Reciprocal adaptation of rice and Xanthomonas oryzae pv. oryzae: cross-species 2D GWAS reveals the underlying genetics

Identification of the novel bacterial blight resistance gene Xa46(t) by mapping and expression analysis of the rice mutant H120

(2020) Shen Chen et al.   Scientific Reports

A novel resistance gene for bacterial blight in rice, Xa43(t) identified by GWAS, confirmed by QTL mapping using a bi-parental population

(2019) Suk-Man Kim et al.   PLoS One

Interactive Tree Of Life (iTOL) v4: recent updates and new developments

(2019) Ivica Letunic et al.   NUCLEIC ACIDS RESEARCH

Biosynthesis and secretion of the microbial sulfated peptide RaxX and binding to the rice XA21 immune receptor

(2019) Dee Dee Luu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Cell surface immune receptors: the guardians of the plant’s extracellular spaces

(2019) Kostya Kanyuka et al.   CURRENT OPINION IN PLANT BIOLOGY

High-resolution genetic mapping of a novel bacterial blight resistance gene xa-45(t) identified from Oryza glaberrima and transferred to Oryza sativa

(2019) Kumari Neelam et al.   THEORETICAL AND APPLIED GENETICS

Plant NLRs: From discovery to application

(2018) Paul Kapos et al.   PLANT SCIENCE

Two-way mixed-effects methods for joint association analysis using both host and pathogen genomes

(2018) Miaoyan Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Receptor networks underpin plant immunity

(2018) Chih-Hang Wu et al.   SCIENCE

Genomic variation in 3,010 diverse accessions of Asian cultivated rice

(2018) Wensheng Wang et al.   NATURE

Identification of novel recessive gene xa44(t) conferring resistance to bacterial blight races in rice by QTL linkage analysis using an SNP chip

(2018) Suk-Man Kim   THEORETICAL AND APPLIED GENETICS

PopLDdecay: a fast and effective tool for linkage disequilibrium decay analysis based on variant call format files

(2018) Chi Zhang et al.   BIOINFORMATICS

Rice Routes of Countering Xanthomonas oryzae

(2018) Zhiyuan Ji et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Role of the Genes of Type VI Secretion System in Virulence of Rice Bacterial Brown Stripe Pathogen Acidovorax avenae subsp. avenae Strain RS-2

(2017) Md. Masum et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

A fungal wheat pathogen evolved host specialization by extensive chromosomal rearrangements

(2017) Fanny E Hartmann et al.   ISME Journal

CRISPR-GE: A Convenient Software Toolkit for CRISPR-Based Genome Editing

(2017) Xianrong Xie et al.   Molecular Plant

Nature's genetic screens: using genome-wide association studies for effector discovery

(2017) Andrea Sánchez-Vallet et al.   MOLECULAR PLANT PATHOLOGY

agriGO v2.0: a GO analysis toolkit for the agricultural community, 2017 update

(2017) Tian Tian et al.   NUCLEIC ACIDS RESEARCH

NLR network mediates immunity to diverse plant pathogens

(2017) Chih-Hang Wu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Association Genetics in Plant Pathogens: Minding the Gap between the Natural Variation and the Molecular Function

(2017) Anne Genissel et al.   Frontiers in Plant Science

Genome-Wide Association Studies In Plant Pathosystems: Toward an Ecological Genomics Approach

(2017) Claudia Bartoli et al.   Frontiers in Plant Science

funRiceGenes dataset for comprehensive understanding and application of rice functional genes

(2017) Wen Yao et al.   GigaScience

Population genomic insights into variation and evolution of Xanthomonas oryzae pv. oryzae

(2017) Samriti Midha et al.   Scientific Reports

Identification and linkage analysis of a new rice bacterial blight resistance gene from XM14, a mutant line from IR24

