Evolutionary and ecological functional genomics, from lab to the wild

Transgenerational epigenetics: Inheritance of global cytosine methylation and methylation-related epigenetic markers in the shrub Lavandula latifolia

(2018) Carlos M. Herrera et al.   AMERICAN JOURNAL OF BOTANY

Dissection of complicate genetic architecture and breeding perspective of cottonseed traits by genome-wide association study

(2018) Xiongming Du et al.   BMC GENOMICS

Rice nucleosome patterns undergo remodeling coincident with stress-induced gene expression

(2018) Qi Zhang et al.   BMC GENOMICS

Genome-wide association of yield traits in a nested association mapping population of barley reveals new gene diversity for future breeding

(2018) Rajiv Sharma et al.   JOURNAL OF EXPERIMENTAL BOTANY

Environmental drivers and genomic architecture of trait differentiation in fire-adapted Banksia attenuata ecotypes

(2018) Tianhua He et al.   Journal of Integrative Plant Biology

Genome-wide association mapping in Arabidopsis identifies novel genes underlying quantitative disease resistance to Alternaria brassicae

(2018) Sivasubramanian Rajarammohan et al.   MOLECULAR PLANT PATHOLOGY

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

Ecological genomics of variation in bud-break phenology and mechanisms of response to climate warming in Populus trichocarpa

(2018) Athena D. McKown et al.   NEW PHYTOLOGIST

Chromatin-based mechanisms of temperature memory in plants

(2018) Thomas Friedrich et al.   PLANT CELL AND ENVIRONMENT

Genome wide association and gene validation studies for early root vigor to improve direct seeding of rice

(2018) Fanmiao Wang et al.   PLANT CELL AND ENVIRONMENT

Changes in chromatin accessibility between Arabidopsis stem cells and mesophyll cells illuminate cell type-specific transcription factor networks

(2018) Paja Sijacic et al.   PLANT JOURNAL

Asymmetrical changes of gene expression, small RNAs and chromatin in two resynthesized wheat allotetraploids

(2018) Wu Jiao et al.   PLANT JOURNAL

Comparative epigenomics reveals evolution of duplicated genes in potato and tomato

(2018) Lin Wang et al.   PLANT JOURNAL

Molecular diversity and landscape genomics of the crop wild relative Triticum urartu across the Fertile Crescent

(2018) Alice Brunazzi et al.   PLANT JOURNAL

Natural Genetic Variation Shapes Root System Responses to Phytohormones in Arabidopsis

(2018) Daniela Ristova et al.   PLANT JOURNAL

Coexpression network revealing the plasticity and robustness of population transcriptome during the initial stage of domesticating energy crop Miscanthus lutarioriparius

(2018) Shilai Xing et al.   PLANT MOLECULAR BIOLOGY

Large-scale comparative epigenomics reveals hierarchical regulation of non-CG methylation inArabidopsis

(2018) Yu Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transcriptome landscape of a bacterial pathogen under plant immunity

(2018) Tatsuya Nobori et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Genome-wide association study dissects yield components associated with low-phosphorus stress tolerance in maize

(2018) Cheng Xu et al.   THEORETICAL AND APPLIED GENETICS

Translating High-Throughput Phenotyping into Genetic Gain

(2018) José Luis Araus et al.   TRENDS IN PLANT SCIENCE

Absence of warmth permits epigenetic memory of winter in Arabidopsis

(2018) Jo Hepworth et al.   Nature Communications

Ecology and genomics of an important crop wild relative as a prelude to agricultural innovation

(2018) Eric J.B. von Wettberg et al.   Nature Communications

Genome-wide association mapping and genomic prediction for CBSD resistance in Manihot esculenta

(2018) Siraj Ismail Kayondo et al.   Scientific Reports

Comparative transcriptome analysis of field- and chamber-grown samples of Colobanthus quitensis (Kunth) Bartl, an Antarctic flowering plant

(2018) Sung Mi Cho et al.   Scientific Reports

Epigenetic population differentiation in field- and common garden-grown Scabiosa columbaria plants

(2018) Maartje P. Groot et al.   Ecology and Evolution

Molecular Mechanisms of Acclimatization to Phosphorus Starvation and Recovery Underlying Full-Length Transcriptome Profiling in Barley (Hordeum vulgare L.)

