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The Setaria viridis genome and diversity panel enables discovery of a novel domestication gene

https://doi.org/10.1101/744557
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Outgoing claims: the papers this work cites, builds on, or argues with.

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Inflorescence Abscission Zones in Grasses: Diversity and Genetic Regulation
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Agrobacterium tumefaciens-Mediated Transformation of Setaria viridis
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Flowering plants, Eudicots : Malpighiales
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Genomics of Plant Genetic Resources
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Maintaining Food Value of Wild Rice (Zizania palustris L.) Using Comparative Genomics
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Traditional maintenance and multiplication of foxtail millet (Setaria italica (L.) P. Beauv.) landraces in China
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Genetic dissection of seed shattering, agronomic, and color traits in American wildrice (Zizania palustris var. interior L.) with a comparative map
inferredcites →https://doi.org/10.1007/s001220050705openalex-snapshot
Construction of RFLP-based maps of foxtail millet, Setaria italica (L.) P. Beauv.
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Assessment of genetic relationships between Setaria italica and its wild relative S. viridis using AFLP markers
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Millets across Eurasia: chronology and context of early records of the genera Panicum and Setaria from archaeological sites in the Old World
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The lignin toolbox of the model grass Setaria viridis
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To Have and to Hold
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Genotype Imputation with Millions of Reference Samples
inferredcites →https://doi.org/10.1016/j.plantsci.2016.06.011openalex-snapshot
Effects of abiotic stress on physiological plasticity and water use of Setaria viridis (L.)
inferredcites →https://doi.org/10.1016/j.plantsci.2019.110329openalex-snapshot
Setaria viridis as a model for translational genetic studies of jasmonic acid-related insect defenses in Zea mays
inferredcites →https://doi.org/10.1016/s0022-2836(05)80360-2openalex-snapshot
Basic Local Alignment Search Tool
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Statistical methods for detecting molecular adaptation
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The hitch-hiking effect of a favourable gene
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Sub1A is an ethylene-response-factor-like gene that confers submergence tolerance to rice
inferredcites →https://doi.org/10.1038/nbt.2196openalex-snapshot
Reference genome sequence of the model plant Setaria
inferredcites →https://doi.org/10.1038/nbt1173openalex-snapshot
Erect leaves caused by brassinosteroid deficiency increase biomass production and grain yield in rice
inferredcites →https://doi.org/10.1038/ng.169openalex-snapshot
Deletion in a gene associated with grain size increased yields during rice domestication
inferredcites →https://doi.org/10.1038/ng.2281openalex-snapshot
Parallel domestication of the Shattering1 genes in cereals
inferredcites →https://doi.org/10.1038/ng.2309openalex-snapshot
Comparative population genomics of maize domestication and improvement
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Genome-wide efficient mixed-model analysis for association studies
inferredcites →https://doi.org/10.1038/ng.2673openalex-snapshot
A haplotype map of genomic variations and genome-wide association studies of agronomic traits in foxtail millet (Setaria italica)
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Genome-wide association study of leaf architecture in the maize nested association mapping population
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Nonhybrid, finished microbial genome assemblies from long-read SMRT sequencing data
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Efficient multivariate linear mixed model algorithms for genome-wide association studies
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MECAT: fast mapping, error correction, and de novo assembly for single-molecule sequencing reads
inferredcites →https://doi.org/10.1038/nplants.2017.54openalex-snapshot
Sparse panicle1 is required for inflorescence development in Setaria viridis and maize
inferredcites →https://doi.org/10.1038/s41467-017-02292-8openalex-snapshot
Extensive gene content variation in the Brachypodium distachyon pan-genome correlates with population structure
inferredcites →https://doi.org/10.1038/s41467-018-07669-xopenalex-snapshot
The genomic landscape of molecular responses to natural drought stress in Panicum hallii
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Accurate detection of complex structural variations using single-molecule sequencing
inferredcites →https://doi.org/10.1038/s42003-019-0561-9openalex-snapshot
Overexpression of the Rieske FeS protein of the Cytochrome b6f complex increases C4 photosynthesis in Setaria viridis
inferredcites →https://doi.org/10.1039/c8ta04218gopenalex-snapshot
A biomimetic Setaria viridis -inspired electrode with polyaniline nanowire arrays aligned on MoO 3 @polypyrrole core–shell nanobelts
inferredcites →https://doi.org/10.1071/fp17322openalex-snapshot
High-throughput chlorophyll fluorescence screening of Setaria viridis for mutants with altered CO2 compensation points
inferredcites →https://doi.org/10.1073/pnas.201394398openalex-snapshot
Structure of linkage disequilibrium and phenotypic associations in the maize genome
inferredcites →https://doi.org/10.1073/pnas.93.19.10274openalex-snapshot
Substitution rate comparisons between grasses and palms: synonymous rate differences at the nuclear gene Adh parallel rate differences at the plastid gene rbcL.
