The development of a genome wide SNP set for the Barnacle goose Branta leucopsis.
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.
Resource Ecology Group, Wageningen University, Wageningen, the Netherlands. mrjonker@gmail.com
Rudy M
RM
Jonker
Qiong
Q
Zhang
Pim
P
Van Hooft
Maarten J J E
MJ
Loonen
Henk P
HP
Van der Jeugd
Richard P M A
RP
Crooijmans
Martien A M
MA
Groenen
Herbert H T
HH
Prins
Robert H S
RH
Kraus
D000483:Alleles; D000818:Animals; D002874:Chromosome Mapping; D017931:DNA Primers; D005777:Geese / Q000145:classification / Q000235:genetics*; D005787:Gene Frequency; D005819:Genetic Markers; D016678:Genome; D005838:Genotype; D060005:Genotyping Techniques; D058974:Phylogeography; D020641:Polymorphism, Single Nucleotide; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA
D017931:DNA Primers; D005819:Genetic Markers