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      A molecular framework for grain number determination in barley

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          Abstract

          Flowering plants with indeterminate inflorescences often produce more floral structures than they require. We found that floral primordia initiations in barley ( Hordeum vulgare L.) are molecularly decoupled from their maturation into grains. While initiation is dominated by flowering-time genes, floral growth is specified by light signaling, chloroplast, and vascular developmental programs orchestrated by barley CCT MOTIF FAMILY 4 ( HvCMF4), which is expressed in the inflorescence vasculature. Consequently, mutations in HvCMF4 increase primordia death and pollination failure, mainly through reducing rachis greening and limiting plastidial energy supply to developing heterotrophic floral tissues. We propose that HvCMF4 is a sensory factor for light that acts in connection with the vascular-localized circadian clock to coordinate floral initiation and survival. Notably, stacking beneficial alleles for both primordia number and survival provides positive implications on grain production. Our findings provide insights into the molecular underpinnings of grain number determination in cereal crops.

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          Abstract

          Signaling from inflorescence vasculature via CCT MOTIF FAMILY4 determine distal floral fate and yield traits in barley.

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          Most cited references79

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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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            Trimmomatic: a flexible trimmer for Illumina sequence data

            Motivation: Although many next-generation sequencing (NGS) read preprocessing tools already existed, we could not find any tool or combination of tools that met our requirements in terms of flexibility, correct handling of paired-end data and high performance. We have developed Trimmomatic as a more flexible and efficient preprocessing tool, which could correctly handle paired-end data. Results: The value of NGS read preprocessing is demonstrated for both reference-based and reference-free tasks. Trimmomatic is shown to produce output that is at least competitive with, and in many cases superior to, that produced by other tools, in all scenarios tested. Availability and implementation: Trimmomatic is licensed under GPL V3. It is cross-platform (Java 1.5+ required) and available at http://www.usadellab.org/cms/index.php?page=trimmomatic Contact: usadel@bio1.rwth-aachen.de Supplementary information: Supplementary data are available at Bioinformatics online.
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              Fiji: an open-source platform for biological-image analysis.

              Fiji is a distribution of the popular open-source software ImageJ focused on biological-image analysis. Fiji uses modern software engineering practices to combine powerful software libraries with a broad range of scripting languages to enable rapid prototyping of image-processing algorithms. Fiji facilitates the transformation of new algorithms into ImageJ plugins that can be shared with end users through an integrated update system. We propose Fiji as a platform for productive collaboration between computer science and biology research communities.
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                Author and article information

                Contributors
                Role: ConceptualizationRole: Formal analysisRole: InvestigationRole: MethodologyRole: Project administrationRole: ResourcesRole: ValidationRole: VisualizationRole: Writing - original draftRole: Writing - review & editing
                Role: Formal analysisRole: InvestigationRole: MethodologyRole: Software
                Role: ConceptualizationRole: Formal analysisRole: InvestigationRole: MethodologyRole: ResourcesRole: ValidationRole: Writing - review & editing
                Role: Formal analysisRole: InvestigationRole: ValidationRole: Writing - review & editing
                Role: InvestigationRole: MethodologyRole: Project administrationRole: Writing - review & editing
                Role: InvestigationRole: MethodologyRole: ResourcesRole: Validation
                Role: MethodologyRole: Resources
                Role: Investigation
                Role: ConceptualizationRole: InvestigationRole: MethodologyRole: ResourcesRole: ValidationRole: Writing - original draft
                Role: InvestigationRole: MethodologyRole: ResourcesRole: SupervisionRole: ValidationRole: Writing - review & editing
                Role: MethodologyRole: Resources
                Role: InvestigationRole: MethodologyRole: Validation
                Role: Formal analysisRole: Investigation
                Role: MethodologyRole: ResourcesRole: SupervisionRole: Validation
                Role: InvestigationRole: ResourcesRole: Writing - review & editing
                Role: InvestigationRole: Resources
                Role: Formal analysisRole: ResourcesRole: SoftwareRole: SupervisionRole: Writing - review & editing
                Role: InvestigationRole: MethodologyRole: Resources
                Role: ConceptualizationRole: Funding acquisitionRole: MethodologyRole: Project administrationRole: SupervisionRole: ValidationRole: Writing - review & editing
                Journal
                Sci Adv
                Sci Adv
                sciadv
                advances
                Science Advances
                American Association for the Advancement of Science
                2375-2548
                March 2023
                03 March 2023
                : 9
                : 9
                : eadd0324
                Affiliations
                [ 1 ]Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, OT Gatersleben, 06466 Seeland, Germany.
                [ 2 ]Nordic Genetic Resource Center, Alnarp SE-23053, Sweden.
                [ 3 ]Center for Integrated Breeding Research (CiBreed), Georg-August-University, Göttingen, Germany.
                [ 4 ]German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Leipzig, Germany.
                [ 5 ]Martin Luther University Halle-Wittenberg, Faculty of Natural Sciences III, Institute of Agricultural and Nutritional Sciences, 06120 Halle, Germany.
                Author notes
                [†]

                Present address: Institute for Plant Genetics, Cluster of Excellence on Plant Sciences (CEPLAS), Heinrich Heine University, 40225 Düsseldorf, Germany.

                [‡]

                Present address: Centre for Plant Genome Engineering, Institute of Plant Biochemistry, Heinrich Heine University, 40225 Düsseldorf, Germany.

                [§]

                Deceased.

                [* ]Corresponding author. Email: huang@ 123456ipk-gatersleben.de (Y.H.); thor@ 123456ipk-gatersleben.de (T.S.)
                Author information
                https://orcid.org/0000-0002-7476-1350
                https://orcid.org/0000-0001-7707-8365
                https://orcid.org/0000-0001-6301-909X
                https://orcid.org/0000-0001-5891-6503
                https://orcid.org/0000-0002-7814-5475
                https://orcid.org/0000-0002-5539-3097
                https://orcid.org/0000-0002-7511-0779
                https://orcid.org/0000-0002-9537-0121
                https://orcid.org/0000-0001-7338-0946
                https://orcid.org/0000-0002-9712-3810
                https://orcid.org/0000-0001-7080-7983
                https://orcid.org/0000-0003-3011-8731
                https://orcid.org/0000-0002-4966-425X
                https://orcid.org/0000-0001-6373-6013
                https://orcid.org/0000-0002-5213-4030
                https://orcid.org/0000-0002-5267-0677
                Article
                add0324
                10.1126/sciadv.add0324
                9984178
                36867700
                0bb18433-babb-4a59-8756-aae2b20b9284
                Copyright © 2023 The Authors, some rights reserved; exclusive licensee American Association for the Advancement of Science. No claim to original U.S. Government Works. Distributed under a Creative Commons Attribution License 4.0 (CC BY).

                This is an open-access article distributed under the terms of the Creative Commons Attribution license, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

                History
                : 16 May 2022
                : 01 February 2023
                Funding
                Funded by: European Research Council (ERC);
                Award ID: ‘LUSH SPIKE’ (ERC-2015-CoG, agreement 681686)
                Funded by: HEISENBERG Program of the German Research Foundation;
                Award ID: SCHN 768/8-1 and SCHN 768/15-1
                Funded by: European Fund for Regional Development (EFRE) and the State of Saxony-Anhalt;
                Award ID: ZS/2018/09/94616
                Funded by: IPK;
                Award ID: Core budget
                Categories
                Research Article
                Biomedicine and Life Sciences
                SciAdv r-articles
                Plant Sciences
                Custom metadata
                Eunice Ann Alesin

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