GWAS, MWAS and mGWAS provide insights into precision agriculture based on genotype-dependent microbial effects in foxtail millet

Specialized metabolic functions of keystone taxa sustain soil microbiome stability

(2021) Weibing Xun et al.   Microbiome

Genome wide association study reveals plant loci controlling heritability of the rhizosphere microbiome

(2021) Siwen Deng et al.   ISME Journal

Microbiota-root-shoot-environment axis and stress tolerance in plants

(2021) Shiji Hou et al.   CURRENT OPINION IN PLANT BIOLOGY

Identification of blast-resistance loci through genome-wide association analysis in foxtail millet (Setaria italica (L.) Beauv.)

(2021) Zhi-jiang LI et al.   Journal of Integrative Agriculture

Differentiation strategies of soil rare and abundant microbial taxa in response to changing climatic regimes

(2020) Yuting Liang et al.   ENVIRONMENTAL MICROBIOLOGY

Modulation of the Root Microbiome by Plant Molecules: The Basis for Targeted Disease Suppression and Plant Growth Promotion

(2020) Alberto Pascale et al.   Frontiers in Plant Science

A plant genetic network for preventing dysbiosis in the phyllosphere

(2020) Tao Chen et al.   NATURE

Rare taxa maintain the stability of crop mycobiomes and ecosystem functions

(2020) Chao Xiong et al.   ENVIRONMENTAL MICROBIOLOGY

A single bacterial genus maintains root growth in a complex microbiome

(2020) Omri M. Finkel et al.   NATURE

The R package Rsubread is easier, faster, cheaper and better for alignment and quantification of RNA sequencing reads

(2019) Yang Liao et al.   NUCLEIC ACIDS RESEARCH

Causal relationships among the gut microbiome, short-chain fatty acids and metabolic diseases

(2019) Serena Sanna et al.   NATURE GENETICS

Systems Biology of Plant-Microbiome Interactions

(2019) Patricia A. Rodriguez et al.   Molecular Plant

NRT1.1B is associated with root microbiota composition and nitrogen use in field-grown rice

(2019) Jingying Zhang et al.   NATURE BIOTECHNOLOGY

Genetic Interactions Among Ghd7, Ghd8, OsPRR37 and Hd1 Contribute to Large Variation in Heading Date in Rice

(2019) Bo Zhang et al.   Rice

A heritable subset of the core rumen microbiome dictates dairy cow productivity and emissions

(2019) R. John Wallace et al.   Science Advances

The AabHLH35 Transcription Factor Identified from Anthurium andraeanum is Involved in Cold and Drought Tolerance

(2019) Li Jiang et al.   Plants-Basel

Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype

(2019) Daehwan Kim et al.   NATURE BIOTECHNOLOGY

GWAS Atlas: a curated resource of genome-wide variant-trait associations in plants and animals

(2019) Dongmei Tian et al.   NUCLEIC ACIDS RESEARCH

Occurrence of autophagy during pioneer root and stem development in Populus trichocarpa

(2019) Natalia Wojciechowska et al.   PLANTA

Pathogen-induced activation of disease-suppressive functions in the endophytic root microbiome

(2019) Víctor J. Carrión et al.   SCIENCE

Resequencing of 243 diploid cotton accessions based on an updated A genome identifies the genetic basis of key agronomic traits

(2018) Xiongming Du et al.   NATURE GENETICS

MYB72-dependent coumarin exudation shapes root microbiome assembly to promote plant health

(2018) Ioannis A. Stringlis et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Large-scale replicated field study of maize rhizosphere identifies heritable microbes

(2018) William A. Walters et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2018) Wensheng Wang et al.   NATURE

Comparative performance of the BGISEQ-500 and Illumina HiSeq4000 sequencing platforms for transcriptome analysis in plants

(2018) Fu-Yuan Zhu et al.   Plant Methods

Rhizosphere microbiome structure alters to enable wilt resistance in tomato

(2018) Min-Jung Kwak et al.   NATURE BIOTECHNOLOGY

Genome-wide association studies on the phyllosphere microbiome: Embracing complexity in host-microbe interactions

(2018) Kathleen Beilsmith et al.   PLANT JOURNAL

Substrate (un)specificity of Arabidopsis NRT1/PTR FAMILY (NPF) proteins

(2017) Claire Corratgé-Faillie et al.   JOURNAL OF EXPERIMENTAL BOTANY

Root microbiota drive direct integration of phosphate stress and immunity

(2017) Gabriel Castrillo et al.   NATURE

Metagenome-Wide Association Study and Machine Learning Prediction of Bulk Soil Microbiome and Crop Productivity

(2017) Hao-Xun Chang et al.   Frontiers in Microbiology

Taxonomic structure and functional association of foxtail millet root microbiome

(2017) Tao Jin et al.   GigaScience

A high density genetic map and QTL for agronomic and yield traits in Foxtail millet [Setaria italica (L.) P. Beauv.]

