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      Genomic mechanisms of climate adaptation in polyploid bioenergy switchgrass

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      1 , , 2 , 1 , 2 , 1 , 2 , 1 , 1 , 3 , 4 , 3 , 3 , 5 , 1 , 3 , 3 , 3 , 1 , 2 , 6 , 7 , 8 , 3 , 9 , 10 , 11 , 1 , 9 , 12 , 2 , 13 , 1 , 14 , 15 , 1 , 3 , 16 , 17 , 1 , 2 , 1 , 3 , 3 , 3 , 2 , 16 , 2 , 18 , 19 , 20 , 21 , 22 , 23 , 21 , 24 , 25 , 26 , 27 , 16 , 28 , 16 , 8 , 29 , 30 , 31 , 32 , 33 , 9 , 10 , 11 , 34 , 7 , 35 , 3 , 4 , 36 , 37 , 1 , 2 , , 1 , 3 ,
      Nature
      Nature Publishing Group UK
      Evolutionary genetics, Genetic variation, Genome evolution, Bioalcohols, Plant breeding

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          Abstract

          Long-term climate change and periodic environmental extremes threaten food and fuel security 1 and global crop productivity 24 . Although molecular and adaptive breeding strategies can buffer the effects of climatic stress and improve crop resilience 5 , these approaches require sufficient knowledge of the genes that underlie productivity and adaptation 6 —knowledge that has been limited to a small number of well-studied model systems. Here we present the assembly and annotation of the large and complex genome of the polyploid bioenergy crop switchgrass ( Panicum virgatum). Analysis of biomass and survival among 732 resequenced genotypes, which were grown across 10 common gardens that span 1,800 km of latitude, jointly revealed extensive genomic evidence of climate adaptation. Climate–gene–biomass associations were abundant but varied considerably among deeply diverged gene pools. Furthermore, we found that gene flow accelerated climate adaptation during the postglacial colonization of northern habitats through introgression of alleles from a pre-adapted northern gene pool. The polyploid nature of switchgrass also enhanced adaptive potential through the fractionation of gene function, as there was an increased level of heritable genetic diversity on the nondominant subgenome. In addition to investigating patterns of climate adaptation, the genome resources and gene–trait associations developed here provide breeders with the necessary tools to increase switchgrass yield for the sustainable production of bioenergy.

          Abstract

          The genome of the biofuel crop switchgrass ( Panicum virgatum) reveals climate–gene–biomass associations that underlie adaptation in nature and will facilitate improvements of the yield of this crop for bioenergy production.

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          Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2

          In comparative high-throughput sequencing assays, a fundamental task is the analysis of count data, such as read counts per gene in RNA-seq, for evidence of systematic changes across experimental conditions. Small replicate numbers, discreteness, large dynamic range and the presence of outliers require a suitable statistical approach. We present DESeq2, a method for differential analysis of count data, using shrinkage estimation for dispersions and fold changes to improve stability and interpretability of estimates. This enables a more quantitative analysis focused on the strength rather than the mere presence of differential expression. The DESeq2 package is available at http://www.bioconductor.org/packages/release/bioc/html/DESeq2.html. Electronic supplementary material The online version of this article (doi:10.1186/s13059-014-0550-8) contains supplementary material, which is available to authorized users.
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            The Sequence Alignment/Map format and SAMtools

            Summary: The Sequence Alignment/Map (SAM) format is a generic alignment format for storing read alignments against reference sequences, supporting short and long reads (up to 128 Mbp) produced by different sequencing platforms. It is flexible in style, compact in size, efficient in random access and is the format in which alignments from the 1000 Genomes Project are released. SAMtools implements various utilities for post-processing alignments in the SAM format, such as indexing, variant caller and alignment viewer, and thus provides universal tools for processing read alignments. Availability: http://samtools.sourceforge.net Contact: rd@sanger.ac.uk
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              Fitting Linear Mixed-Effects Models Usinglme4

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                Author and article information

