4.6 Review

Epigenomics as Potential Tools for Enhancing Magnitude of Breeding Approaches for Developing Climate Resilient Chickpea

Related references

Note: Only part of the references are listed.
Article Ecology

Fitness effects of somatic mutations accumulating during vegetative growth

Mitchell B. Cruzan et al.

Summary: The accumulation of somatic mutations in plants can be passed on to offspring, but the consequences for offspring fitness are not well known. This study found different fitness effects of somatic mutations, with some self-pollinated progeny showing increased fitness.

EVOLUTIONARY ECOLOGY (2022)

Review Biology

Epigenetics for Crop Improvement in Times of Global Change

Ioanna Kakoulidou et al.

Summary: Research on plant epigenetics aims to understand how various factors regulate plant development independently of genome changes. Epigenetic changes can be heritable and impact plant growth and crop tolerance, particularly in response to environmental stimuli. Harnessing epigenetic diversity can lead to engineered plants with advantageous traits for optimal crop production.

BIOLOGY-BASEL (2021)

Article Biochemistry & Molecular Biology

First Report of CRISPR/Cas9 Mediated DNA-Free Editing of 4CL and RVE7 Genes in Chickpea Protoplasts

Sapna Badhan et al.

Summary: The current genome editing system CRISPR/Cas9 has been proven effective in plant applications, with the DNA-free editing showing promise in achieving targeted mutagenesis in chickpea. By selecting drought tolerance-related genes 4CL and RVE7 for editing in chickpea protoplast, this study demonstrated high efficiency in editing the RVE7 gene, providing insights into gene functions under drought stress in chickpea.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2021)

Article Multidisciplinary Sciences

A chickpea genetic variation map based on the sequencing of 3,366 genomes

Rajeev K. Varshney et al.

Summary: By studying the genetic diversity of chickpea, the research team estimated the divergence of Cicer over the last 21 million years and identified chromosomal locations of deleterious mutations in elite germplasm. They also found targets for purging deleterious alleles through genomics-assisted breeding and proposed three crop breeding strategies.

NATURE (2021)

Review Immunology

Epigenetic regulation in antiviral innate immunity

Xiao Wang et al.

Summary: The emergence of life-threatening viruses poses challenges to public health, with epigenetics playing a crucial role in host-virus interactions. Understanding these interactions through an epigenetic lens may offer therapeutic opportunities. This review discusses the roles of chromatin remodeling, histone modification, and m6A RNA modification in modulating chromatin openness during host defense against viruses, highlighting the need for future research in this area.

EUROPEAN JOURNAL OF IMMUNOLOGY (2021)

Article Plant Sciences

The Genome-Wide EMS Mutagenesis Bias Correlates With Sequence Context and Chromatin Structure in Rice

Wei Yan et al.

Summary: By investigating 52 rice EMS mutants, it was found that EMS exhibits a preference for G/C sites with higher GC contents in flanking sequences. The composition of local dinucleotides and trinucleotides is also associated with the efficiency of EMS mutagenesis.

FRONTIERS IN PLANT SCIENCE (2021)

Review Plant Sciences

Exploration of Epigenetics for Improvement of Drought and Other Stress Resistance in Crops: A Review

Chao Sun et al.

Summary: Crop plants adapt to biotic and abiotic stresses by expressing specific genes, and epigenetic changes enable them to remember past stress events for better future stress responses. Plant stress memory enhances plants' ability to cope with challenges efficiently, contributing to increased yield potential in changing climatic conditions.

PLANTS-BASEL (2021)

Review Physiology

Phenotypic Switching Resulting From Developmental Plasticity: Fixed or Reversible?

Warren W. Burggren

FRONTIERS IN PHYSIOLOGY (2020)

Review Biochemistry & Molecular Biology

Application of the MSAP Technique to Evaluate Epigenetic Changes in Plant Conservation

Maria Elena Gonzalez-Benito et al.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2020)

Review Forestry

Advances and Promises of Epigenetics for Forest Trees

Joana Amaral et al.