(2018) Panrong Ren et al.   Frontiers in Plant Science

Functional Characterization of a Flavonoid Glycosyltransferase in Sweet Orange (Citrus sinensis)

(2018) Xiaogang Liu et al.   Frontiers in Plant Science

Mapping of HKT1;5 Gene in Barley Using GWAS Approach and Its Implication in Salt Tolerance Mechanism

(2018) Khaled M. Hazzouri et al.   Frontiers in Plant Science

Genome-Wide Association Studies and Comparison of Models and Cross-Validation Strategies for Genomic Prediction of Quality Traits in Advanced Winter Wheat Breeding Lines

(2018) Peter S. Kristensen et al.   Frontiers in Plant Science

Microbiome and ecotypic adaption of Holcus lanatus (L.) to extremes of its soil pH range, investigated through transcriptome sequencing

(2018) Ellen Young et al.   Microbiome

Gene Regulatory Divergence Between Locally Adapted Ecotypes in Their Native Habitats

(2018) Billie A. Gould et al.   MOLECULAR ECOLOGY

Loci and natural alleles underlying robust roots and adaptive domestication of upland ecotype rice in aerobic conditions

(2018) Yan Zhao et al.   PLoS Genetics

The molecular genetic basis of herbivory between butterflies and their host plants

(2018) Sumitha Nallu et al.   Nature Ecology & Evolution

Transcriptomic characterization of candidate genes responsive to salt tolerance of Miscanthus energy crops

(2017) Zhihong Song et al.   Global Change Biology Bioenergy

The Genomic Architecture of Flowering Time Varies Across Space and Time in Mimulus guttatus

(2017) Patrick J. Monnahan et al.   GENETICS

Getting back to nature: a reality check for experiments in controlled environments

(2017) Maria Grazia Annunziata et al.   JOURNAL OF EXPERIMENTAL BOTANY

Evolutionary Epigenomics of Retrotransposon-Mediated Methylation Spreading in Rice

(2017) Jae Young Choi et al.   MOLECULAR BIOLOGY AND EVOLUTION

The emergence of the hyperinvasive vine, Mikania micrantha (Asteraceae), via admixture and founder events inferred from population transcriptomics

(2017) Ming Yang et al.   MOLECULAR ECOLOGY

Natural variation in life history strategy of Arabidopsis thaliana determines stress responses to drought and insects of different feeding guilds

(2017) Nelson H. Davila Olivas et al.   MOLECULAR ECOLOGY

Population transcriptomic characterization of the genetic and expression variation of a candidate progenitor of Miscanthus energy crops

(2017) Juan Yan et al.   MOLECULAR ECOLOGY

Comparative Transcriptome Analysis Reveals Adaptive Evolution of Notopterygium incisum and Notopterygium franchetii, Two High-Alpine Herbal Species Endemic to China

(2017) Yun Jia et al.   MOLECULES

Genomic analyses in cotton identify signatures of selection and loci associated with fiber quality and yield traits

(2017) Lei Fang et al.   NATURE GENETICS

A study of allelic diversity underlying flowering-time adaptation in maize landraces

(2017) J Alberto Romero Navarro et al.   NATURE GENETICS

High-quality de novo assembly of the apple genome and methylome dynamics of early fruit development

(2017) Nicolas Daccord et al.   NATURE GENETICS

Exploiting induced and natural epigenetic variation for crop improvement

(2017) Nathan M. Springer et al.   NATURE REVIEWS GENETICS

Novel Loci Underlie Natural Variation in Vitamin E Levels in Maize Grain

(2017) Christine H. Diepenbrock et al.   PLANT CELL

The Molecular Dialog between Flowering Plant Reproductive Partners Defined by SNP-Informed RNA-Sequencing

(2017) Alexander R. Leydon et al.   PLANT CELL

Profiling of Accessible Chromatin Regions across Multiple Plant Species and Cell Types Reveals Common Gene Regulatory Principles and New Control Modules

