Search for informative polymorphisms in candidate genes: clock genes and circadian behaviour in blue tits
Open Access
- 16 September 2008
- journal article
- research article
- Published by Springer Science and Business Media LLC in Genetica
- Vol. 136 (1), 109-117
- https://doi.org/10.1007/s10709-008-9318-y
Abstract
The identification of functional polymorphisms in genes that underlie behavioural trait variation is a challenging but intriguing task in evolutionary biology. Given the wealth of genomic data and the increasing number of genotype–phenotype association studies in model organisms, one can ask whether and how this information can be used for non-model organisms. Here we describe two strategies to search for likely functional polymorphisms in candidate genes in a bird species that has been intensively studied by behavioural and population ecologists, the blue tit Cyanistes caeruleus. In the first approach we searched for repeating elements in coding regions of the genome using information about repeats in Gallus gallus genes. The rationale is that tandem-repeat elements have a high potential to be polymorphic and functional. The second strategy aimed to replicate reported genotype–phenotype association studies by extrapolating results from model organisms to our study species. Both strategies showed high success rates with respect to finding homologous gene regions and potentially informative genetic variants in the genes AANAT, ADCYAP1, CKIε, CLOCK, CREB1, NPAS2 and PERIOD2.Keywords
This publication has 68 references indexed in Scilit:
- GenBankNucleic Acids Research, 2007
- Successful design and conduct of genome-wide association studiesHuman Molecular Genetics, 2007
- Drd4 gene polymorphisms are associated with personality variation in a passerine birdProceedings Of The Royal Society B-Biological Sciences, 2007
- Candidate-gene approaches for studying complex genetic traits: practical considerationsNature Reviews Genetics, 2002
- Listening to silence and understanding nonsense: exonic mutations that affect splicingNature Reviews Genetics, 2002
- BLAT—The BLAST-Like Alignment ToolGenome Research, 2002
- Gapped BLAST and PSI-BLAST: a new generation of protein database search programsNucleic Acids Research, 1997
- Absence of expression of the FMR-1 gene in fragile X syndromeCell, 1991
- Identification of a gene (FMR-1) containing a CGG repeat coincident with a breakpoint cluster region exhibiting length variation in fragile X syndromeCell, 1991