title: Genetic differentiation, clinal variation and phenotypic associations with growth cessation across the Populus tremula photoperiodic pathway.
abstract: Perennial plants monitor seasonal changes through changes in environmental conditions such as the quantity and quality of light. To ensure a correct initiation of critical developmental processes, such as the initiation and cessation of growth, plants have adapted to a spatially variable light regime and genes in the photoperiodic pathway have been implicated as likely sources for these adaptations. Here we examine genetic variation in genes from the photoperiodic pathway in Populus tremula (Salicaceae) for signatures diversifying selection in response to varying light regimes across a latitudinal gradient. We fail to identify any loci with unusually high levels of genetic differentiation among populations despite identifying four SNPs that show significant allele frequency clines with latitude. We do, however, observe large covariance in allelic effects across populations for growth cessation, a highly adaptive trait in P. tremula. High covariance in allelic effects is a signature compatible with diversifying selection along an environmental gradient. We also observe significantly higher heterogeneity in genetic differentiation among SNPs from the photoperiod genes than among SNPs from randomly chosen genes. This suggests that spatially variable selection could be affecting genes from the photoperiod pathway even if selection is not strong enough to cause individual loci to be identified as outliers. SNPs from three genes in the photoperiod pathway (PHYB2, LHY1, and LHY2) show significant associations with natural variation in growth cessation. Collectively these SNPs explain 10-15% of the phenotypic variation in growth cessation. Covariances in allelic effects across populations help explain an additional 5-7% of the phenotypic variation in growth cessation.
authors.affiliation: Department of Ecology and Environmental Science, Umeå Plant Science Centre, Umeå University, SE-90187 Umeå, Sweden.
authors.forename: Xiao-Fei
authors.initials: XF
authors.lastname: Ma
authors.forename: David
authors.initials: D
authors.lastname: Hall
authors.forename: Katherine R St
authors.initials: KR
authors.lastname: Onge
authors.forename: Stefan
authors.initials: S
authors.lastname: Jansson
authors.forename: Pär K
authors.initials: PK
authors.lastname: Ingvarsson
mesh_terms: D000483:Alleles; D003198:Computer Simulation; D017753:Ecosystem; D005787:Gene Frequency / Q000235:genetics; D014644:Genetic Variation; D005838:Genotype; D010641:Phenotype; D017440:Photoperiod; D020641:Polymorphism, Single Nucleotide / Q000235:genetics; D032107:Populus / Q000235:genetics* / Q000254:growth & development*
references.citation: Annu Rev Genet. 2004;38:87-117
references.pmid: 15568973
references.citation: Am Nat. 1998 Mar;151(3):283-92
references.pmid: 18811359
references.citation: Genetics. 2008 Sep;180(1):329-40
references.pmid: 18716330
references.citation: Mol Ecol. 2004 Apr;13(4):969-80
references.pmid: 15012769
references.citation: New Phytol. 2009 Mar;181(4):808-819
references.pmid: 19140936
references.citation: Mol Ecol. 2008 Apr;17(8):1885-96
references.pmid: 18363667
references.citation: Genet Res. 1999 Dec;74(3):223-36
references.pmid: 10689800
references.citation: Mol Ecol. 2010 Apr;19(8):1638-50
references.pmid: 20345678
references.citation: Plant Physiol. 2003 Jun;132(2):732-8
references.pmid: 12805602
references.citation: Annu Rev Plant Biol. 2004;55:141-72
references.pmid: 15377217
references.citation: Genetics. 2008 Apr;178(4):2217-26
references.pmid: 18245834
references.citation: Evolution. 2007 Dec;61(12):2849-60
references.pmid: 17908247
references.citation: Genetics. 2008 Oct;180(2):977-93
references.pmid: 18780740
references.citation: Nucleic Acids Res. 2004 Feb 18;32(3):e32
references.pmid: 14973328
references.citation: Plant Physiol. 2007 May;144(1):248-57
references.pmid: 17369429
references.citation: Mol Ecol. 2009 Feb;18(3):375-402
references.pmid: 19143936
references.citation: Science. 2000 May 5;288(5467):859-63
references.pmid: 10797009
references.citation: Trends Plant Sci. 2003 Sep;8(9):405-7
references.pmid: 13678904
references.citation: Genetics. 1982 May;101(1):139-55
references.pmid: 17246079
references.citation: Curr Opin Plant Biol. 2003 Feb;6(1):13-9
references.pmid: 12495746
references.citation: Genetics. 2006 Mar;172(3):1845-53
references.pmid: 16361240
references.citation: PLoS Genet. 2007 Mar 30;3(3):e45
references.pmid: 17397259
references.citation: Genetics. 2002 Mar;160(3):1191-202
references.pmid: 11901133
references.citation: Science. 2006 May 19;312(5776):1040-3
references.pmid: 16675663
references.citation: Science. 2001 Aug 3;293(5531):880-3
references.pmid: 11486091
references.citation: Genetics. 2000 Feb;154(2):837-45
references.pmid: 10655234
references.citation: Genetics. 2003 Jul;164(3):1205-19
references.pmid: 12871925
references.citation: Trends Ecol Evol. 2005 Aug;20(8):435-40
references.pmid: 16701414
references.citation: Proc Natl Acad Sci U S A. 2007 Oct 23;104(43):16986-91
references.pmid: 17940010
references.citation: Proc Natl Acad Sci U S A. 2003 Aug 5;100(16):9440-5
references.pmid: 12883005
references.citation: Genetics. 2000 Jun;155(2):945-59
references.pmid: 10835412
references.citation: Am J Hum Genet. 2002 Mar;70(3):575-85
references.pmid: 11836648
references.citation: Nature. 2009 Oct 8;461(7265):747-53
references.pmid: 19812666
references.citation: Genetics. 2008 Sep;180(1):367-79
references.pmid: 18716337
references.citation: Genetics. 1973 May;74(1):175-95
references.pmid: 4711903
references.citation: Nat Genet. 2006 Feb;38(2):203-8
references.pmid: 16380716