(2017) Kelsey A. Maher et al.   PLANT CELL

Transgenerational stress-adaption: an opportunity for ecological epigenetics

(2017) Arne Weinhold   PLANT CELL REPORTS

Plant small RNAs: the essential epigenetic regulators of gene expression for salt-stress responses and tolerance

(2017) Vinay Kumar et al.   PLANT CELL REPORTS

Two-stage identification of SNP effects on dynamic poplar growth

(2017) Jingyuan Liu et al.   PLANT JOURNAL

Domestication rewired gene expression and nucleotide diversity patterns in tomato

(2017) Christopher Sauvage et al.   PLANT JOURNAL

Seasonal below-ground metabolism in switchgrass

(2017) Nathan A. Palmer et al.   PLANT JOURNAL

A genome-wide association study of 23 agronomic traits in Chinese wheat landraces

(2017) Yaxi Liu et al.   PLANT JOURNAL

Transcriptome analysis of the Brassica napus -Leptosphaeria maculans pathosystem identifies receptor, signaling and structural genes underlying plant resistance

(2017) Michael G. Becker et al.   PLANT JOURNAL

Transcriptome Profiling of Wheat Inflorescence Development from Spikelet Initiation to Floral Patterning Identified Stage-Specific Regulatory Genes

(2017) Nan Feng et al.   PLANT PHYSIOLOGY

Topological features of a gene co-expression network predict patterns of natural diversity in environmental response

(2017) David L. Des Marais et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Epigenetics for Plant Improvement: Current Knowledge and Modeling Avenues

(2017) Philippe Gallusci et al.   TRENDS IN PLANT SCIENCE

Piecing together cis -regulatory networks: insights from epigenomics studies in plants

(2017) Shao-shan C. Huang et al.   Wiley Interdisciplinary Reviews-Systems Biology and Medicine

Integrated DNA methylome and transcriptome analysis reveals the ethylene-induced flowering pathway genes in pineapple

(2017) Jiabin Wang et al.   Scientific Reports

Transgenerational epimutations induced by multi-generation drought imposition mediate rice plant’s adaptation to drought condition

(2017) Xiaoguo Zheng et al.   Scientific Reports

Genetic Architecture of a Rice Nested Association Mapping Population

(2017) Christopher A. Fragoso et al.   G3-Genes Genomes Genetics

Genomic Prediction and Association Mapping of Curd-Related Traits in Gene Bank Accessions of Cauliflower

(2017) Patrick Thorwarth et al.   G3-Genes Genomes Genetics

Gene co-expression network connectivity is an important determinant of selective constraint

(2017) Niklas Mähler et al.   PLoS Genetics

Genome-Wide Association Mapping of Flowering and Ripening Periods in Apple

(2017) Jorge Urrestarazu et al.   Frontiers in Plant Science

Comparative Analysis of Transcriptomes in Rhizophoraceae Provides Insights into the Origin and Adaptive Evolution of Mangrove Plants in Intertidal Environments

(2017) Wuxia Guo et al.   Frontiers in Plant Science

The Genomic Architecture of Flowering Time Varies Across Space and Time in Mimulus guttatus

(2017) Patrick J. Monnahan et al.   GENETICS

High altitude population of Arabidopsis thaliana is more plastic and adaptive under common garden than controlled condition

(2017) Akanksha Singh et al.   BMC ECOLOGY

Young inversion with multiple linked QTLs under selection in a hybrid zone

(2017) Cheng-Ruei Lee et al.   Nature Ecology & Evolution

Field-based high throughput phenotyping rapidly identifies genomic regions controlling yield components in rice

(2017) Paul Tanger et al.   Scientific Reports

Transcriptomic insight into terpenoid and carbazole alkaloid biosynthesis and functional characterization of two terpene synthases in curry tree (Murraya koenigii)

(2017) Seema Meena et al.   Scientific Reports

A systems approach to a spatio-temporal understanding of the drought stress response in maize

(2017) Zhenyan Miao et al.   Scientific Reports

Genome-wide association study Identified multiple Genetic Loci on Chilling Resistance During Germination in Maize