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Rapid and Accurate Haplotype Phasing and Missing-Data Inference for Whole-Genome Association Studies By Use of Localized Haplotype Clustering
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A Phylogeny ofSetaria(Poaceae, Panicoideae, Paniceae) and Related Genera Based on the Chloroplast GenendhF
inferredcites →https://doi.org/10.1093/aob/mcm048openalex-snapshot
Contrasting Patterns in Crop Domestication and Domestication Rates: Recent Archaeobotanical Insights from the Old World
inferredcites →https://doi.org/10.1093/aob/mcx217openalex-snapshot
Anatomy and ultrastructure of embryonic leaves of the C4 species Setaria viridis
inferredcites →https://doi.org/10.1093/bioinformatics/18.2.337openalex-snapshot
Generating samples under a Wright–Fisher neutral model of genetic variation
inferredcites →https://doi.org/10.1093/bioinformatics/btl140openalex-snapshot
Improved scoring of functional groups from gene expression data by decorrelating GO graph structure
inferredcites →https://doi.org/10.1093/bioinformatics/btm039openalex-snapshot
Gepard: a rapid and sensitive tool for creating dotplots on genome scale
inferredcites →https://doi.org/10.1093/bioinformatics/btp324openalex-snapshot
Fast and accurate short read alignment with Burrows–Wheeler transform
inferredcites →https://doi.org/10.1093/bioinformatics/btp352openalex-snapshot
The Sequence Alignment/Map format and SAMtools
inferredcites →https://doi.org/10.1093/bioinformatics/btr330openalex-snapshot
The variant call format and VCFtools
inferredcites →https://doi.org/10.1093/bioinformatics/btr521openalex-snapshot
adegenet 1.3-1 : new tools for the analysis of genome-wide SNP data
inferredcites →https://doi.org/10.1093/bioinformatics/btu033openalex-snapshot
RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies
inferredcites →https://doi.org/10.1093/bioinformatics/btv195openalex-snapshot
PROVEAN web server: a tool to predict the functional effect of amino acid substitutions and indels
inferredcites →https://doi.org/10.1093/gbe/evs009openalex-snapshot
Genome-Wide Analysis of Syntenic Gene Deletion in the Grasses
inferredcites →https://doi.org/10.1093/genetics/123.3.585openalex-snapshot
Statistical method for testing the neutral mutation hypothesis by DNA polymorphism.
inferredcites →https://doi.org/10.1093/jxb/erw357openalex-snapshot
Effects of reduced carbonic anhydrase activity on CO2assimilation rates inSetaria viridis: a transgenic analysis
inferredcites →https://doi.org/10.1093/jxb/erz495openalex-snapshot
Sugar sensing responses to low and high light in leaves of the C4 model grass Setaria viridis
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hapbin: An Efficient Program for Performing Haplotype-Based Scans for Positive Selection in Large Genomic Datasets: Fig. 1.
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BUSCO Applications from Quality Assessments to Gene Prediction and Phylogenomics
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KEGG: Kyoto Encyclopedia of Genes and Genomes
inferredcites →https://doi.org/10.1093/nar/28.1.27openalex-snapshot
KEGG: Kyoto Encyclopedia of Genes and Genomes
inferredcites →https://doi.org/10.1093/nar/gkg770openalex-snapshot
Improving the Arabidopsis genome annotation using maximal transcript alignment assemblies
inferredcites →https://doi.org/10.1093/nar/gkn668openalex-snapshot
Genomics of bacteria and archaea: the emerging dynamic view of the prokaryotic world
inferredcites →https://doi.org/10.1093/nar/gkr1293openalex-snapshot
MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity
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InParanoid 8: orthology analysis between 273 proteomes, mostly eukaryotic
inferredcites →https://doi.org/10.1094/mpmi-06-19-0174-ropenalex-snapshot
In-Situ Metabolomic Analysis of Setaria viridis Roots Colonized by Beneficial Endophytic Bacteria
inferredcites →https://doi.org/10.1094/pbiomes-04-19-0023-ropenalex-snapshot
Heritability and Functional Importance of the Setaria viridis Bacterial Seed Microbiome
inferredcites →https://doi.org/10.1101/642041openalex-snapshot
Characterizing the serotonin biosynthesis pathway upon aphid infestation in Setaria viridis leaves
inferredcites →https://doi.org/10.1101/gad.12.2.208openalex-snapshot
The maize geneliguleless2 encodes a basic leucine zipper protein involved in the establishment of the leaf blade–sheath boundary