FORESTS (2020)

Article Multidisciplinary Sciences

Site-specific manipulation of Arabidopsis loci using CRISPR-Cas9 SunTag systems

Ashot Papikian et al.

NATURE COMMUNICATIONS (2019)

Article Biochemistry & Molecular Biology

The miRNA-Mediated Post-Transcriptional Regulation of Maize in Response to High Temperature

Moubiao Zhang et al.

INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES (2019)

Article Biotechnology & Applied Microbiology

Continuous salt stress-induced long non-coding RNAs and DNA methylation patterns in soybean roots

Rui Chen et al.

BMC GENOMICS (2019)

Review Biochemistry & Molecular Biology

Translational genomics and multi-omics integrated approaches as a useful strategy for crop breeding

Hong-Kyu Choi

GENES & GENOMICS (2019)

Review Agronomy

Toward the sequence-based breeding in legumes in the post-genome sequencing era

Rajeev K. Varshney et al.

THEORETICAL AND APPLIED GENETICS (2019)

Review Genetics & Heredity

Histone H3 lysine K4 methylation and its role in learning and memory

Bridget E. Collins et al.

EPIGENETICS & CHROMATIN (2019)

Article Plant Sciences

Drought tolerance of sugarcane is improved by previous exposure to water deficit

Fernanda C. C. Marcos et al.

JOURNAL OF PLANT PHYSIOLOGY (2018)

Review Cell Biology

Dynamics and function of DNA methylation in plants

Huiming Zhang et al.

NATURE REVIEWS MOLECULAR CELL BIOLOGY (2018)

Article Biotechnology & Applied Microbiology

An epigenetic breeding system in soybean for increased yield and stability

Sunil K. Kenchanmane Raju et al.

PLANT BIOTECHNOLOGY JOURNAL (2018)

Article Multidisciplinary Sciences

Genome-wide bisulphite-sequencing reveals organ-specific methylation patterns in chickpea

Himanshi Bhatia et al.

SCIENTIFIC REPORTS (2018)

Article Multidisciplinary Sciences

Drought tolerance of sugarcane propagules is improved when origin material faces water deficit

Fernanda C. C. Marcos et al.

PLOS ONE (2018)

Article Plant Sciences

The legume miR1514a modulates a NAC transcription factor transcript to trigger phasiRNA formation in response to drought

Guadalupe Sosa-Valencia et al.

JOURNAL OF EXPERIMENTAL BOTANY (2017)

Review Biochemistry & Molecular Biology

Crop Breeding Chips and Genotyping Platforms: Progress, Challenges, and Perspectives

Awais Rasheed et al.

MOLECULAR PLANT (2017)

Review Genetics & Heredity

Exploiting induced and natural epigenetic variation for crop improvement

Nathan M. Springer et al.

NATURE REVIEWS GENETICS (2017)

Article Multidisciplinary Sciences

Critical roles of DNA demethylation in the activation of ripening-induced genes and inhibition of ripening-repressed genes in tomato fruit

Zhaobo Lang et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2017)

Review Plant Sciences

Epigenetics for Plant Improvement: Current Knowledge and Modeling Avenues

Philippe Gallusci et al.

TRENDS IN PLANT SCIENCE (2017)

Article Multidisciplinary Sciences

Micro RNAs and DNA methylation are regulatory players in human cells with altered X chromosome to autosome balance

Shriram N. Rajpathak et al.

SCIENTIFIC REPORTS (2017)

Article Biotechnology & Applied Microbiology

Epigenetic and chromatin-based mechanisms in environmental stress adaptation and stress memory in plants

Jorn Laemke et al.

GENOME BIOLOGY (2017)

Review Biochemistry & Molecular Biology

Writing, erasing and reading histone lysine methylations

Kwangbeom Hyun et al.

EXPERIMENTAL AND MOLECULAR MEDICINE (2017)

Review Biochemistry & Molecular Biology

Chromatin-Based Epigenetic Regulation of Plant Abiotic Stress Response

Garima Pandey et al.

