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A reference-guided TILLING by amplicon-sequencing platform supports forward and reverse genetics in barley

Plant Communications 2022年第4期3卷 37-53页

作者： Congcong Jiang Miaomiao Lei Yu Guo Guangqi Gao Lijie Shi Yanlong Jin Yu Cai Axel Himmelbach Shenghui Zhou Qiang He Xuefeng Yao Jinhong Kan georg haberer Fengying Duan Lihui Li Jun Liu Jing Zhang Manuel Spannagl Chunming Liu Nils Stein Zongyun Feng Martin Mascher Ping Yang Institute of Crop Sciences Chinese Academy of Agricultural SciencesBeijingChina College of Agronomy Sichuan Agricultural UniversityChengduChina Leibniz Institute of Plant Genetics and Crop Plant Research(IPK) SeelandGermany Institute of Botany Chinese Academy of SciencesBeijingChina Plant Genome and Systems Biology(PGSB) Helmholtz Center MunichGerman Research Center for Environmental HealthNeuherbergGermany

Barley is a diploid species with a genome smaller than those of other members of the Triticeae tribe,making it an attractive model for genetic studies in Triticeae crops.The recent development of barley genomics has created a need for a high-throughput platform to identify genetically uniform mutants for gene function investigations.In this study,we report an ethyl methanesulfonate(EMS)-mutagenized population consisting of 8525M_(3) lines in the barley landrace“Hatiexi”(HTX),which we complement with a high-quality de novo assembly of a reference genome for this genotype.The mutation rate within the population ranged from 1.51 to 4.09 mutations per megabase,depending on the treatment dosage of EMS and the mutation discrimination platform used for genotype analysis.We implemented a three-dimensional DNA pooling strategy combined with multiplexed amplicon sequencing to create a highly efficient and cost-effective TILLING(targeting induced locus lesion in genomes)platform in barley.Mutations were successfully identified from 72 mixed amplicons within a DNA pool containing 64 individual mutants and from 56 mixed amplicons within a pool containing 144 individuals.We discovered abundant allelic mutants for dozens of genes,including the barley Green Revolution contributor gene Brassinosteroid insensitive 1(BRI1).As a proof of concept,we rapidly determined the causal gene responsible for a chlorotic mutant by following the MutMap strategy,demonstrating the value of this resource to support forward and reverse genetic studies in barley.

关键词： barley mutagenesis TILLING amplicon-seq genetics

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Meta-Analysis of Retrograde Signaling in Arabidopsis thaliana Reveals a Core Module of Genes Embedded in Complex Cellular Signaling Networks

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Molecular Plant 2014年第7期7卷 1167-1190页

作者： Christine GlaiBer georg haberer Iris Finkemeier Thomas Pfannschmidt Tatjana Kleine Dario Leister KarI-Josef Dietz Rainer Erich Haiusler Bernhard Grimm Klaus Franz Xaver Mayer Helmholtz Zentrum Munchen German Research Center for Environmental Health Institute of Bioinformatics and Systems Biology(IBIS) Ingolstadter Landstr. 1 D-85764 Neuherberg Germany Biozentrum der LMU Munchen Department of Biologie I-Botanik Groβhaderner Str. 2-4 D-82152 Planegg-Martinsried Germany Friedrich-Schiller-Universitat Jena Institut fur AIIgemeine Botanik und Pflanzenphysiologie Dornburger Str. 159 D-07743 JenaGermany Laboratoire de Physiologie Cellulaire Vegetale (LPCV) CEA/CNRS/UJF iRTSV CEA Grenoble 17 rue des Martyrs 38054 Grenoble cedex 9France Biochemistry and Physiology of Plants Faculty of Biology Bielefeld University Universit~tsstrai3e 25 D-33615 Bielefeld Germany University of Cologne Botanical Institute Cologne Biocenter Zu1picher Str. 47B D-50674 Cologne Germany Humboldt-Universitat zu Berlin Institut fur Biologie AG Pflanzenphysiologie Philippstrasse 13 D-10115 Berlin Germany

Plastid-to-nucleus signaling is essential for the coordination and adjustment of cellular metabolism in response to environmental and developmental cues of plant cells. A variety of operational retrograde signaling path- ways have been described that are thought to be triggered by reactive oxygen species, photosynthesis redox imbalance, tetrapyrrole intermediates, and other metabolic traits. Here we report a meta-analysis based on transcriptome and pro- tein interaction data. Comparing the output of these pathways reveals the commonalities and peculiarities stimulated by six different sources impinging on operational retrograde signaling. Our study provides novel insights into the interplay of these pathways, supporting the existence of an as-yet unknown core response module of genes being regulated under all conditions tested. Our analysis further highlights affiliated regulatory cis-elements and classifies abscisic acid and auxin-based signaling as secondary components involved in the response cascades following a plastidial signal. Our study provides a global analysis of structure and interfaces of different pathways involved in plastid-to-nucleus signaling and a new view on this complex cellular communication network.

关键词： retrograde signaling meta-analysis abscisic acid auxin.

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Fifteen Million Years of Evolution in the Oryza Genus Shows Extensive Gene Family Expansion

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Molecular Plant 2014年第4期7卷 642-656页

作者： Julie Jacquemin Jetty S.S. Ammiraju georg haberer Dean D. Billheimer Yeisoo Yu Liana C. Liu Luis F. Rivera Klaus Mayer Mingsheng Chen Rod A. Wing Arizona Genomics Institute School of Plant Sciences University of Arizona Tucson AZ 85721 USA MIPS/IBIS Helmholtz Center Munich Ingoistaedter Landstrasse 1 85764 Neuherberg Germany Arizona Statistics Consulting Laboratory School of Plant Sciences University of Arizona Tucson AZ 85721 USA State Key Laboratory of Plant Genomics Institute of Genetics and Developmental Biology Chinese Academy of Sciences 8eijing 100101 China

In analyzing gene families in the whole-genome sequences available for O. sativa （AA）, O. glaberrima （AA）, and O. brachyantha （FF）, we observed large size expansions in the AA genomes compared to FF genomes for the superfamilies F-box and NB-ARC, and five additional families： the Aspartic proteases, BTB/POZ proteins （BTB）, Glutaredoxins, Trypsin a-amylase inhibitor proteins, and Zf-Dof proteins. Their evolutionary dynamic was investigated to understand how and why such important size variations are observed between these closely related species. We show that expansions resulted from both amplification, largely by tandem duplications, and contraction by gene losses. For the F-box and NB-ARC gene families, the genes conserved in all species were under strong purifying selection while expanded orthologous genes were under more relaxed purifying selection. In F-box, NB-ARC, and BTB, the expanded groups were enriched in genes with little evidence of expression, in comparison with conserved groups. We also detected 87 loci under positive selection in the expanded groups. These results show that most of the duplicated copies in the expanded groups evolve neutrally after duplication because of functional redundancy but a fraction of these genes were preserved following neofunctionalization. Hence, the lineage-specific expansions observed between Oryza species were partly driven by directional selection.

关键词： gene family expansion Oryza tandem duplication duplicated gene evolution.

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