(2017) Guanghui Hu et al.   Scientific Reports

Genome-wide association study and genomic prediction in citrus: Potential of genomics-assisted breeding for fruit quality traits

(2017) Mai F. Minamikawa et al.   Scientific Reports

Genome-wide and gene-based association mapping for rice eating and cooking characteristics and protein content

(2017) Xiaoqian Wang et al.   Scientific Reports

From the laboratory to the field: assaying histone methylation at FLOWERING LOCUS C in naturally growing Arabidopsis halleri

(2016) Haruki Nishio et al.   GENES & GENETIC SYSTEMS

Plant adaptation or acclimation to rising CO2? Insight from first multigenerational RNA-Seq transcriptome

(2016) Alexander Watson-Lazowski et al.   GLOBAL CHANGE BIOLOGY

Modulation ofR-gene expression across environments

(2016) Alice MacQueen et al.   JOURNAL OF EXPERIMENTAL BOTANY

Photosynthetic response to fluctuating environments and photoprotective strategies under abiotic stress

(2016) Wataru Yamori   JOURNAL OF PLANT RESEARCH

Next-generation biology: Sequencing and data analysis approaches for non-model organisms

(2016) Rute R. da Fonseca et al.   Marine Genomics

Extreme QTL mapping of germination speed in Arabidopsis thaliana

(2016) Wei Yuan et al.   MOLECULAR ECOLOGY

Rapid genome-wide evolution in Brassica rapa populations following drought revealed by sequencing of ancestral and descendant gene pools

(2016) Steven J. Franks et al.   MOLECULAR ECOLOGY

Identification of Regulatory DNA Elements Using Genome-wide Mapping of DNase I Hypersensitive Sites during Tomato Fruit Development

(2016) Zhengkun Qiu et al.   Molecular Plant

Bacteria establish an aqueous living space in plants crucial for virulence

(2016) Xiu-Fang Xin et al.   NATURE

Exome sequencing of geographically diverse barley landraces and wild relatives gives insights into environmental adaptation

(2016) Joanne Russell et al.   NATURE GENETICS

Domestication history and geographical adaptation inferred from a SNP map of African rice

(2016) Rachel S Meyer et al.   NATURE GENETICS

Genome-wide association analysis reveals distinct genetic architectures for single and combined stress responses inArabidopsis thaliana

(2016) Nelson H. Davila Olivas et al.   NEW PHYTOLOGIST

Genetic architecture of plant stress resistance: multi-trait genome-wide association mapping

(2016) Manus P. M. Thoen et al.   NEW PHYTOLOGIST

Regional heritability mapping and genome-wide association identify loci for complex growth, wood and disease resistance traits in Eucalyptus

(2016) Rafael Tassinari Resende et al.   NEW PHYTOLOGIST

Combining ATAC-seq with nuclei sorting for discovery of cis-regulatory regions in plant genomes

(2016) Zefu Lu et al.   NUCLEIC ACIDS RESEARCH

Association mapping of leaf traits in spinach (Spinacia oleraceaL.)

(2016) Jianbing Ma et al.   PLANT BREEDING

EGRINs (Environmental Gene Regulatory Influence Networks) in Rice That Function in the Response to Water Deficit, High Temperature, and Agricultural Environments

(2016) Olivia Wilkins et al.   PLANT CELL

Molecular, genetic and evolutionary analysis of a paracentric inversion inArabidopsis thaliana

(2016) Paul Fransz et al.   PLANT JOURNAL

Transcriptome and Degradome Sequencing Reveals Dormancy Mechanisms of Cunninghamia lanceolata Seeds

(2016) Dechang Cao et al.   PLANT PHYSIOLOGY

Nested Association Mapping of Stem Rust Resistance in Wheat Using Genotyping by Sequencing

(2016) Prabin Bajgain et al.   PLoS One

Predicting the evolutionary dynamics of seasonal adaptation to novel climates inArabidopsis thaliana

(2016) Alexandre Fournier-Level et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mobile small RNAs regulate genome-wide DNA methylation