                Contributors
                jlovell@hudsonalpha.org
                tjuenger@mail.utexas.edu
                jschmutz@hudsonalpha.org
                Journal
                Nature
                Nature
                Nature
                Nature Publishing Group UK (London )
                0028-0836
                1476-4687
                27 January 2021
                27 January 2021
                2021
                : 590
                : 7846
                : 438-444
                Affiliations
                [1 ]GRID grid.417691.c, ISNI 0000 0004 0408 3720, Genome Sequencing Center, , HudsonAlpha Institute for Biotechnology, ; Huntsville, AL USA
                [2 ]GRID grid.89336.37, ISNI 0000 0004 1936 9924, Department of Integrative Biology, , University of Texas at Austin, ; Austin, TX USA
                [3 ]GRID grid.184769.5, ISNI 0000 0001 2231 4551, Department of Energy Joint Genome Institute, , Lawrence Berkeley National Laboratory, ; Berkeley, CA USA
                [4 ]GRID grid.47840.3f, ISNI 0000 0001 2181 7878, Department of Molecular and Cell Biology, , University of California, Berkeley, ; Berkeley, CA USA
                [5 ]GRID grid.430387.b, ISNI 0000 0004 1936 8796, Department of Plant Biology, , Rutgers University, ; New Brunswick, NJ USA
                [6 ]Plant Genetic Resources Conservation Unit, USDA-ARS, Griffin, GA USA
                [7 ]GRID grid.17088.36, ISNI 0000 0001 2150 1785, Department of Plant Biology, , Michigan State University, ; East Lansing, MI USA
                [8 ]GRID grid.134563.6, ISNI 0000 0001 2168 186X, Arizona Genomics Institute, , University of Arizona, ; Tucson, AZ USA
                [9 ]GRID grid.213876.9, ISNI 0000 0004 1936 738X, Institute of Plant Breeding, Genetics and Genomics, , University of Georgia, ; Athens, GA USA
                [10 ]GRID grid.213876.9, ISNI 0000 0004 1936 738X, Department of Crop and Soil Sciences, , University of Georgia, ; Athens, GA USA
                [11 ]GRID grid.213876.9, ISNI 0000 0004 1936 738X, Department of Plant Biology, , University of Georgia, ; Athens, GA USA
                [12 ]GRID grid.26090.3d, ISNI 0000 0001 0665 0280, Department of Plant and Environmental Sciences, , Clemson University, ; Clemson, SC USA
                [13 ]GRID grid.259676.9, ISNI 0000 0001 2214 9920, Department of Biological Sciences, , Marshall University, ; Huntington, WV USA
                [14 ]GRID grid.10706.30, ISNI 0000 0004 0498 924X, School of Biotechnology, , Jawaharlal Nehru University, ; New Delhi, India
                [15 ]GRID grid.10706.30, ISNI 0000 0004 0498 924X, School of Computational and Integrative Sciences, , Jawaharlal Nehru University, ; New Delhi, India
                [16 ]GRID grid.419447.b, ISNI 0000 0004 0370 5663, Noble Research Institute LLC, ; Ardmore, OK USA
                [17 ]GRID grid.24434.35, ISNI 0000 0004 1937 0060, Department of Agronomy and Horticulture, , University of Nebraska, ; Lincoln, NE USA
                [18 ]GRID grid.263791.8, ISNI 0000 0001 2167 853X, Department of Agronomy, Horticulture and Plant Science, , South Dakota State University, ; Brookings, SD USA
                [19 ]GRID grid.463419.d, ISNI 0000 0001 0946 3608, Grassland, Soil and Water Research Laboratory, USDA-ARS, ; Temple, TX USA
                [20 ]GRID grid.134936.a, ISNI 0000 0001 2162 3504, Division of Plant Sciences, , University of Missouri, ; Columbia, MO USA
                [21 ]GRID grid.187073.a, ISNI 0000 0001 1939 4845, Environmental Science Division, , Argonne National Laboratory, ; Lemont, IL USA
                [22 ]GRID grid.482950.2, ISNI 0000 0001 1942 3888, Kika de la Garza Plant Materials Center, , USDA-NRCS, ; Kingsville, TX USA
                [23 ]Plant Breeding Department, Antonio Narro Agrarian Autonomous University, Saltillo, Mexico
