Genetic differentiation, clinal variation and phenotypic associations with growth cessation across the Populus tremula photoperiodic pathway.
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.
Ma
Xiao-Fei
XF
Department of Ecology and Environmental Science, Umeå Plant Science Centre, Umeå University, SE-90187 Umeå, Sweden.
Hall
David
D
Onge
Katherine R St
KR
Jansson
Stefan
S
Ingvarsson
Pär K
PK
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*
Annu Rev Genet. 2004;38:87-117
15568973
Am Nat. 1998 Mar;151(3):283-92
18811359
Genetics. 2008 Sep;180(1):329-40
18716330
Mol Ecol. 2004 Apr;13(4):969-80
15012769
New Phytol. 2009 Mar;181(4):808-819
19140936
Mol Ecol. 2008 Apr;17(8):1885-96
18363667
Genet Res. 1999 Dec;74(3):223-36
10689800
Mol Ecol. 2010 Apr;19(8):1638-50
20345678
Plant Physiol. 2003 Jun;132(2):732-8
12805602
Annu Rev Plant Biol. 2004;55:141-72
15377217
Genetics. 2008 Apr;178(4):2217-26
18245834
Evolution. 2007 Dec;61(12):2849-60
17908247
Genetics. 2008 Oct;180(2):977-93
18780740
Nucleic Acids Res. 2004 Feb 18;32(3):e32
14973328
Plant Physiol. 2007 May;144(1):248-57
17369429
Mol Ecol. 2009 Feb;18(3):375-402
19143936
Science. 2000 May 5;288(5467):859-63
10797009
Trends Plant Sci. 2003 Sep;8(9):405-7
13678904
Genetics. 1982 May;101(1):139-55
17246079
Curr Opin Plant Biol. 2003 Feb;6(1):13-9
12495746
Genetics. 2006 Mar;172(3):1845-53
16361240
PLoS Genet. 2007 Mar 30;3(3):e45
17397259
Genetics. 2002 Mar;160(3):1191-202
11901133
Science. 2006 May 19;312(5776):1040-3
16675663
Science. 2001 Aug 3;293(5531):880-3
11486091
Genetics. 2000 Feb;154(2):837-45
10655234
Genetics. 2003 Jul;164(3):1205-19
12871925
Trends Ecol Evol. 2005 Aug;20(8):435-40
16701414
Proc Natl Acad Sci U S A. 2007 Oct 23;104(43):16986-91
17940010
Proc Natl Acad Sci U S A. 2003 Aug 5;100(16):9440-5
12883005
Genetics. 2000 Jun;155(2):945-59
10835412
Am J Hum Genet. 2002 Mar;70(3):575-85
11836648
Nature. 2009 Oct 8;461(7265):747-53
19812666
Genetics. 2008 Sep;180(1):367-79
18716337
Genetics. 1973 May;74(1):175-95
4711903
Nat Genet. 2006 Feb;38(2):203-8
16380716