ena-STUDY-SCUOLA SUPERIORE SANT'ANNA-02-09-2014-11:40:25:411-164
Targeting environmental adaptation in the monocot  model Brachypodium distachyon: a multi-faceted approach
The local environment plays a major role in the spatial distribution of plant populations. Natural plant populations have an extremely poor displacing capacity, so their continued survival in a given environment depends on how well they adapt to local pedoclimatic conditions. Genomic tools can be used to identify adaptive traits at a DNA level and to further our understanding of evolutionary processes. Such knowledge might be of great value from an agronomic perspective, as the environment might be seen as a breeder that selects for favourable alleles leading to resilience towards climate challenges. Targeting crop relatives in order to discover adaptive variation might then provide valuable information. Here we report the first use of genotyping-by-sequencing on local groups of the sequenced monocot model species Brachypodium distachyon. Exploiting population genetics, landscape genomics and genome wide association studies, we evaluate B. distachyon role as a natural probe for identifying genomic loci involved in environmental adaptation in a model for cereals. Brachypodium distachyon individuals were sampled in nine locations with different ecologies. They were then characterized with 16,697 SNPs derived from the sequencing of reduced genomic libraries. The observed pattern of genetic diversity was not ascribable to the spatial distance of samples. Variations in sequencing depth showed consistent patterns at 8,072 genomic bins, which were significantly enriched in transposable elements. We investigated the structuration and diversity of this collection of B. distachyon, and exploited climatic data to identify loci with adaptive significance through i) two different approaches for genome wide association analyses considering climatic variation, ii) an outlier loci approach, and iii) a canonical correlation analysis on differentially sequenced bins. We applied a linkage disequilibrium-corrected Bonferroni method to filter associations, and by this identified at set of SNPs significantly related to climate according to the different methods tested. The two association methods jointly identified a set of 15 genes significantly related to environmental adaptation. The outlier loci approach revealed that 5.7% of the loci analysed were under selection. The canonical correlation analysis on differentially sequenced regions showed for some a significant relation with the environmental variation of the sampling area.We show that the multi-faceted approach used here targeted different components of B. distachyon adaptive variation, and may lead to the discovery of genes related to environmental adaptation in natural populations. Its application to a model species with a fully-sequenced genome is a modular strategy that enables the stratification of biological material and thus improves our knowledge of the functional loci determining adaptation in near-crop species. When coupled with population genetics on the landscape and measures of genomic structuration, methods coming from genome wide association studies may lead to the exploitation of model species as natural probes to identify loci related to environmental adaptation.
The local environment plays a major role in the spatial distribution of plant populations. Natural plant populations have an extremely poor displacing capacity, so their continued survival in a given environment depends on how well they adapt to local pedoclimatic conditions. Genomic tools can be used to identify adaptive traits at a DNA level and to further our understanding of evolutionary processes. Such knowledge might be of great value from an agronomic perspective, as the environment might be seen as a breeder that selects for favourable alleles leading to resilience towards climate challenges. Targeting crop relatives in order to discover adaptive variation might then provide valuable information. Here we report the first use of genotyping-by-sequencing on local groups of the sequenced monocot model species Brachypodium distachyon. Exploiting population genetics, landscape genomics and genome wide association studies, we evaluate B. distachyon role as a natural probe for identifying genomic loci involved in environmental adaptation in a model for cereals. Brachypodium distachyon individuals were sampled in nine locations with different ecologies. They were then characterized with 16,697 SNPs derived from the sequencing of reduced genomic libraries. The observed pattern of genetic diversity was not ascribable to the spatial distance of samples. Variations in sequencing depth showed consistent patterns at 8,072 genomic bins, which were significantly enriched in transposable elements. We investigated the structuration and diversity of this collection of B. distachyon, and exploited climatic data to identify loci with adaptive significance through i) two different approaches for genome wide association analyses considering climatic variation, ii) an outlier loci approach, and iii) a canonical correlation analysis on differentially sequenced bins. We applied a linkage disequilibrium-corrected Bonferroni method to filter associations, and by this identified at set of SNPs significantly related to climate according to the different methods tested. The two association methods jointly identified a set of 15 genes significantly related to environmental adaptation. The outlier loci approach revealed that 5.7% of the loci analysed were under selection. The canonical correlation analysis on differentially sequenced regions showed for some a significant relation with the environmental variation of the sampling area.We show that the multi-faceted approach used here targeted different components of B. distachyon adaptive variation, and may lead to the discovery of genes related to environmental adaptation in natural populations. Its application to a model species with a fully-sequenced genome is a modular strategy that enables the stratification of biological material and thus improves our knowledge of the functional loci determining adaptation in near-crop species. When coupled with population genetics on the landscape and measures of genomic structuration, methods coming from genome wide association studies may lead to the exploitation of model species as natural probes to identify loci related to environmental adaptation.