(2016) Xiaomei Fang et al.   BMC GENOMICS

The sucrose non-fermenting 1-related kinase 2 gene SAPK9 improves drought tolerance and grain yield in rice by modulating cellular osmotic potential, stomatal closure and stress-responsive gene expression

(2016) Avishek Dey et al.   BMC PLANT BIOLOGY

Association of host genome with intestinal microbial composition in a large healthy cohort

(2016) Williams Turpin et al.   NATURE GENETICS

Population-based metagenomics analysis reveals markers for gut microbiome composition and diversity

(2016) Alexandra Zhernakova et al.   SCIENCE

bio-samtools 2: a package for analysis and visualization of sequence and alignment data with SAMtools in Ruby: Fig. 1.

(2015) Graham J. Etherington et al.   BIOINFORMATICS

(Pro)cambium formation and proliferation: two sides of the same coin?

(2015) Virginie Jouannet et al.   CURRENT OPINION IN PLANT BIOLOGY

Resequencing 302 wild and cultivated accessions identifies genes related to domestication and improvement in soybean

(2015) Zhengkui Zhou et al.   NATURE BIOTECHNOLOGY

Genome-environment associations in sorghum landraces predict adaptive traits

(2015) J. R. Lasky et al.   Science Advances

Improved plant resistance to drought is promoted by the root-associated microbiome as a water stress-dependent trait

(2014) Eleonora Rolli et al.   ENVIRONMENTAL MICROBIOLOGY

Performance of different wheat genotypes inoculated with the plant growth promoting bacterium Herbaspirillum seropedicae

(2014) Adeline Neiverth et al.   EUROPEAN JOURNAL OF SOIL BIOLOGY

Mapping of Quantitative Trait Locus (QTLs) that Contribute to Germination and Early Seedling Drought Tolerance in the Interspecific Cross Setaria italica×Setaria viridis

(2014) Lufeng Qie et al.   PLoS One

Genome-wide association study of Arabidopsis thaliana leaf microbial community

(2014) Matthew W. Horton et al.   Nature Communications

The Impact of Beneficial Plant-Associated Microbes on Plant Phenotypic Plasticity

(2013) Chooi-Hua Goh et al.   JOURNAL OF CHEMICAL ECOLOGY

A haplotype map of genomic variations and genome-wide association studies of agronomic traits in foxtail millet (Setaria italica)

(2013) Guanqing Jia et al.   NATURE GENETICS

Diversity and heritability of the maize rhizosphere microbiome under field conditions

(2013) J. A. Peiffer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff

(2012) Pablo Cingolani et al.   FLY

A Novel Nuclear Protein Phosphatase 2C Negatively Regulated by ABL1 is Involved in Abiotic Stress and Panicle Development in Rice

(2012) Yu-Sheng Li et al.   MOLECULAR BIOTECHNOLOGY

Genome sequence of foxtail millet (Setaria italica) provides insights into grass evolution and biofuel potential

(2012) Gengyun Zhang et al.   NATURE BIOTECHNOLOGY

Genome-wide efficient mixed-model analysis for association studies

(2012) Xiang Zhou et al.   NATURE GENETICS

Identification of an abscisic acid transporter by functional screening using the receptor complex as a sensor

(2012) Y. Kanno et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

SOAPdenovo2: an empirically improved memory-efficient short-read de novo assembler

(2012) Ruibang Luo et al.   GigaScience

Direct Ubiquitination of Pattern Recognition Receptor FLS2 Attenuates Plant Innate Immunity

(2011) D. Lu et al.   SCIENCE

Genome-wide patterns of genetic variation in sweet and grain sorghum (Sorghum bicolor)

(2011) Lei-Ying Zheng et al.   GENOME BIOLOGY

GCTA: A Tool for Genome-wide Complex Trait Analysis

(2010) Jian Yang et al.   AMERICAN JOURNAL OF HUMAN GENETICS

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

(2010) A. McKenna et al.   GENOME RESEARCH

Genome-wide patterns of genetic variation among elite maize inbred lines

(2010) Jinsheng Lai et al.   NATURE GENETICS

Genetic analysis of pathway regulation for enhancing branched-chain amino acid biosynthesis in plants

(2010) Hao Chen et al.   PLANT JOURNAL

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

A Unified Approach to Genotype Imputation and Haplotype-Phase Inference for Large Data Sets of Trios and Unrelated Individuals

(2009) Brian L. Browning et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Rank-Based Inverse Normal Transformations are Increasingly Used, But are They Merited?

(2009) T. Mark Beasley et al.   BEHAVIOR GENETICS

MAPK cascade signalling networks in plant defence

(2009) Andrea Pitzschke et al.   CURRENT OPINION IN PLANT BIOLOGY

Soil Bacteria Elevate Essential Oil Accumulation and Emissions in Sweet Basil

(2009) Erika Banchio et al.   JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY

Pectin activation of MAP kinase and gene expression is WAK2 dependent

(2009) Bruce D. Kohorn et al.   PLANT JOURNAL

Evolution of F-box genes in plants: Different modes of sequence divergence and their relationships with functional diversification

(2009) Guixia Xu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Substrate-induced growth and isolation of Acidobacteria from acidic Sphagnum peat

(2008) Timofei A Pankratov et al.   ISME Journal