CURRENT GENOMICS (2016)

Article Plant Sciences

Expression analysis of six chromatin and remodeling complex genes (SWR1) in chickpea in different tissues and during heat stress

Parameswaran Chidambaranathan et al.

INDIAN JOURNAL OF GENETICS AND PLANT BREEDING (2016)

Article Biotechnology & Applied Microbiology

Genome-wide dissection of AP2/ERF and HSP90 gene families in five legumes and expression profiles in chickpea and pigeonpea

Gaurav Agarwal et al.

PLANT BIOTECHNOLOGY JOURNAL (2016)

Article Multidisciplinary Sciences

Methylation interactions in Arabidopsis hybrids require RNA-directed DNA methylation and are influenced by genetic variation

Qingzhu Zhang et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2016)

Article Genetics & Heredity

miR408 overexpression causes increased drought tolerance in chickpea

Mortaza Hajyzadeh et al.

Article Biochemical Research Methods

Quantitative profiling of polar primary metabolites of two chickpea cultivars with contrasting responses to salinity

Daniel Anthony Dias et al.

JOURNAL OF CHROMATOGRAPHY B-ANALYTICAL TECHNOLOGIES IN THE BIOMEDICAL AND LIFE SCIENCES (2015)

Article Multidisciplinary Sciences

Loss of Karma transposon methylation underlies the mantled somaclonal variant of oil palm

Meilina Ong-Abdullah et al.

NATURE (2015)

Article Plant Sciences

DNA methylation changes in fusarium wilt resistant and sensitive chickpea genotypes (Cicer arietinum L.)

Parvin Mohammadi et al.

PHYSIOLOGICAL AND MOLECULAR PLANT PATHOLOGY (2015)

Review Biochemistry & Molecular Biology

Low temperature tolerance in plants: Changes at the protein level

Mohsen Janmohammadi et al.

PHYTOCHEMISTRY (2015)

Article Cell Biology

Histone Variants and Epigenetics

Steven Henikoff et al.

COLD SPRING HARBOR PERSPECTIVES IN BIOLOGY (2015)

Article Biochemistry & Molecular Biology

Genotyping-by-sequencing based intra-specific genetic map refines a ''QTL-hotspot region for drought tolerance in chickpea

Deepa Jaganathan et al.

MOLECULAR GENETICS AND GENOMICS (2015)

Review Genetics & Heredity

The Genetic Control of Apomixis: Asexual Seed Formation

Melanie L. Hand et al.

GENETICS (2014)

Review Plant Sciences

Epigenetic Memory for Stress Response and Adaptation in Plants

Tetsu Kinoshita et al.

PLANT AND CELL PHYSIOLOGY (2014)

Review Agronomy

Abiotic stresses, constraints and improvement strategies in chickpea

Uday C. Jha et al.

PLANT BREEDING (2014)

Article Multidisciplinary Sciences

Mapping the Epigenetic Basis of Complex Traits

Sandra Cortijo et al.

SCIENCE (2014)

Article Agronomy

Genetic dissection of drought tolerance in chickpea (Cicer arietinum L.)

Rajeev K. Varshney et al.

THEORETICAL AND APPLIED GENETICS (2014)

Article Cell Biology

Epigenetic Regulation in Plants

Craig S. Pikaard et al.

COLD SPRING HARBOR PERSPECTIVES IN BIOLOGY (2014)

Article Cell Biology

Genomic Imprinting in Mammals

Denise P. Barlow et al.

COLD SPRING HARBOR PERSPECTIVES IN BIOLOGY (2014)

Article Plant Sciences

Halopriming of seeds imparts tolerance to NaCl and PEG induced stress in Vigna radiata (L.) Wilczek varieties

K. C. Jisha et al.

PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS (2014)

Review Biotechnology & Applied Microbiology

Achievements and prospects of genomics-assisted breeding in three legume crops of the semi-arid tropics

Rajeev K. Varshney et al.

BIOTECHNOLOGY ADVANCES (2013)

Article Plant Sciences

Overexpression of miR160 affects root growth and nitrogen-fixing nodule number in Medicago truncatula

Pilar Bustos-Sanmamed et al.

