Epigenetics: possible applications in climate-smart crop breeding

Stress-responsive miRNAome of Glycine max (L.) Merrill: molecular insights and way forward

(2019) S. V. Ramesh et al.   PLANTA

Dynamic changes in histone modification are associated with upregulation of Hsf and rRNA genes during heat stress in maize seedlings

(2019) Haoli Hou et al.   PROTOPLASMA

Drought Response in Rice: The miRNA Story

(2019) Kalaivani Nadarajah et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

CRISPR / dC as9 platforms in plants: strategies and applications beyond genome editing

(2019) Mahdi Moradpour et al.   PLANT BIOTECHNOLOGY JOURNAL

Environmental and epigenetic regulation of Rider retrotransposons in tomato

(2019) Matthias Benoit et al.   PLoS Genetics

Overexpression of native Musa-miR397 enhances plant biomass without compromising abiotic stress tolerance in banana

(2019) Prashanti Patel et al.   Scientific Reports

Control of Maize Vegetative and Reproductive Development, Fertility, and rRNAs Silencing byHISTONE DEACETYLASE 108

(2018) Cristian Forestan et al.   GENETICS

Pseudomonas putida modulates the expression of miRNAs and their target genes in response to drought and salt stresses in chickpea ( Cicer arietinum L.)

(2018) Ram Jatan et al.   GENOMICS

Dynamics and function of DNA methylation in plants

(2018) Huiming Zhang et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

Differentially Expressed microRNAs Link Cellular Physiology to Phenotypic Changes in Rice under Stress Conditions

(2018) Rumdeep K Grewal et al.   PLANT AND CELL PHYSIOLOGY

An epigenetic breeding system in soybean for increased yield and stability

(2018) Sunil K. Kenchanmane Raju et al.   PLANT BIOTECHNOLOGY JOURNAL

A dicistronic precursor encoding miR398 and the legume-specific miR2119 coregulates CSD1 and ADH1 mRNAs in response to water deficit

(2018) Carlos De la Rosa et al.   PLANT CELL AND ENVIRONMENT

Preparing plants for improved cold tolerance by priming

(2018) Margarete Baier et al.   PLANT CELL AND ENVIRONMENT

Transcriptome analysis of microRNA156 overexpression alfalfa roots under drought stress

(2018) Muhammad Arshad et al.   Scientific Reports

Resequencing of Common Bean Identifies Regions of Inter–Gene Pool Introgression and Provides Comprehensive Resources for Molecular Breeding

(2018) Juan David Lobaton et al.   Plant Genome

Control of Maize Vegetative and Reproductive Development, Fertility, and rRNAs Silencing byHISTONE DEACETYLASE 108

(2018) Cristian Forestan et al.   GENETICS

Epigenetic responses to abiotic stresses during reproductive development in cereals

(2018) Kevin Begcy et al.   Plant Reproduction

Plant epigenetic mechanisms: role in abiotic stress and their generational heritability

(2018) Jebi Sudan et al.   3 Biotech

Plant epigenetic mechanisms: role in abiotic stress and their generational heritability

(2018) Jebi Sudan et al.   3 Biotech

Shifting the limits in wheat research and breeding using a fully annotated reference genome

(2018) et al.   SCIENCE

Exploring miRNAs for developing climate-resilient crops: A perspective review

(2018) Jin Xu et al.   SCIENCE OF THE TOTAL ENVIRONMENT

Analysis of DNA methylation patterns associated with drought stress response in faba bean ( Vicia faba L.) using methylation-sensitive amplification polymorphism (MSAP)

(2017) Ghassen Abid et al.   ENVIRONMENTAL AND EXPERIMENTAL BOTANY

A chromosome conformation capture ordered sequence of the barley genome

(2017) Martin Mascher et al.   NATURE

Exploiting induced and natural epigenetic variation for crop improvement

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

Divergent cytosine DNA methylation patterns in single-cell, soybean root hairs

(2017) Md Shakhawat Hossain et al.   NEW PHYTOLOGIST

Natural antisense transcripts are significantly involved in regulation of drought stress in maize

(2017) Jie Xu et al.   NUCLEIC ACIDS RESEARCH

A Histone Code Reader and a Transcriptional Activator Interact to Regulate Genes for Salt Tolerance

(2017) Wei Wei et al.   PLANT PHYSIOLOGY

Epigenetics for Plant Improvement: Current Knowledge and Modeling Avenues

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

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

(2017) Xiaoguo Zheng et al.   Scientific Reports

Physiological, Biochemical, Epigenetic and Molecular Analyses of Wheat (Triticum aestivum) Genotypes with Contrasting Salt Tolerance