(2016) Mathew G. Lewsey et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Open chromatin reveals the functional maize genome

(2016) Eli Rodgers-Melnick et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

DNA methylome of the 20-gigabase Norway spruce genome

(2016) Israel Ausin et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Power of Natural Variation for Model Organism Biology

(2016) Audrey P. Gasch et al.   TRENDS IN GENETICS

Open access resources for genome-wide association mapping in rice

(2016) Susan R. McCouch et al.   Nature Communications

Dissection of genetic architecture of rice plant height and heading date by multiple-strategy-based association studies

(2016) Liyuan Zhou et al.   Scientific Reports

High light intensity plays a major role in emergence of population level variation in Arabidopsis thaliana along an altitudinal gradient

(2016) Antariksh Tyagi et al.   Scientific Reports

Environmental Association Analyses Identify Candidates for Abiotic Stress Tolerance in Glycine soja , the Wild Progenitor of Cultivated Soybeans

(2016) Justin E. Anderson et al.   G3-Genes Genomes Genetics

Metatranscriptomic Study of Common and Host-Specific Patterns of Gene Expression between Pines and Their Symbiotic Ectomycorrhizal Fungi in the Genus Suillus

(2016) Hui-Ling Liao et al.   PLoS Genetics

Multiple alleles at a single locus control seed dormancy in Swedish Arabidopsis

(2016) Envel Kerdaffrec et al.   eLife

Using Transcriptomics to Identify Differential Gene Expression in Response to Salinity among Australian Phragmites australis Clones

(2016) Gareth D. Holmes et al.   Frontiers in Plant Science

Phenotypic variation and differentiated gene expression of Australian plants in response to declining rainfall

(2016) Haylee D'Agui et al.   Royal Society Open Science

Unmanned Aerial Vehicles for High-Throughput Phenotyping and Agronomic Research

(2016) Yeyin Shi et al.   PLoS One

Population transcriptomics uncovers the regulation of gene expression variation in adaptation to changing environment

(2016) Qin Xu et al.   Scientific Reports

Transcriptome analyses provide insights into the phylogeny and adaptive evolution of the mangrove fern genus Acrostichum

(2016) Zhang Zhang et al.   Scientific Reports

Transcriptome analysis of the Holly mangrove Acanthus ilicifolius and its terrestrial relative, Acanthus leucostachyus, provides insights into adaptation to intertidal zones

(2015) Yuchen Yang et al.   BMC GENOMICS

Modelling the genetic architecture of flowering time control in barley through nested association mapping

(2015) Andreas Maurer et al.   BMC GENOMICS

Prediction of Plant Height inArabidopsis thalianaUsing DNA Methylation Data

(2015) Yaodong Hu et al.   GENETICS

Determinants of nucleosome positioning and their influence on plant gene expression

(2015) Ming-Jung Liu et al.   GENOME RESEARCH

LeasyScan: a novel concept combining 3D imaging and lysimetry for high-throughput phenotyping of traits controlling plant water budget

(2015) Vincent Vadez et al.   JOURNAL OF EXPERIMENTAL BOTANY

Ten years of transcriptomics in wild populations: what have we learned about their ecology and evolution?

(2015) Mariano Alvarez et al.   MOLECULAR ECOLOGY

Genomic, Transcriptomic, and Phenomic Variation Reveals the Complex Adaptation of Modern Maize Breeding

(2015) Haijun Liu et al.   Molecular Plant

Molecular phenology in plants: in natura systems biology for the comprehensive understanding of seasonal responses under natural environments

(2015) Hiroshi Kudoh   NEW PHYTOLOGIST

Transcriptional regulatory networks inArabidopsis thalianaduring single and combined stresses

(2015) Pankaj Barah et al.   NUCLEIC ACIDS RESEARCH

Genome-Wide Nucleosome Occupancy and Positioning and Their Impact on Gene Expression and Evolution in Plants

(2015) Tao Zhang et al.   PLANT PHYSIOLOGY

Coselected genes determine adaptive variation in herbivore resistance throughout the native range ofArabidopsis thaliana

