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      Landscape genomics reveal signatures of local adaptation in barley ( Hordeum vulgare L.)

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          Abstract

          Land plants are sessile organisms that cannot escape the adverse climatic conditions of a given environment. Hence, adaptation is one of the solutions to surviving in a challenging environment. This study was aimed at detecting adaptive loci in barley landraces that are affected by selection. To that end, a diverse population of barley landraces was analyzed using the genotyping by sequencing approach. Climatic data for altitude, rainfall and temperature were collected from 61 weather sites near the origin of selected landraces across Ethiopia. Population structure analysis revealed three groups whereas spatial analysis accounted significant similarities at shorter geographic distances (< 40 Km) among barley landraces. Partitioning the variance between climate variables and geographic distances indicated that climate variables accounted for most of the explainable genetic variation. Markers by climatic variables association analysis resulted in altogether 18 and 62 putative adaptive loci using Bayenv and latent factor mixed model (LFMM), respectively. Subsequent analysis of the associated SNPs revealed putative candidate genes for plant adaptation. This study highlights the presence of putative adaptive loci among barley landraces representing original gene pool of the farming communities.

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          Most cited references35

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          Heat tolerance in plants: An overview

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            Association mapping in structured populations.

            The use, in association studies, of the forthcoming dense genomewide collection of single-nucleotide polymorphisms (SNPs) has been heralded as a potential breakthrough in the study of the genetic basis of common complex disorders. A serious problem with association mapping is that population structure can lead to spurious associations between a candidate marker and a phenotype. One common solution has been to abandon case-control studies in favor of family-based tests of association, such as the transmission/disequilibrium test (TDT), but this comes at a considerable cost in the need to collect DNA from close relatives of affected individuals. In this article we describe a novel, statistically valid, method for case-control association studies in structured populations. Our method uses a set of unlinked genetic markers to infer details of population structure, and to estimate the ancestry of sampled individuals, before using this information to test for associations within subpopulations. It provides power comparable with the TDT in many settings and may substantially outperform it if there are conflicting associations in different subpopulations.
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              Ecology and the origin of species.

              The ecological hypothesis of speciation is that reproductive isolation evolves ultimately as a consequence of divergent natural selection on traits between environments. Ecological speciation is general and might occur in allopatry or sympatry, involve many agents of natural selection, and result from a combination of adaptive processes. The main difficulty of the ecological hypothesis has been the scarcity of examples from nature, but several potential cases have recently emerged. I review the mechanisms that give rise to new species by divergent selection, compare ecological speciation with its alternatives, summarize recent tests in nature, and highlight areas requiring research.
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                Author and article information

                Contributors
                Journal
                Front Plant Sci
                Front Plant Sci
                Front. Plant Sci.
                Frontiers in Plant Science
                Frontiers Media S.A.
                1664-462X
                02 October 2015
                2015
                : 6
                : 813
                Affiliations
                Department of Crop Genetics and Biotechnology, Institute of Crop Science and Resource Conservation, Rhenish Friedrich-Wilhelm University of Bonn Bonn, Germany
                Author notes

                Edited by: Stéphane Joost, Ecole Polytechnique Fédérale de Lausanne, Switzerland

                Reviewed by: Jacob A. Tennessen, Oregon State University, USA; Sevan Suni, Harvard University, USA; Torsten Günther, Uppsala University, Sweden

                *Correspondence: Ali A. Naz, Department of Crop Genetics and Biotechnology, Institute of Crop Science and Resource Conservation, Rhenish Friedrich-Wilhelm University of Bonn, Katzenburgweg 5, D-53115 Bonn, Germany a.naz@ 123456uni-bonn.de

                This article was submitted to Evolutionary and Population Genetics, a section of the journal Frontiers in Plant Science

                Article
                10.3389/fpls.2015.00813
                4591487
                26483825
                1bba65ff-bfc4-4cd3-af6f-bab58b63c963
                Copyright © 2015 Abebe, Naz and Léon.

                This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

                History
                : 29 June 2015
                : 17 September 2015
                Page count
                Figures: 7, Tables: 3, Equations: 0, References: 92, Pages: 17, Words: 11862
                Funding
                Funded by: Alexander von Humboldt-Stiftung 10.13039/100005156
                Categories
                Genetics
                Original Research

                Plant science & Botany
                landscape genomics,local adaptation,hordeum vulgare,genotyping by sequencing,spatial genetic structure,adaptive loci

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