Data from: Disentangling the roles of history and local selection in shaping clinal variation of allele frequencies and gene expression in Norway spruce (Picea abies)

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 are 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.

解析本地适应的遗传基础极具挑战，因为参与其建立与维持的各类相互拮抗的进化动力之间存在微妙的制衡关系。厘清这类研究难题的一个有效体系是适应性性状的渐变群（cline）。本研究针对沿北纬47°至68°纬度梯度分布的18个挪威云杉（Picea abies）种群，分析了其芽封顶这一高度可遗传且具适应性的性状的遗传与表型变异。我们利用其中5个种群的子集验证了芽封顶的变异呈现显著的渐变群模式。我们针对两类单核苷酸多态性（single nucleotide polymorphism, SNP）展开基因分型分析：137个SNP取自18个推测参与芽封顶调控的候选基因，另有308个对照SNP取自264个随机选取的基因，以此解析种群遗传结构特征及其与环境因子的关联。结果显示，种群遗传分化程度较低（遗传分化系数FST=0.05），但斯堪的纳维亚半岛的种群间呈现出显著的纬度分布模式。因此，观测到的部分渐变群变异可归因于种群动态过程。在校正种群遗传结构的影响后，候选基因内的SNP与纬度的关联呈现富集现象。另有29个SNP在FST分析中被鉴定为异常分化位点。候选基因（即PaGI、PaPhyP、PaPhyN、PaPRR7及PaFTL2）内的SNP存在渐变群变异富集现象，这表明18个种群所经历的本地选择，以及其近期祖先种群所承受的选择压力，共同塑造了本次观测到的渐变群模式。通过表达分析对上述基因进行验证的结果显示，PaFTL2的表达水平与纬度呈显著关联，从而证实了该基因在植物物候调控中发挥的核心作用。