(2015) Benjamin Brachi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Flux Control in a Defense Pathway in Arabidopsis thaliana Is Robust to Environmental Perturbations and Controls Variation in Adaptive Traits

(2015) Carrie F. Olson-Manning et al.   G3-Genes Genomes Genetics

Target Enrichment Improves Mapping of Complex Traits by Deep Sequencing

(2015) Jianjun Guo et al.   G3-Genes Genomes Genetics

Genome-Wide Association Analysis of Adaptation Using Environmentally Predicted Traits

(2015) Joost van Heerwaarden et al.   PLoS Genetics

Multiple abiotic stimuli are integrated in the regulation of rice gene expression under field conditions

(2015) Anne Plessis et al.   eLife

Next Generation Sequencing Technologies: The Doorway to the Unexplored Genomics of Non-Model Plants

(2015) Chibuikem I. N. Unamba et al.   Frontiers in Plant Science

Prediction of Plant Height inArabidopsis thalianaUsing DNA Methylation Data

(2015) Yaodong Hu et al.   GENETICS

Field pathogenomics reveals the emergence of a diverse wheat yellow rust population

(2015) Amelia Hubbard et al.   GENOME BIOLOGY

Genome-environment associations in sorghum landraces predict adaptive traits

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

Targeting environmental adaptation in the monocot model Brachypodium distachyon: a multi-faceted approach

(2014) Matteo Dell’Acqua et al.   BMC GENOMICS

Natural soil microbes alter flowering phenology and the intensity of selection on flowering time in a wild Arabidopsis relative

(2014) Maggie R. Wagner et al.   ECOLOGY LETTERS

Transcriptome analysis reveals diversified adaptation of Stipa purpurea along a drought gradient on the Tibetan Plateau

(2014) Yunqiang Yang et al.   FUNCTIONAL & INTEGRATIVE GENOMICS

Natural Variation in Abiotic Stress Responsive Gene Expression and Local Adaptation to Climate in Arabidopsis thaliana

(2014) Jesse R. Lasky et al.   MOLECULAR BIOLOGY AND EVOLUTION

Abiotic and biotic stress combinations

(2014) Nobuhiro Suzuki et al.   NEW PHYTOLOGIST

Epigenetics: Beyond Chromatin Modifications and Complex Genetic Regulation

(2014) S. R. Eichten et al.   PLANT PHYSIOLOGY

Mapping the Epigenetic Basis of Complex Traits

(2014) S. Cortijo et al.   SCIENCE

Get your high-quality low-cost genome sequence

(2014) Luigi Faino et al.   TRENDS IN PLANT SCIENCE

Genome-wide association study of Arabidopsis thaliana leaf microbial community

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

Combining high-throughput phenotyping and genome-wide association studies to reveal natural genetic variation in rice

(2014) Wanneng Yang et al.   Nature Communications

Association Mapping across Numerous Traits Reveals Patterns of Functional Variation in Maize

(2014) Jason G. Wallace et al.   PLoS Genetics

Genotype-by-Environment Interaction and Plasticity: Exploring Genomic Responses of Plants to the Abiotic Environment

(2013) David L. Des Marais et al.   Annual Review of Ecology Evolution and Systematics

Screening of rice Genebank germplasm for yield and selection of new drought tolerance donors

(2013) Rolando O. Torres et al.   FIELD CROPS RESEARCH

Comparative metatranscriptomics reveals kingdom level changes in the rhizosphere microbiome of plants

(2013) Thomas R Turner et al.   ISME Journal

Mass flowering of the tropical treeShorea beccarianawas preceded by expression changes in flowering and drought-responsive genes

(2013) Masaki J. Kobayashi et al.   MOLECULAR ECOLOGY

Are long-lived trees poised for evolutionary change? Single locus effects in the evolution of gene expression networks in spruce

(2013) Jukka-Pekka Verta et al.   MOLECULAR ECOLOGY

Single-base resolution methylomes of tomato fruit development reveal epigenome modifications associated with ripening

(2013) Silin Zhong et al.   NATURE BIOTECHNOLOGY

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

Genome-wide association studies and prediction of 17 traits related to phenology, biomass and cell wall composition in the energy grassMiscanthus sinensis

