Adaptive genetic structure in ecologically marginalpopulations of European Silver Fir (Abies alba MILL.) atthe south-western Mediterranean pre-Alps of France.

Coniferous trees are of major economic and ecologic importance. Yet, they are genomically poorly studied, because their long generation times, their high levels of heterozygosity and their huge genomes impede the access to conifer genomic resources. The European silver fir (Abies alba MILL) is widely distributed across diverse habitats in mountainous areas of temperate Europe. The species is of high value for forestry due to its high quality timber and its ecosystem functions such as erosion control and landslide prevention. Using next-generation sequencing the first silver fir transcriptome was sequenced and annotated. The annotation protocol lead to the identification of 460 candidate genes that are putatively involved in environmental stress resistance. Additionally, the transcriptomes of twelve more individuals were sequenced. Subsequent SNP detection produced on average 24580 SNPs per individual. For the SNPs that lie on the annotated candidate genes, a KASP genotyping assay was designed that allows for the fast and cost efficient genotyping of many A. alba trees. In the Mediterranean Basin, A. alba occurs in isolated and comparatively small populations. Recently, strong die-off events were observed in these populations, likely as a result of severe droughts. In the course of climate change, droughts are predicted to increase further in frequency and severity endangering the persistence of Mediterranean A. alba populations. Particularly these populations may, however, be of special value for the adaptive potential of the whole species since they may harbor genetic resources preadapted to relatively xeric environments. There is an ongoing debate about assisted migration, i.e. the transplantation of Mediterranean A. alba populations to more northern population in order to use them as donors of drought adapted alleles. To elucidate the question whether the idea of assisted migration is practical, knowledge about the state of local adaptation, its molecular basis and its environmental drivers is needed. Here, 376 individuals from high and low elevational populations which are located along a 170 km eastwest transect across four mountains in the south-western Mediterranean pre-Alps of France were investigated at 267 SNP loci distributed across 175 candidate genes. The methodological framework of landscape genetics was applied. Results of Bayesian cluster analysis showed that the dominant genetic pattern coincides with an east-west isolation-by-distance genetic structure, likely a result of post-glacial recolonization movement. Fst-outlier tests revealed 16 SNPs under divergent selection. Significant associations of allele frequencies of eight SNPs and winter drought were detected suggesting that this variable is a strong driver of local adaptation. Correlations tests of genetic distance of a subset of outlier loci and environmental distance demonstrated that isolation-by-environment occurs along altitude. Reanalysis of published common garden phenotypic data using Qst-Fst comparisons revealed adaptive divergence of bud flush and growth rate at the coldest and most humid site. The thesis illustrates a complex pattern of genetic structure in ecologically marginal populations that is shaped by demography and natural selection. It highlights that local adaptation is site specific in terms of both the genes under selection and the environmental drivers. Hence, whether a population is suitable to be the subject of assisted migration would have to be answered individually. Since this is highly impractical, the thesis states that in-situ conservation of marginal populations is the best option to ensure the capacity of evolutionary change in A. alba and to support the species’ ability to cope with the challenges of a rapidly changing climate

Canonical correlations reveal adaptive loci and phenotypic responses to climate in perennial ryegrass

Germplasm from perennial ryegrass (Lolium perenne L.) natural populations is useful for breeding because of its adaptation to a wide range of climates. Climate‐adaptive genes can be detected from associations between genotype, phenotype and climate but an integrated framework for the analysis of these three sources of information is lacking. We used two approaches to identify adaptive loci in perennial ryegrass and their effect on phenotypic traits. First, we combined Genome‐Environment Association (GEA) and GWAS analyses. Then, we implemented a new test based on a Canonical Correlation Analysis (CANCOR) to detect adaptive loci. Furthermore, we improved the previous perennial ryegrass gene set by de novo gene prediction and functional annotation of 39,967 genes. GEA‐GWAS revealed eight outlier loci associated with both environmental variables and phenotypic traits. CANCOR retrieved 633 outlier loci associated with two climatic gradients, characterized by cold‐dry winter versus mild‐wet winter and long rainy season versus long summer, and pointed out traits putatively conferring adaptation at the extremes of these gradients. Our CANCOR test also revealed the presence of both polygenic and oligogenic climatic adaptations. Our gene annotation revealed that 374 of the CANCOR outlier loci were positioned within or close to a gene. Co‐association networks of outlier loci revealed a potential utility of CANCOR for investigating the interaction of genes involved in polygenic adaptations. The CANCOR test provides an integrated framework to analyse adaptive genomic diversity and phenotypic responses to environmental selection pressures that could be used to facilitate the adaptation of plant species to climate change

Adaptive genetic structure in ecologically marginalpopulations of European Silver Fir (Abies alba MILL.) atthe south-western Mediterranean pre-Alps of France.

Coniferous trees are of major economic and ecologic importance. Yet, they are genomically poorly studied, because their long generation times, their high levels of heterozygosity and their huge genomes impede the access to conifer genomic resources. The European silver fir (Abies alba MILL) is widely distributed across diverse habitats in mountainous areas of temperate Europe. The species is of high value for forestry due to its high quality timber and its ecosystem functions such as erosion control and landslide prevention. Using next-generation sequencing the first silver fir transcriptome was sequenced and annotated. The annotation protocol lead to the identification of 460 candidate genes that are putatively involved in environmental stress resistance. Additionally, the transcriptomes of twelve more individuals were sequenced. Subsequent SNP detection produced on average 24580 SNPs per individual. For the SNPs that lie on the annotated candidate genes, a KASP genotyping assay was designed that allows for the fast and cost efficient genotyping of many A. alba trees. In the Mediterranean Basin, A. alba occurs in isolated and comparatively small populations. Recently, strong die-off events were observed in these populations, likely as a result of severe droughts. In the course of climate change, droughts are predicted to increase further in frequency and severity endangering the persistence of Mediterranean A. alba populations. Particularly these populations may, however, be of special value for the adaptive potential of the whole species since they may harbor genetic resources preadapted to relatively xeric environments. There is an ongoing debate about assisted migration, i.e. the transplantation of Mediterranean A. alba populations to more northern population in order to use them as donors of drought adapted alleles. To elucidate the question whether the idea of assisted migration is practical, knowledge about the state of local adaptation, its molecular basis and its environmental drivers is needed. Here, 376 individuals from high and low elevational populations which are located along a 170 km eastwest transect across four mountains in the south-western Mediterranean pre-Alps of France were investigated at 267 SNP loci distributed across 175 candidate genes. The methodological framework of landscape genetics was applied. Results of Bayesian cluster analysis showed that the dominant genetic pattern coincides with an east-west isolation-by-distance genetic structure, likely a result of post-glacial recolonization movement. Fst-outlier tests revealed 16 SNPs under divergent selection. Significant associations of allele frequencies of eight SNPs and winter drought were detected suggesting that this variable is a strong driver of local adaptation. Correlations tests of genetic distance of a subset of outlier loci and environmental distance demonstrated that isolation-by-environment occurs along altitude. Reanalysis of published common garden phenotypic data using Qst-Fst comparisons revealed adaptive divergence of bud flush and growth rate at the coldest and most humid site. The thesis illustrates a complex pattern of genetic structure in ecologically marginal populations that is shaped by demography and natural selection. It highlights that local adaptation is site specific in terms of both the genes under selection and the environmental drivers. Hence, whether a population is suitable to be the subject of assisted migration would have to be answered individually. Since this is highly impractical, the thesis states that in-situ conservation of marginal populations is the best option to ensure the capacity of evolutionary change in A. alba and to support the species’ ability to cope with the challenges of a rapidly changing climate