inferredcites →https://doi.org/10.1101/gr.094052.109openalex-snapshot
Fast model-based estimation of ancestry in unrelated individuals
inferredcites →https://doi.org/10.1101/gr.107524.110openalex-snapshot
The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data
inferredcites →https://doi.org/10.1101/gr.129684.111openalex-snapshot
VarScan 2: Somatic mutation and copy number alteration discovery in cancer by exome sequencing
inferredcites →https://doi.org/10.1101/gr.229202openalex-snapshot
BLAT —The BLAST -Like Alignment Tool
inferredcites →https://doi.org/10.1104/pp.108.129627openalex-snapshot
Foxtail Millet: A Sequence-Driven Grass Model System
inferredcites →https://doi.org/10.1104/pp.18.00146openalex-snapshot
Components of Water Use Efficiency Have Unique Genetic Signatures in the Model C 4 Grass Setaria
inferredcites →https://doi.org/10.1105/tpc.110.075309openalex-snapshot
Setaria viridis: A Model for C4 Photosynthesis
inferredcites →https://doi.org/10.1105/tpc.111.094383openalex-snapshot
Genetic Control of Seed Shattering in Rice by the APETALA2 Transcription Factor SHATTERING ABORTION1
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A Multipurpose Toolkit to Enable Advanced Genome Engineering in Plants
inferredcites →https://doi.org/10.1105/tpc.17.00816openalex-snapshot
Brassinosteroids Modulate Meristem Fate and Differentiation of Unique Inflorescence Morphology in Setaria viridis
inferredcites →https://doi.org/10.1111/jse.12262openalex-snapshot
A worldwide phylogenetic classification of the Poaceae (Gramineae) II: An update and a comparison of two 2015 classifications
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Take up the challenge! Opportunities for evolution research from resolving conflict in integrative taxonomy
inferredcites →https://doi.org/10.1111/mec.12907openalex-snapshot
Population genetics of Setaria viridis, a new model system
inferredcites →https://doi.org/10.1111/nph.14970openalex-snapshot
Suppression of a single BAHD gene in Setaria viridis causes large, stable decreases in cell wall feruloylation and increases biomass digestibility
inferredcites →https://doi.org/10.1111/nph.16087openalex-snapshot
Divergent gene expression networks underlie morphological diversity of abscission zones in grasses
inferredcites →https://doi.org/10.1126/science.1072831openalex-snapshot
Plant Development: Regulation by Protein Degradation
inferredcites →https://doi.org/10.1126/science.1123604openalex-snapshot
Rice Domestication by Reducing Shattering
inferredcites →https://doi.org/10.1126/science.1124635openalex-snapshot
How Fast Was Wild Wheat Domesticated?
inferredcites →https://doi.org/10.1126/science.1126410openalex-snapshot
An SNP Caused Loss of Seed Shattering During Rice Domestication
inferredcites →https://doi.org/10.1128/aem.02411-13openalex-snapshot
GET_HOMOLOGUES, a Versatile Software Package for Scalable and Robust Microbial Pangenome Analysis
inferredcites →https://doi.org/10.1186/1471-2156-11-94openalex-snapshot
Discriminant analysis of principal components: a new method for the analysis of genetically structured populations
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Estimating variation within the genes and inferring the phylogeny of 186 sequenced diverse Escherichia coli genomes
inferredcites →https://doi.org/10.1186/s12859-019-2941-zopenalex-snapshot
A mass and charge balanced metabolic model of Setaria viridis revealed mechanisms of proton balancing in C4 plants
inferredcites →https://doi.org/10.1186/s13068-016-0457-6openalex-snapshot
A developing Setaria viridis internode: an experimental system for the study of biomass generation in a C4 model species
inferredcites →https://doi.org/10.1186/s13742-015-0047-8openalex-snapshot
Second-generation PLINK: rising to the challenge of larger and richer datasets
inferredcites →https://doi.org/10.1371/journal.pbio.0040072openalex-snapshot
A Map of Recent Positive Selection in the Human Genome
inferredcites →https://doi.org/10.1534/genetics.108.095034openalex-snapshot
Two Adjacent Nucleotide-Binding Site–Leucine-Rich Repeat Class Genes Are Required to Confer Pikm-Specific Rice Blast Resistance
inferredcites →https://doi.org/10.1534/genetics.114.164350openalex-snapshot
fastSTRUCTURE: Variational Inference of Population Structure in Large SNP Data Sets
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dbscan: Fast Density-Based Clustering with R