(2013) Gancho T. Slavov et al.   NEW PHYTOLOGIST

QTL-seq: rapid mapping of quantitative trait loci in rice by whole genome resequencing of DNA from two bulked populations

(2013) Hiroki Takagi et al.   PLANT JOURNAL

The advantages and limitations of trait analysis with GWAS: a review

(2013) Arthur Korte et al.   Plant Methods

Identification of Genes Involved in the Response of Arabidopsis to Simultaneous Biotic and Abiotic Stresses

(2013) N. J. Atkinson et al.   PLANT PHYSIOLOGY

Simultaneous Application of Heat, Drought, and Virus to Arabidopsis Plants Reveals Significant Shifts in Signaling Networks

(2013) C. M. Prasch et al.   PLANT PHYSIOLOGY

Transcriptome Responses to Combinations of Stresses in Arabidopsis

(2013) S. Rasmussen et al.   PLANT PHYSIOLOGY

The impact of climate change on plant epigenomes

(2013) Qiong A. Liu   TRENDS IN GENETICS

A Genome-Wide Association Study Reveals Genes Associated with Fusarium Ear Rot Resistance in a Maize Core Diversity Panel

(2013) Charles T. Zila et al.   G3-Genes Genomes Genetics

Single-base resolution maps of cultivated and wild rice methylomes and regulatory roles of DNA methylation in plant gene expression

(2012) Xin Li et al.   BMC GENOMICS

Transcriptomic and metabolomic analysis of Yukon Thellungiella plants grown in cabinets and their natural habitat show phenotypic plasticity

(2012) David R Guevara et al.   BMC PLANT BIOLOGY

Arabidopsis plants grown in the field and climate chambers significantly differ in leaf morphology and photosystem components

(2012) Yogesh Mishra et al.   BMC PLANT BIOLOGY

Deciphering and Prediction of Transcriptome Dynamics under Fluctuating Field Conditions

(2012) Atsushi J. Nagano et al.   CELL

Evolution of Flux Control in the Glucosinolate Pathway in Arabidopsis thaliana

(2012) Carrie F. Olson-Manning et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genome-wide genetic changes during modern breeding of maize

(2012) Yinping Jiao et al.   NATURE GENETICS

Genome-Wide Identification of Regulatory DNA Elements and Protein-Binding Footprints Using Signatures of Open Chromatin in Arabidopsis

(2012) W. Zhang et al.   PLANT CELL

Physiological Genomics of Response to Soil Drying in Diverse Arabidopsis Accessions

(2012) D. L. Des Marais et al.   PLANT CELL

Reshaping of the maize transcriptome by domestication

(2012) R. Swanson-Wagner et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Widespread dynamic DNA methylation in response to biotic stress

(2012) R. H. Dowen et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Transcriptome and methylome interactions in rice hybrids

(2012) Ramakrishna K. Chodavarapu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Gain-of-Function Polymorphism Controlling Complex Traits and Fitness in Nature

(2012) K. V. S. K. Prasad et al.   SCIENCE

Natural Enemies Drive Geographic Variation in Plant Defenses

(2012) T. Zust et al.   SCIENCE

Insect Herbivores Drive Real-Time Ecological and Evolutionary Change in Plant Populations

(2012) A. A. Agrawal et al.   SCIENCE

Genome-Wide Patterns of Arabidopsis Gene Expression in Nature

(2012) Christina L. Richards et al.   PLoS Genetics

Plant sexual reproduction during climate change: gene function in natura studied by ecological and evolutionary systems biology

(2011) Kentaro K. Shimizu et al.   ANNALS OF BOTANY

High-resolution mapping of open chromatin in the rice genome

(2011) W. Zhang et al.   GENOME RESEARCH

Multiple reference genomes and transcriptomes for Arabidopsis thaliana

(2011) Xiangchao Gan et al.   NATURE

Genome-wide association study of flowering time and grain yield traits in a worldwide collection of rice germplasm

