title: Targeting environmental adaptation in the monocot model Brachypodium distachyon: a multi-faceted approach.
abstract: BACKGROUND
  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. 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.
  
  
  RESULTS
  Brachypodium 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.
  
  
  CONCLUSIONS
  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 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.
authors.forename: Matteo
authors.initials: M
authors.lastname: Dell'Acqua
authors.forename: Andrea
authors.initials: A
authors.lastname: Zuccolo
authors.forename: Metin
authors.initials: M
authors.lastname: Tuna
authors.forename: Luca
authors.initials: L
authors.lastname: Gianfranceschi
authors.affiliation: Institute of Life Sciences, Scuola Superiore Sant'Anna, Pisa, Italy. marioenrico.pe@sssup.it.
authors.forename: Mario Enrico
authors.initials: ME
authors.lastname: Pè
mesh_terms: D000222:Adaptation, Physiological / Q000235:genetics*; D058431:Brachypodium / Q000235:genetics* / Q000502:physiology*; D004777:Environment; D017343:Genes, Plant / Q000235:genetics; D056426:Genetic Loci / Q000235:genetics; D023281:Genomics; D060005:Genotyping Techniques; D010802:Phylogeny; D020641:Polymorphism, Single Nucleotide; D017421:Sequence Analysis