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454 Transcriptome sequencing; Genetics of migration; Phylloscopus
Abstract:
Background: Animal migration requires adaptations in morphological, physiological and behavioural traits. Several
of these traits have been shown to possess a strong heritable component in birds, but little is known about their
genetic architecture. Here we used 454 sequencing of brain-derived transcriptomes from two differentially
migrating subspecies of the willow warbler Phylloscopus trochilus to detect genes potentially underlying traits
associated with migration.
Results: The transcriptome sequencing resulted in 1.8 million reads following filtering steps. Most of the reads
(84%) were successfully mapped to the genome of the zebra finch Taeniopygia gutatta. The mapped reads were
situated within at least 12,101 predicted zebra finch genes, with the greatest sequencing depth in exons. Reads
that were mapped to intergenic regions were generally located close to predicted genes and possibly located in
uncharacterized untranslated regions (UTRs). Out of 85,000 single nucleotide polymorphisms (SNPs) with a
minimum sequencing depth of eight reads from each of two subspecies-specific pools, only 55 showed high
differentiation, confirming previous studies showing that most of the genetic variation is shared between the
subspecies. Validation of a subset of the most highly differentiated SNPs using Sanger sequencing demonstrated
that several of them also were differentiated between an independent set of individuals of each subspecies. These
SNPs were clustered in two chromosome regions that are likely to be influenced by divergent selection between
the subspecies and that could potentially be associated with adaptations to their different migratory strategies.
Conclusions: Our study represents the first large-scale sequencing analysis aiming at detecting genes underlying
migratory phenotypes in birds and provides new candidates for genes potentially involved in migration.