(2017) Suresh Kumar et al.   Frontiers in Plant Science

Drought Stress-Related Physiological Changes and Histone Modifications in Barley Primary Leaves at HSP17 Gene

(2017) Aslihan Temel et al.   Agronomy-Basel

MicroRNA profiling provides insights into post-transcriptional regulation of gene expression in chickpea root apex under salinity and water deficiency

(2017) Hitaishi Khandal et al.   Scientific Reports

Water-deficit stress-responsive microRNAs and their targets in four durum wheat genotypes

(2016) Haipei Liu et al.   FUNCTIONAL & INTEGRATIVE GENOMICS

Transgenerational response to stress in plants and its application for breeding

(2016) Andriy Bilichak et al.   JOURNAL OF EXPERIMENTAL BOTANY

Water-deficiency conditions differently modulate the methylome of roots and leaves in barley (Hordeum vulgareL.)

(2016) Karolina Chwialkowska et al.   JOURNAL OF EXPERIMENTAL BOTANY

Genome-wide characterization of maize small RNA loci and their regulation in the required to maintain repression6-1 (rmr6-1) mutant and long-term abiotic stresses

(2016) Alice Lunardon et al.   PLANT PHYSIOLOGY

Pseudomonas putida attunes morphophysiological, biochemical and molecular responses in Cicer arietinum L. during drought stress and recovery

(2016) Shalini Tiwari et al.   PLANT PHYSIOLOGY AND BIOCHEMISTRY

Characterization of Small RNAs Derived from tRNAs, rRNAs and snoRNAs and Their Response to Heat Stress in Wheat Seedlings

(2016) Yu Wang et al.   PLoS One

Chilling-induced tomato flavor loss is associated with altered volatile synthesis and transient changes in DNA methylation

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

Stress-induced and epigenetic-mediated maize transcriptome regulation study by means of transcriptome reannotation and differential expression analysis

(2016) Cristian Forestan et al.   Scientific Reports

Genomic Selection in Multi-environment Crop Trials

(2016) Helena Oakey et al.   G3-Genes Genomes Genetics

Arabidopsis FORGETTER1 mediates stress-induced chromatin memory through nucleosome remodeling

(2016) Krzysztof Brzezinka et al.   eLife

MicroRNAs As Potential Targets for Abiotic Stress Tolerance in Plants

(2016) Varsha Shriram et al.   Frontiers in Plant Science

Reconsidering plant memory: Intersections between stress recovery, RNA turnover, and epigenetics

(2016) P. A. Crisp et al.   Science Advances

DNA-methylation changes induced by salt stress in wheat Triticum aestivum

(2016) Zhong Lan et al.   AFRICAN JOURNAL OF BIOTECHNOLOGY

Transcriptome Analysis of Sunflower Genotypes with Contrasting Oxidative Stress Tolerance Reveals Individual- and Combined- Biotic and Abiotic Stress Tolerance Mechanisms

(2016) Vemanna S. Ramu et al.   PLoS One

DNA methylation and gene expression in Mimulus guttatus

(2015) Jack M. Colicchio et al.   BMC GENOMICS

Stress-induced chromatin changes in plants: of memories, metabolites and crop improvement

(2015) Cécile Vriet et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

A hit-and-run heat shock factor governs sustained histone methylation and transcriptional stress memory

(2015) J. La mke et al.   EMBO JOURNAL

miR408 overexpression causes increased drought tolerance in chickpea

(2015) Mortaza Hajyzadeh et al.   GENE

Prediction of Plant Height inArabidopsis thalianaUsing DNA Methylation Data

(2015) Yaodong Hu et al.   GENETICS

Epigenome editing by a CRISPR-Cas9-based acetyltransferase activates genes from promoters and enhancers

(2015) Isaac B Hilton et al.   NATURE BIOTECHNOLOGY

MutS HOMOLOG1-Derived Epigenetic Breeding Potential in Tomato

(2015) Xiaodong Yang et al.   PLANT PHYSIOLOGY

The R2R3-type MYB gene OsMYB91 has a function in coordinating plant growth and salt stress tolerance in rice

(2015) Ning Zhu et al.   PLANT SCIENCE

Hybrid mimics and hybrid vigor inArabidopsis

(2015) Li Wang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

From Genetics to Functional Genomics: Improvement in Drought Signaling and Tolerance in Wheat

