Search for informative polymorphisms in candidate genes: clock genes and circadian behaviour in blue tits.
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, CKIepsilon, CLOCK, CREB1, NPAS2 and PERIOD2.
Steinmeyer
C
C
Max Planck Institute for Ornithology (Seewiesen), Postfach 1564, 82305 Starnberg, Seewiesen, Germany.
Mueller
J C
JC
Kempenaers
B
B
D000818:Animals; D030161:Avian Proteins / Q000235:genetics*; D056926:CLOCK Proteins; D002940:Circadian Rhythm / Q000235:genetics*; D016678:Genome; D005838:Genotype; D006801:Humans; D046109:Passeriformes / Q000235:genetics*; D010641:Phenotype; D011110:Polymorphism, Genetic; D015534:Trans-Activators / Q000235:genetics*
D030161:Avian Proteins; D015534:Trans-Activators; D056926:CLOCK Proteins; C538943:CLOCK protein, human
Nature. 2005 Mar 31;434(7033):640-4
15800623
Nat Genet. 2002 Oct;32(2):290-5
12244319
Psychiatr Genet. 1999 Jun;9(2):107-9
10412192
Chronobiol Int. 2004 Mar;21(2):229-37
15332344
Nat Genet. 2004 Sep;36(9):921-4
15340423
J Biol Chem. 1995 Sep 8;270(36):20898-900
7673112
J Hum Genet. 2006;51(12):1122-1125
17051316
Gene. 2004 Oct 27;341:149-65
15474298
Proc Biol Sci. 2005 Nov 7;272(1578):2289-98
16191642
Science. 1994 Jul 29;265(5172):669-71
8036515
Mol Endocrinol. 1996 Dec;10(12):1527-35
8961263
Neurogenetics. 2003 Apr;4(3):151-3
12736803
Nat Protoc. 2007;2(11):2734-46
18007609
Nature. 2007 Jun 21;447(7147):932-40
17581576
Nat Rev Genet. 2001 Jun;2(6):437-45
11389460
Science. 2007 Jan 26;315(5811):525-8
17185560
J Biochem Biophys Methods. 2004 Jul 30;60(1):1-12
15236905
J Sleep Res. 2002 Dec;11(4):305-12
12464098
Annu Rev Neurosci. 2007;30:575-621
17417937
EMBO Rep. 2001 Apr;2(4):342-6
11306557
Nat Rev Genet. 2005 Jul;6(7):544-56
15951747
Cell. 1991 Aug 23;66(4):817-22
1878973
Annu Rev Genomics Hum Genet. 2006;7:339-67
16756480
Sleep Res Online. 2000;3(2):73-6
11382904
Science. 2001 Feb 9;291(5506):1040-3
11232563
Am J Med Genet B Neuropsychiatr Genet. 2005 Feb 5;133B(1):101-4
15578592
Mol Ecol. 2006 Apr;15(5):1299-320
16626455
Psychiatry Clin Neurosci. 1999 Aug;53(4):527-9
10498237
Trends Ecol Evol. 2005 Feb;20(2):96-104
16701349
Neuropsychopharmacology. 2003 Apr;28(4):734-9
12655319
Psychiatry Res. 2002 Mar 15;109(2):121-8
11927136
Science. 1996 Mar 8;271(5254):1423-7
8596916
Chronobiol Int. 2007;24(1):1-8
17364575
Proc Biol Sci. 2007 Jul 22;274(1619):1685-91
17472912
Nature. 2006 Aug 3;442(7102):563-7
16885984
Neuropsychopharmacology. 2004 Oct;29(10):1901-9
15187983
Nat Genet. 2002 Mar;30(3):315-20
11919562
Sleep. 2003 Jun 15;26(4):413-5
12841365
Nat Rev Genet. 2002 Apr;3(4):285-98
11967553
Cell. 1998 Jul 10;94(1):97-107
9674431
J Sleep Res. 2007 Mar;16(1):12-6
17309758
Neurosci Lett. 2000 Feb 11;280(1):29-32
10696804
Sleep. 1998 Sep 15;21(6):569-76
9779516
Ann Med. 2005;37(8):580-9
16338760
Hum Mol Genet. 2003 Feb 1;12(3):205-16
12554675
Genetics. 2000 Mar;154(3):1053-68
10757753
Proc Natl Acad Sci U S A. 1999 Jul 6;96(14):7871-6
10393914
Biochem Biophys Res Commun. 1999 Sep 7;262(3):832-7
10471411
Genome Res. 2002 Apr;12(4):656-64
11932250
Mol Psychiatry. 1998 Jan;3(1):21-31
9491809
Mol Ecol. 1996 Jun;5(3):365-78
8688957
Nature. 1988 Mar 17;332(6161):278-81
3347271
Mol Ecol. 2007 Nov;16(22):4867-80
17927702
Int J Chronobiol. 1976;4(2):97-110
1027738
Nucleic Acids Res. 1997 Sep 1;25(17):3389-402
9254694
Mol Ecol. 2008 Feb;17(4):964-80
17927703
Hum Mol Genet. 2007 Oct 15;16 Spec No. 2:R220-5
17597095
Nucleic Acids Res. 2008 Jan;36(Database issue):D25-30
18073190
J Sleep Res. 2005 Sep;14(3):293-7
16120104
Genetika. 2004 Oct;40(10):1301-18
15575498
Cell. 1991 May 31;65(5):905-14
1710175
Science. 2000 Apr 21;288(5465):483-92
10775102
Nat Rev Genet. 2002 May;3(5):391-7
11988764
Mol Ecol. 2005 Oct;14(12):3623-42
16202085