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Field Investigations of the Relationships of Leaf Angle in Corn (Zea mays L.) to Grain Yield and Apparent Photosynthesis1
inferredcites →https://doi.org/10.2307/3298585openalex-snapshot
Phylogeny and Subfamilial Classification of the Grasses (Poaceae)
inferredcites →https://doi.org/10.2307/623100openalex-snapshot
Foraging and Farming: The Evolution of Plant Exploitation
inferredcites →https://doi.org/10.3389/fpls.2017.00865openalex-snapshot
Overexpression of BdMATE Gene Improves Aluminum Tolerance in Setaria viridis
inferredcites →https://doi.org/10.3389/fpls.2018.00918openalex-snapshot
QTL Mapping Combined With Comparative Analyses Identified Candidate Genes for Reduced Shattering in Setaria italica
inferredcites →https://doi.org/10.3389/fpls.2018.01309openalex-snapshot
A Dynamic Co-expression Map of Early Inflorescence Development in Setaria viridis Provides a Resource for Gene Discovery and Comparative Genomics
inferredcites →https://doi.org/10.3732/ajb.1300428openalex-snapshot
Morphological, phylogenetic, and ecological diversity of the new model species Setaria viridis (Poaceae: Paniceae) and its close relatives
inferredcites →https://doi.org/10.3732/ajb.1400186openalex-snapshot
Morphological diversity and genetic regulation of inflorescence abscission zones in grasses
inferredcites →https://doi.org/10.3732/ajb.1500499openalex-snapshot
Abscission zone development in Setaria viridis and its domesticated relative, Setaria italica
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Methods for Performing Crosses in Setaria viridis, a New Model System for the Grasses
inferredcites →https://doi.org/10.4161/fly.19695openalex-snapshot
A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff
inferredcites →https://doi.org/10.4324/9781003060765-2openalex-snapshot
An evolutionary continuum of people–plant interaction
inferredcites →https://doi.org/10.48550/arxiv.1608.01031openalex-snapshot
Meraculous2: fast accurate short-read assembly of large polymorphic genomes
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Potential role of biotechnology tools for genetic improvement of lost crops of Africa: the case of fonio (Digitaria exilis and Digitaria iburua)
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Aligning sequence reads, clone sequences and assembly con*gs with BWA-MEM

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

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Gramene: A Resource for Comparative Analysis of Plants Genomes and Pathways
inferred← citeshttps://doi.org/10.1007/978-3-030-75875-2_7openalex-snapshot
Genomic Designing for Abiotic Stress Tolerance in Foxtail Millet (Setaria Italica L.)
inferred← citeshttps://doi.org/10.1007/978-3-030-75879-0_7openalex-snapshot
Genomic Designing for Biotic Stress Tolerance in Foxtail Millet (Setaria italica L.)
inferred← citeshttps://doi.org/10.1007/978-981-99-5890-0_7openalex-snapshot
Genome Editing and Opportunities for Trait Improvement in Pearl Millet
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Orphan Crops and their Wild Relatives in the Genomic Era
inferred← citeshttps://doi.org/10.1093/plphys/kiab169openalex-snapshot
The SvFUL2 transcription factor is required for inflorescence determinacy and timely flowering in Setaria viridis
inferred← citeshttps://doi.org/10.1093/plphys/kiad220openalex-snapshot
DNA methylation signatures of duplicate gene evolution in angiosperms
inferred← citeshttps://doi.org/10.1111/tpj.14949openalex-snapshot
Optimization of multiplexed CRISPR/Cas9 system for highly efficient genome editing in Setaria viridis
inferred← citeshttps://doi.org/10.1111/tpj.15781openalex-snapshot
Genome‐wide loss of CHH methylation with limited transcriptome changes in Setaria viridis DOMAINS REARRANGED METHYLTRANSFERASE ( DRM ) mutants
inferred← citeshttps://doi.org/10.1534/g3.120.401122openalex-snapshot
QTG-Finder2: A Generalized Machine-Learning Algorithm for Prioritizing QTL Causal Genes in Plants
inferred← citeshttps://doi.org/10.1534/g3.120.401345openalex-snapshot
Reference Genome for the Highly Transformable Setaria viridis ME034V
inferred← citeshttps://doi.org/10.5511/plantbiotechnology.21.0407aopenalex-snapshot
Efficient genome editing and gene knockout in Setaria viridis with CRISPR/Cas9 directed gene editing by the non-homologous end-joining pathway
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