(2011) Xuehui Huang et al.   NATURE GENETICS

Non–model organisms

(2011) Tal Nawy   NATURE METHODS

A Map of Local Adaptation in Arabidopsis thaliana

(2011) A. Fournier-Level et al.   SCIENCE

Adaptation to Climate Across the Arabidopsis thaliana Genome

(2011) A. M. Hancock et al.   SCIENCE

Evolutionary genetics of plant adaptation

(2011) Jill T. Anderson et al.   TRENDS IN GENETICS

Growth habit determination by the balance of histone methylation activities in Arabidopsis

(2010) Jong-Hyun Ko et al.   EMBO JOURNAL

The Next Generation of Molecular Markers From Massively Parallel Sequencing of Pooled DNA Samples

(2010) Andreas Futschik et al.   GENETICS

Applications of next generation sequencing in molecular ecology of non-model organisms

(2010) R Ekblom et al.   HEREDITY

Natural allelic variation underlying a major fitness trade-off in Arabidopsis thaliana

(2010) Marco Todesco et al.   NATURE

Dissection of genetically complex traits with extremely large pools of yeast segregants

(2010) Ian M. Ehrenreich et al.   NATURE

Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines

(2010) Susanna Atwell et al.   NATURE

Genome-wide association studies of 14 agronomic traits in rice landraces

(2010) Xuehui Huang et al.   NATURE GENETICS

Chromatin immunoprecipitation (ChIP) of plant transcription factors followed by sequencing (ChIP-SEQ) or hybridization to whole genome arrays (ChIP-CHIP)

(2010) Kerstin Kaufmann et al.   Nature Protocols

Transcriptome profiles of hybrid poplar (Populus trichocarpa × deltoides) reveal rapid changes in undamaged, systemic sink leaves after simulated feeding by forest tent caterpillar (Malacosoma disstria)

(2010) Ryan N. Philippe et al.   NEW PHYTOLOGIST

Robust control of the seasonal expression of the Arabidopsis FLC gene in a fluctuating environment

(2010) S. Aikawa et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome-wide survey of Arabidopsis natural variation in downy mildew resistance using combined association and linkage mapping

(2010) A. Nemri et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Linkage and Association Mapping of Arabidopsis thaliana Flowering Time in Nature

(2010) Benjamin Brachi et al.   PLoS Genetics

A transposon-induced epigenetic change leads to sex determination in melon

(2009) Antoine Martin et al.   NATURE

Genetic Properties of the Maize Nested Association Mapping Population

(2009) M. D. McMullen et al.   SCIENCE

The Genetic Architecture of Maize Flowering Time

(2009) E. S. Buckler et al.   SCIENCE

Effects of Genetic Perturbation on Seasonal Life History Plasticity

(2009) A. M. Wilczek et al.   SCIENCE

A Multiparent Advanced Generation Inter-Cross to Fine-Map Quantitative Traits in Arabidopsis thaliana

(2009) Paula X. Kover et al.   PLoS Genetics

Connecting Genes, Coexpression Modules, and Molecular Signatures to Environmental Stress Phenotypes in Plants

(2008) David J Weston et al.   BMC Systems Biology

Highly Integrated Single-Base Resolution Maps of the Epigenome in Arabidopsis

(2008) Ryan Lister et al.   CELL

Natural Variation in Gene Expression Between Wild and Weedy Populations of Helianthus annuus

(2008) Z. Lai et al.   GENETICS

Genetic Design and Statistical Power of Nested Association Mapping in Maize

(2008) Jianming Yu et al.   GENETICS

Next-generation genetics in plants

(2008) Magnus Nordborg et al.   NATURE

Regulatory change in YABBY-like transcription factor led to evolution of extreme fruit size during tomato domestication

(2008) Bin Cong et al.   NATURE GENETICS

Mapping and quantifying mammalian transcriptomes by RNA-Seq

(2008) Ali Mortazavi et al.   NATURE METHODS

Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers

(2008) Nathan A. Baird et al.   PLoS One

The Transcriptional Landscape of the Yeast Genome Defined by RNA Sequencing

(2008) U. Nagalakshmi et al.   SCIENCE