Disentangling the Roles of History and Local Selection in Shaping Clinal Variation of Allele Frequencies and Gene Expression in Norway Spruce (Picea Abies)
Chen, Jun, Källman, Thomas, Ma, Xiaofei, Gyllenstrand, Niclas, Zaina, Giusi, Morgante, Michele, Bousquet, Jean, Eckert, Andrew, Wegrzyn, Jill, Neale, David, Lagercrantz, Ulf, Lascoux, Martin, Genetics
ABSTRACT Understanding the genetic basis of local adaptation is challenging due to the subtle balance among conflicting evolutionary forces that are involved in its establishment and maintenance. One system with which to tease apart these difficulties is clines in adaptive characters. Here we analyzed genetic and phenotypic variation in bud set, a highly heritable and adaptive trait, among 18 populations of Norway spruce (Picea abies), arrayed along a latitudinal gradient ranging from 47°N to 68°N. We confirmed that variation in bud set is strongly clinal, using a subset of five populations. Genotypes for 137 single-nucleotide polymorphisms (SNPs) chosen from 18 candidate genes putatively affecting bud set and 308 control SNPs chosen from 264 random genes were analyzed for patterns of genetic structure and correlation to environment. Population genetic structure was low (FST = 0.05), but latitudinal patterns were apparent among Scandinavian populations. Hence, part of the observed clinal variation should be attributable to population demography. Conditional on patterns of genetic structure, there was enrichment of SNPs within candidate genes for correlations with latitude. Twenty-nine SNPs were also outliers with respect to FST. The enrichment for clinal variation at SNPs within candidate genes (i.e., SNPs in PaGI, PaPhyP, PaPhyN, PaPRR7, and PaFTL2) indicated that local selection in the 18 populations, and/or selection in the ancestral populations from which they were recently derived, shaped the observed cline. Validation of these genes using expression studies also revealed that PaFTL2 expression is significantly associated with latitude, thereby confirming the central role played by this gene in the control of phenology in plants.
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LOCAL adaptation is a key process in the evolution of species. Understanding how local adaptation is established and maintained, however, is especially difficult as its establishment is contingent upon historical conditions and its maintenance depends on the balance among conflicting evolutionary forces (e.g., Yeaman and Otto 2011). It is a particularly challenging task in forest trees, because they have long generation times and therefore cannot be easily manipulated experimentally. For instance, transfer experiments are theoretically possible but practically difficult to implement. On the other hand, the analysis of the strong latitudinal clines displayed by forest trees for potentially adaptive traits such as bud set (Dormling 1973; Savolainen et al. 2007; Aitken et al. 2008) can provide crucial information on the forces involved in local adaptation and, in particular, on the relative parts played by demography and selection in the establishment of the cline. Furthermore, phenology in general, and flowering time and bud set in particular, have been extensively studied and strong candidate genes are available, many of which belong to the photoperiodic pathway including the circadian clock (Gyllenstrand et al. 2007; Albani and Coupland 2010; Bergelson and Roux 2010; Fornara et al. 2010; Holliday et al. 2010; Hsu et al. 2011). Recent candidate gene studies on the genetic basis of clinal variation in phenology in European aspen (Ma et al. 2010) and Sitka spruce (Holliday et al. 2010; Lobo 2011) illustrate well the promises of this approach.
In the present study we focus on a conifer species, Norway spruce [Picea abies (L.) Kar.] and more specifically on clinal variation in the northwest part of its natural range. The clines in phenological traits observed in this species and in this part of its range are intriguing for several reasons. First, as in many other forest tree species (Jaramillo-Correa et al. 2001; Savolainen et al. 2007; Alberto et al. 2011; Kremer et al. 2010; Prunier et al. 2011), Norway spruce populations are strongly differentiated for bud set [QST = 0.74 (R. Liesch, unpublished data)], a trait with high heritability [average h2 = 0. …