(2015) Hikmet Budak et al.   Frontiers in Plant Science

Prediction of Plant Height inArabidopsis thalianaUsing DNA Methylation Data

(2015) Yaodong Hu et al.   GENETICS

Salt Tolerant and Sensitive Rice Varieties Display Differential Methylome Flexibility under Salt Stress

(2015) Liliana J. Ferreira et al.   PLoS One

Divergent DNA methylation patterns associated with gene expression in rice cultivars with contrasting drought and salinity stress response

(2015) Rohini Garg et al.   Scientific Reports

Comparative proteomic analysis of leaves between photoperiod-sensitive and photoperiod-insensitive maize inbred seedlings under long day treatments

(2014) Ning Wang et al.   ACTA PHYSIOLOGIAE PLANTARUM

pENCODE: A Plant Encyclopedia of DNA Elements

(2014) Amanda K. Lane et al.   Annual Review of Genetics

Comparison of the heat stress induced variations in DNA methylation between heat-tolerant and heat-sensitive rapeseed seedlings

(2014) Guizhen Gao et al.   BREEDING SCIENCE

Epigenetic memory in plants

(2014) M. Iwasaki et al.   EMBO JOURNAL

SRA- and SET-domain-containing proteins link RNA polymerase V occupancy to DNA methylation

(2014) Lianna M. Johnson et al.   NATURE

RNA-directed DNA methylation: an epigenetic pathway of increasing complexity

(2014) Marjori A. Matzke et al.   NATURE REVIEWS GENETICS

Epigenetic Memory for Stress Response and Adaptation in Plants

(2014) Tetsu Kinoshita et al.   PLANT AND CELL PHYSIOLOGY

An Atlas of Soybean Small RNAs Identifies Phased siRNAs from Hundreds of Coding Genes

(2014) Siwaret Arikit et al.   PLANT CELL

Genetic Perturbation of the Maize Methylome

(2014) Qing Li et al.   PLANT CELL

ThemiR156-SPL9-DFRpathway coordinates the relationship between development and abiotic stress tolerance in plants

(2014) Long-Gang Cui et al.   PLANT JOURNAL

Epigenetics: Beyond Chromatin Modifications and Complex Genetic Regulation

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

Identification of Maize Long Non-Coding RNAs Responsive to Drought Stress

(2014) Wei Zhang et al.   PLoS One

Inheritance of Trans Chromosomal Methylation patterns fromArabidopsisF1 hybrids

(2014) Ian K. Greaves et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mutation of a major CG methylase in rice causes genome-wide hypomethylation, dysregulated genome expression, and seedling lethality

(2014) L. Hu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mapping the Epigenetic Basis of Complex Traits

(2014) S. Cortijo et al.   SCIENCE

The Arabidopsis Nucleosome Remodeler DDM1 Allows DNA Methyltransferases to Access H1-Containing Heterochromatin

(2013) Assaf Zemach et al.   CELL

Epigenetic marks in an adaptive water stress-responsive gene in tomato roots under normal and drought conditions

(2013) Rodrigo M González et al.   Epigenetics

Evolution of variety-specific regulatory schema for expression of osa-miR408 inindicarice varieties under drought stress

(2013) Roseeta D. Mutum et al.   FEBS Journal

The role of rice microRNAs in abiotic stress responses

(2013) Dong-Hoon Jeong et al.   JOURNAL OF PLANT BIOLOGY

The RdDM Pathway Is Required for Basal Heat Tolerance in Arabidopsis

(2013) Olga V. Popova et al.   Molecular Plant

Covering Your Bases: Inheritance of DNA Methylation in Plant Genomes

(2013) Chad E. Niederhuth et al.   Molecular Plant

Draft genome sequence of chickpea (Cicer arietinum) provides a resource for trait improvement

(2013) Rajeev K Varshney et al.   NATURE BIOTECHNOLOGY

Overexpression of microRNA319 impacts leaf morphogenesis and leads to enhanced cold tolerance in rice (Oryza sativa L.)

(2013) CHUNHUA YANG et al.   PLANT CELL AND ENVIRONMENT

MicroRNA prediction and its function in regulating drought-related genes in cowpea

(2013) Xiao-Rong Shui et al.   PLANT SCIENCE

Environmental Heat and Salt Stress Induce Transgenerational Phenotypic Changes in Arabidopsis thaliana

(2013) Léonie Suter et al.   PLoS One

Use of MSAP Markers to Analyse the Effects of Salt Stress on DNA Methylation in Rapeseed (Brassica napus var. oleifera)

(2013) Gianpiero Marconi et al.   PLoS One

Warm temperatures induce transgenerational epigenetic release of RNA silencing by inhibiting siRNA biogenesis in Arabidopsis

(2013) S.-H. Zhong et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Does genomic selection have a future in plant breeding?

