Abstract
BackgroundThe 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. Here we report the 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.ResultsBrachypodium distachyon individuals were sampled in nine locations with different ecologies and characterized with 16,697 SNPs. 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, 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. A linkage disequilibrium-corrected Bonferroni method was applied to filter associations. 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 showed that the distribution of some differentially sequenced regions was associated to environmental variation.ConclusionsWe 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 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.Electronic supplementary materialThe online version of this article (doi:10.1186/1471-2164-15-801) contains supplementary material, which is available to authorized users.
Highlights
The local environment plays a major role in the spatial distribution of plant populations
We performed our association approach by considering structuration in order to avoid overrepresentation of false positives. This was done both with a hierarchical structure and a principal component analysis (PCA) with Latent factor mixed models (LFMM) and compressed mixed linear model (CMLM), respectively, and we showed that the two different approaches yield similar results though differing in magnitude in terms of the statistical association found
We strongly support the application of generation sequencing approaches to landscape genomics as a fast and modular tool for the discovery of adaptive traits, in sequenced species
Summary
The local environment plays a major role in the spatial distribution of plant populations. 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. Domestication and breeding, have caused a severe reduction of crop diversity, whose extant genetic variation is much smaller than that of their wild relatives [10,11]. This limits the diversity in which to search for adaptation, hindering our ability to identify favourable allelic combinations. Natural populations might be used to study the relation between the genetic and ecologic diversity in search of adaptive traits. The environment can be considered as an unceasing breeder selecting for successful alleles, providing this approach potential downfalls in an agronomic perspective
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