(2016) Constantine Busungu et al.   BREEDING SCIENCE

RPAN: rice pan-genome browser for ∼3000 rice genomes

(2016) Chen Sun et al.   NUCLEIC ACIDS RESEARCH

Rice SNP-seek database update: new SNPs, indels, and queries

(2016) Locedie Mansueto et al.   NUCLEIC ACIDS RESEARCH

Validation of Genome-Wide Association Studies as a Tool to Identify Virulence Factors inParastagonospora nodorum

(2016) Yuanyuan Gao et al.   PHYTOPATHOLOGY

Targeted promoter editing for rice resistance toXanthomonas oryzaepv.oryzaereveals differential activities forSWEET14-inducing TAL effectors

(2016) Servane Blanvillain-Baufumé et al.   PLANT BIOTECHNOLOGY JOURNAL

Extensive sequence divergence between the reference genomes of two eliteindicarice varieties Zhenshan 97 and Minghui 63

(2016) Jianwei Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Structure of the bacterial plant-ferredoxin receptor FusA

(2016) Rhys Grinter et al.   Nature Communications

Effector Diversification Contributes to Xanthomonas oryzae pv. oryzae Phenotypic Adaptation in a Semi-Isolated Environment

(2016) Ian Lorenzo Quibod et al.   Scientific Reports

Understanding Plant Immunity as a Surveillance System to Detect Invasion

(2015) David E. Cook et al.   Annual Review of Phytopathology

Against friend and foe: Type 6 effectors in plant-associated bacteria

(2015) Choong-Min Ryu   JOURNAL OF MICROBIOLOGY

Fitting Linear Mixed-Effects Models Usinglme4

(2015) Douglas Bates et al.   Journal of Statistical Software

Genetic Architecture of Natural Variation in Rice Chlorophyll Content Revealed by a Genome-Wide Association Study

(2015) Quanxiu Wang et al.   Molecular Plant

XA23 Is an Executor R Protein and Confers Broad-Spectrum Disease Resistance in Rice

(2015) Chunlian Wang et al.   Molecular Plant

A Robust CRISPR/Cas9 System for Convenient, High-Efficiency Multiplex Genome Editing in Monocot and Dicot Plants

(2015) Xingliang Ma et al.   Molecular Plant

Gene targeting by the TAL effector PthXo2 reveals cryptic resistance gene for bacterial blight of rice

(2015) Junhui Zhou et al.   PLANT JOURNAL

A knowledge-based molecular screen uncovers a broad-spectrumOsSWEET14resistance allele to bacterial blight from wild rice

(2015) Mathilde Hutin et al.   PLANT JOURNAL

Identification and fine-mapping of a new resistance gene, Xa40, conferring resistance to bacterial blight races in rice (Oryza sativa L.)

(2015) Suk-Man Kim et al.   THEORETICAL AND APPLIED GENETICS

Novel R tools for analysis of genome-wide population genetic data with emphasis on clonality

(2015) Zhian N. Kamvar et al.   Frontiers in Genetics

The rice immune receptor XA21 recognizes a tyrosine-sulfated protein from a Gram-negative bacterium

(2015) R. N. Pruitt et al.   Science Advances

Novel Insights into Rice Innate Immunity Against Bacterial and Fungal Pathogens

(2014) Wende Liu et al.   Annual Review of Phytopathology

SNPhylo: a pipeline to construct a phylogenetic tree from huge SNP data

(2014) Tae-Ho Lee et al.   BMC GENOMICS

Structure of the bacterial type II NADH dehydrogenase: a monotopic membrane protein with an essential role in energy generation

(2014) Adam Heikal et al.   MOLECULAR MICROBIOLOGY

Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism

(2014) Wei Chen et al.   NATURE GENETICS

The Rice TAL Effector-Dependent Resistance Protein XA10 Triggers Cell Death and Calcium Depletion in the Endoplasmic Reticulum

(2014) D. Tian et al.   PLANT CELL

Xa39, a novel dominant gene conferring broad-spectrum resistance toXanthomonas oryzaepv.oryzaein rice