(2013) Elisabeth Jonas et al.   TRENDS IN BIOTECHNOLOGY

Epigenetic regulation of adaptive responses of forest tree species to the environment

(2013) Katharina Bräutigam et al.   Ecology and Evolution

The Role of Micro-Ribonucleic Acids in Legumes with a Focus on Abiotic Stress Response

(2013) Nitin Mantri et al.   Plant Genome

Epigenetic responses to drought stress in rice (Oryza sativa L.)

(2013) Gayacharan et al.   PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS

High throughput sequencing reveals novel and abiotic stress-regulated microRNAs in the inflorescences of rice

(2012) Blanca E Barrera-Figueroa et al.   BMC PLANT BIOLOGY

Molecular Mechanisms of Epigenetic Variation in Plants

(2012) Ryo Fujimoto et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Salt Stress Induced Variation in DNA Methylation Pattern and Its Influence on Gene Expression in Contrasting Rice Genotypes

(2012) Ratna Karan et al.   PLoS One

Abscisic Acid Refines the Synthesis of Chloroplast Proteins in Maize (Zea mays) in Response to Drought and Light

(2012) Xiuli Hu et al.   PLoS One

Differential expression of proteins in maize roots in response to abscisic acid and drought

(2011) Xiuli Hu et al.   ACTA PHYSIOLOGIAE PLANTARUM

Transgenerational epigenetic inheritance in plants

(2011) Marie-Theres Hauser et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Role of miRNAs and siRNAs in biotic and abiotic stress responses of plants

(2011) Basel Khraiwesh et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Identification of novel soybean microRNAs involved in abiotic and biotic stresses

(2011) Franceli R Kulcheski et al.   BMC GENOMICS

Atypical epigenetic mark in an atypical location: cytosine methylation at asymmetric (CNN) sites within the body of a non-repetitive tomato gene

(2011) Rodrigo M González et al.   BMC PLANT BIOLOGY

DNA methylation changes detected by methylation-sensitive amplified polymorphism in two contrasting rice genotypes under salt stress

(2011) Wensheng Wang et al.   Journal of Genetics and Genomics

Histone Methylation in Higher Plants

(2010) Chunyan Liu et al.   Annual Review of Plant Biology

Regulation of barley miRNAs upon dehydration stress correlated with target gene expression

(2010) Melda Kantar et al.   FUNCTIONAL & INTEGRATIVE GENOMICS

Epigenetic Contribution to Covariance Between Relatives

(2010) O. Tal et al.   GENETICS

Drought-induced site-specific DNA methylation and its association with drought tolerance in rice (Oryza sativa L.)

(2010) Wen-Sheng Wang et al.   JOURNAL OF EXPERIMENTAL BOTANY

Establishing, maintaining and modifying DNA methylation patterns in plants and animals

(2010) Julie A. Law et al.   NATURE REVIEWS GENETICS

Epigenetic Reprogramming in Plant and Animal Development

(2010) Suhua Feng et al.   SCIENCE

LegumeTFDB: an integrative database of Glycine max, Lotus japonicus and Medicago truncatula transcription factors

(2009) Keiichi Mochida et al.   BIOINFORMATICS

Adaptive epigenetic memory of ancestral temperature regime in Arabidopsis thalianaThis paper is one of a selection of papers published in a Special Issue from the National Research Council of Canada – Plant Biotechnology Institute.

(2009) C. A. Whittle et al.   Botany

Epigenetic regulation of stress responses in plants

(2009) Viswanathan Chinnusamy et al.   CURRENT OPINION IN PLANT BIOLOGY

miR398 and miR408 are up-regulated in response to water deficit in Medicago truncatula

(2009) Inês Trindade et al.   PLANTA

Energy use efficiency is characterized by an epigenetic component that can be directed through artificial selection to increase yield

(2009) M. Hauben et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Sequencing and analysis of the gene-rich space of cowpea

(2008) Michael P Timko et al.   BMC GENOMICS

The Arabidopsis NFYA5 Transcription Factor Is Regulated Transcriptionally and Posttranscriptionally to Promote Drought Resistance

(2008) W.-X. Li et al.   PLANT CELL

Microarray-based analysis of stress-regulated microRNAs in Arabidopsis thaliana

(2008) H.-H. Liu et al.   RNA