Targeting environmental adaptation in the monocot model Brachypodium distachyon: a multi-faceted approach

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dc.authorid0000-0002-7644-5968
dc.authorid0000-0001-5703-8382
dc.authorid0000-0001-7574-0714
dc.authorscopusid57211803160
dc.authorscopusid11339149800
dc.authorscopusid57225437022
dc.authorscopusid6701733726
dc.authorscopusid6701433171
dc.authorwosidGianfranceschi, Luca/D-3166-2012
dc.authorwosidDell'Acqua, Matteo/B-4728-2017
dc.authorwosidZuccolo, Andrea/H-5636-2019
dc.authorwosidTuna, Metin/ABA-4295-2020
dc.contributor.authorDell'Acqua, Matteo
dc.contributor.authorZuccolo, Andrea
dc.contributor.authorTuna, Metin
dc.contributor.authorGianfranceschi, Luca
dc.contributor.authorPe, Mario Enrico
dc.date.accessioned2022-05-11T14:45:48Z
dc.date.available2022-05-11T14:45:48Z
dc.date.issued2014
dc.departmentFakülteler, Ziraat Fakültesi, Tarla Bitkileri Bölümü
dc.description.abstractBackground: 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.
dc.description.sponsorshipDoctoral Programme in Agrobiodiversity of Scuola Superiore Sant'Anna, Pisa, Italy
dc.description.sponsorshipThis work was fully supported by the Doctoral Programme in Agrobiodiversity of Scuola Superiore Sant'Anna, Pisa, Italy.
dc.identifier.doi10.1186/1471-2164-15-801
dc.identifier.issn1471-2164
dc.identifier.pmid25236859
dc.identifier.scopus2-s2.0-84908147775
dc.identifier.scopusqualityQ1
dc.identifier.urihttps://doi.org/10.1186/1471-2164-15-801
dc.identifier.urihttps://hdl.handle.net/20.500.11776/10150
dc.identifier.volume15
dc.identifier.wosWOS:000342098200001
dc.identifier.wosqualityQ1
dc.indekslendigikaynakWeb of Science
dc.indekslendigikaynakScopus
dc.indekslendigikaynakPubMed
dc.institutionauthorTuna, Metin
dc.language.isoen
dc.publisherBmc
dc.relation.ispartofBmc Genomics
dc.relation.publicationcategoryMakale - Uluslararası Hakemli Dergi - Kurum Öğretim Elemanıen_US
dc.rightsinfo:eu-repo/semantics/openAccess
dc.subjectLandscape genomics
dc.subjectBrachypodium distachyon
dc.subjectAdaptation
dc.subjectGenotyping by sequencing
dc.subjectPopulation genetics
dc.subjectGWAS
dc.subjectAssociation mapping
dc.subjectGenome-Wide Association
dc.subjectPine Pinus-Taeda
dc.subjectPopulation-Structure
dc.subjectLocal Adaptation
dc.subjectNatural Variation
dc.subjectGenetic-Structure
dc.subjectSpatial-Analysis
dc.subjectComplex Traits
dc.subjectSelection
dc.subjectLandscape
dc.titleTargeting environmental adaptation in the monocot model Brachypodium distachyon: a multi-faceted approach
dc.typeArticle

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