerably less statistical power than the large number of Single Nucleotide Polymorphisms (SNPs) we identified [7]
Despite using a relatively small discovery panel and limited read depth (,106), our distribution of minor allele frequency (MAF) shows that relatively low-frequency SNPs could be detected, which may be especially useful for discriminating populations
Summary
Migration of animals is one of the most visible natural phenomena and as such has attracted much scientific attention. Migratory species can play a key role in understanding how local environmental changes affect populations and habitats at a larger scale [1]. More insight into the genetic population structure of migratory species will be helpful in understanding migration patterns and possible migration changes [4]. Because of the high connectivity between migratory populations high discriminating power is needed to disentangle population structure, especially when insight in recent migratory changes is desired. The Barnacle Goose is one of the model species for migration research, studied especially for its flexibility in adjusting migration schedules to ecological changes [10,11,12,13,14,15]. Barnacle geese are not used in agricultural production, the detection of SNPs in Barnacle Goose may provide potential SNPs for related species and their domesticated forms
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