                [24 ]GRID grid.463419.d, ISNI 0000 0001 0946 3608, Wheat, Sorghum, and Forage Research Unit, USDA-ARS, ; Lincoln, NE USA
                [25 ]GRID grid.264756.4, ISNI 0000 0004 4687 2082, Texas A&M AgriLife Research and Extension Center, , Texas A&M University, ; Overton, TX USA
                [26 ]GRID grid.27860.3b, ISNI 0000 0004 1936 9684, Department of Plant Pathology and the Genome Center, , University of California, Davis, ; Davis, CA USA
                [27 ]GRID grid.451372.6, ISNI 0000 0004 0407 8980, Joint BioEnergy Institute, ; Emeryville, CA USA
                [28 ]GRID grid.507310.0, Western Regional Research Center, USDA-ARS, ; Albany, CA USA
                [29 ]GRID grid.65519.3e, ISNI 0000 0001 0721 7331, Department of Plant and Soil Sciences, , Oklahoma State University, ; Stillwater, OK USA
                [30 ]GRID grid.266900.b, ISNI 0000 0004 0447 0018, Department of Microbiology and Plant Biology, , University of Oklahoma, ; Norman, OK USA
                [31 ]GRID grid.30064.31, ISNI 0000 0001 2157 6568, Institute of Biological Chemistry, , Washington State University, ; Pullman, WA USA
                [32 ]GRID grid.507311.1, US Dairy Forage Research Center, USDA-ARS, ; Madison, WI USA
                [33 ]GRID grid.28803.31, ISNI 0000 0001 0701 8607, DOE Great Lakes Bioenergy Research Center, , University of Wisconsin, ; Madison, WI USA
                [34 ]DOE Center for Bioenergy Innovation, Oak Ridge, TN USA
                [35 ]GRID grid.17088.36, ISNI 0000 0001 2150 1785, DOE Great Lakes Bioenergy Research Center, , Michigan State University, ; East Lansing, MI USA
                [36 ]Center for Advanced Bioenergy and Bioproducts Innovation, Berkeley, CA USA
                [37 ]GRID grid.499295.a, Chan-Zuckerberg Biohub, ; San Francisco, CA USA
                Author information
                http://orcid.org/0000-0002-8938-1166
                http://orcid.org/0000-0002-7943-3997
                http://orcid.org/0000-0002-8557-5086
                http://orcid.org/0000-0001-7336-7012
                http://orcid.org/0000-0002-4336-8994
                http://orcid.org/0000-0002-6435-6140
                http://orcid.org/0000-0002-3092-3629
                http://orcid.org/0000-0001-5681-9662
                http://orcid.org/0000-0002-2780-4274
                http://orcid.org/0000-0003-2689-7410
                http://orcid.org/0000-0002-9983-5707
                http://orcid.org/0000-0003-0825-6855
                http://orcid.org/0000-0001-7069-4560
                http://orcid.org/0000-0002-4107-1345
                http://orcid.org/0000-0001-9850-0828
                http://orcid.org/0000-0001-6633-6226
                http://orcid.org/0000-0003-0802-6881
                http://orcid.org/0000-0001-8610-7551
                http://orcid.org/0000-0002-8704-2224
                http://orcid.org/0000-0002-8356-8325
                http://orcid.org/0000-0001-9550-9288
                http://orcid.org/0000-0001-8062-9172
                Article
                3127
                10.1038/s41586-020-03127-1
                7886653
                33505029
                43424226-d6c4-4c2c-b57e-0c4ff0d91fc7
                © The Author(s) 2021

                Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

                History
                : 1 July 2020
                : 16 December 2020
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                © The Author(s), under exclusive licence to Springer Nature Limited 2021

                Uncategorized
                evolutionary genetics,genetic variation,genome evolution,bioalcohols,plant breeding
                Uncategorized
                evolutionary genetics, genetic variation, genome evolution, bioalcohols, plant breeding

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