Past demography and local adaptation in forest trees : Insights from natural populations and breeding programs of Norway spruce

Abstract: Spatial changes in natural selection patterns can give rise to local adaptation and genetic differentiation between populations. Local adaptation for phenological traits is pronounced in many forest tree species. The Swedish breeding program was established from ‘plus’ trees selected across the country and can therefore be a very good source of information on local adaptation. In the present thesis, we estimated the genetic basis of local adaptation in two Eurasian spruce species Norway spruce (P. abies) and Siberian species (P. obovata) using large-scale whole-exome data and Sanger sequences from samples taken from the Swedish breeding program and from natural populations.To detect signals of local adaptation in Norway spruce (P. abies), we started by studying population genetic clustering and inferring the demographic history of the species. In addition to the already known three main domains in Norway spruce, we also found four genetic clusters created by admixture events between the aforementioned three main clusters. Demographic inferences indicated two recolonizations directions in Scandinavia: east to west (from central Russia and Siberia) and south to north (from Alpine and Carpathian), but also revealed repeated hybridization between P. abies and P. obovata and gene flow among clusters. We next estimated the genetic basis of local adaptation of three phenotypic traits (height, diameter and bud-burst) by multivariate analyses and genome-wide association studies. The results showed that geographical origin is a strong predictor of growth and phenology and trees of southern origins outcompeted local provenances. We further revealed that growth traits were highly polygenic and bud-burst somewhat less.Population genetic structure largely affects the detection of local adaptation. Therefore we further visualized the fine-scale map of population genetic structure through dense sampling of trees from the Swedish breeding program. Trees of Swedish origins were assigned into two main clusters with an admixture zone in central Sweden and the genetic contribution from P. obovata was detected in northern Sweden. A large number of SNPs were found to be associated with environmental variables and exhibited a stronger pattern of isolation-by-distance than random SNPs.Finally we tested for local adaptation in two well-defined candidate genes (FTL2 and GI) of phenology in P. obovata. Clinal variation in FTL2 gene expression, growth cessation, and allele frequency of FLT2 and GI were revealed in populations along Ob River, paralleling the ones in Norway spruce populations in Scandinavia and in Siberian spruce populations along the Yenisei River.