(2014) F. Zhang et al.   PLANT PATHOLOGY

A phylogeny-based sampling strategy and power calculator informs genome-wide associations study design for microbial pathogens

(2014) Maha R Farhat et al.   Genome Medicine

The 3,000 rice genomes project

(2014)   GigaScience

Natural Variations and Genome-Wide Association Studies in Crop Plants

(2013) Xuehui Huang et al.   Annual Review of Plant Biology

Proteome analysis of the plant-pathogenic bacterium Xanthomonas oryzae pv. oryzae

(2013) Shu Xu et al.   BIOCHIMICA ET BIOPHYSICA ACTA-PROTEINS AND PROTEOMICS

Detection of Homologous Recombination Events in Bacterial Genomes

(2013) Wei-Bung Wang et al.   PLoS One

Xanthomonas oryzae pv oryzae triggers immediate transcriptomic modulations in rice

(2012) Rumdeep K Grewal et al.   BMC GENOMICS

Type 6 Secretion Dynamics Within and Between Bacterial Cells

(2012) M. Basler et al.   SCIENCE

Improvement of bacterial blight resistance of hybrid rice in China using the Xa23 gene derived from wild rice (Oryza rufipogon)

(2011) Yong-Li Zhou et al.   CROP PROTECTION

Evaluating the effective numbers of independent tests and significant p-value thresholds in commercial genotyping arrays and public imputation reference datasets

(2011) Miao-Xin Li et al.   HUMAN GENETICS

Phenazine-1-Carboxylic Acid Promotes Bacterial Biofilm Development via Ferrous Iron Acquisition

(2011) Y. Wang et al.   JOURNAL OF BACTERIOLOGY

Characterization of Xanthomonas oryzae-Responsive cis-Acting Element in the Promoter of Rice Race-Specific Susceptibility Gene Xa13

(2011) Ting Yuan et al.   Molecular Plant

Ortholog Alleles at Xa3/Xa26 Locus Confer Conserved Race-Specific Resistance against Xanthomonas oryzae in Rice

(2011) Hong-Jing Li et al.   Molecular Plant

A paralog of the MtN3/saliva family recessively confers race-specific resistance to Xanthomonas oryzae in rice

(2011) QINSONG LIU et al.   PLANT CELL AND ENVIRONMENT

Genome-wide association mapping reveals a rich genetic architecture of complex traits in Oryza sativa

(2011) Keyan Zhao et al.   Nature Communications

XanthomonasAvrBs3 Family-Type III Effectors: Discovery and Function

(2010) Jens Boch et al.   Annual Review of Phytopathology

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

Variance component model to account for sample structure in genome-wide association studies

(2010) Hyun Min Kang et al.   NATURE GENETICS

Xanthomonas oryzaepv.oryzaeXKK.12 Contains an AroQγChorismate Mutase That Is Involved in Rice Virulence

(2010) Giuliano Degrassi et al.   PHYTOPATHOLOGY

New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0

(2010) Stéphane Guindon et al.   SYSTEMATIC BIOLOGY

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Hijacking transferrin bound iron: protein–receptor interactions involved in iron transport in N. gonorrhoeae

(2009) Claire J. Parker Siburt et al.   Metallomics

Fungal effector proteins: past, present and future

(2009) PIERRE J. G. M. DE WIT et al.   MOLECULAR PLANT PATHOLOGY

Host and Pathogen Factors Controlling the Rice-Xanthomonas oryzae Interaction

(2009) F. F. White et al.   PLANT PHYSIOLOGY

Genetics and Improvement of Bacterial Blight Resistance of Hybrid Rice in China

(2009) Qi Zhang   Rice Science

Genome sequence and rapid evolution of the rice pathogen Xanthomonas oryzae pv. oryzae PXO99A

(2008) Steven L Salzberg et al.   BMC GENOMICS