FUNCTIONAL PLANT BIOLOGY (2013)

Article Biochemistry & Molecular Biology

A SWI/SNF Chromatin-Remodeling Complex Acts in Noncoding RNA-Mediated Transcriptional Silencing

Yongyou Zhu et al.

MOLECULAR CELL (2013)

Review Biochemistry & Molecular Biology

Regulation of nucleosome dynamics by histone modifications

Gabriel E. Zentner et al.

NATURE STRUCTURAL & MOLECULAR BIOLOGY (2013)

Review Plant Sciences

Epigenetic mechanisms of plant stress responses and adaptation

Pranav Pankaj Sahu et al.

PLANT CELL REPORTS (2013)

Article Biochemistry & Molecular Biology

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

Xiao-Rong Shui et al.

PLANT SCIENCE (2013)

Article Cell Biology

The Use of Mouse Models to Study Epigenetics

Marnie Blewitt et al.

COLD SPRING HARBOR PERSPECTIVES IN BIOLOGY (2013)

Article Cell Biology

Nucleosome Remodeling and Epigenetics

Peter B. Becker et al.

COLD SPRING HARBOR PERSPECTIVES IN BIOLOGY (2013)

Article Cell Biology

Position-Effect Variegation, Heterochromatin Formation, and Gene Silencing in Drosophila

Sarah C. R. Elgin et al.

COLD SPRING HARBOR PERSPECTIVES IN BIOLOGY (2013)

Article Mathematical & Computational Biology

Significance analysis and statistical dissection of variably methylated regions

Andrew E. Jaffe et al.

BIOSTATISTICS (2012)

Article Biochemical Research Methods

A quantitative genetic and epigenetic model of complex traits

Zhong Wang et al.

BMC BIOINFORMATICS (2012)

Article Public, Environmental & Occupational Health

The Epigenotype

C. H. Waddington

INTERNATIONAL JOURNAL OF EPIDEMIOLOGY (2012)

Review Biochemistry & Molecular Biology

Histone Lysine Methylation Dynamics: Establishment, Regulation, and Biological Impact

Joshua C. Black et al.

MOLECULAR CELL (2012)

Article Plant Sciences

Descendants of Primed Arabidopsis Plants Exhibit Resistance to Biotic Stress

Ana Slaughter et al.

PLANT PHYSIOLOGY (2012)

Article Multidisciplinary Sciences

Widespread dynamic DNA methylation in response to biotic stress

Robert H. Dowen et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2012)

Review Biochemistry & Molecular Biology

Histone modifications in transcriptional activation during plant development

Alexandre Berr et al.

BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS (2011)

Review Biochemistry & Molecular Biology

Epigenetic control of gene regulation in plants

Massimiliano Lauria et al.

BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS (2011)

Review Cell Biology

Regulation of chromatin by histone modifications

Andrew J. Bannister et al.

CELL RESEARCH (2011)

Review Plant Sciences

Histone variants and modifications in plant gene regulation

Roger B. Deal et al.

CURRENT OPINION IN PLANT BIOLOGY (2011)

Review Biochemistry & Molecular Biology

Plant Cohesins, Common Themes and Unique Roles

Li Yuan et al.

CURRENT PROTEIN & PEPTIDE SCIENCE (2011)

Article Plant Sciences

Do plants remember drought? Hints towards a drought-memory in grasses

Julia Walter et al.

ENVIRONMENTAL AND EXPERIMENTAL BOTANY (2011)

Article Genetics & Heredity

Quantitative Epigenetics Through Epigenomic Perturbation of Isogenic Lines

Frank Johannes et al.

GENETICS (2011)

Article Genetics & Heredity

Epigenetic QTL Mapping in Brassica napus

Yan Long et al.

GENETICS (2011)

Review Genetics & Heredity

Studying the epigenome using next generation sequencing

Chee Seng Ku et al.

JOURNAL OF MEDICAL GENETICS (2011)

Review Cell Biology

Multisubunit RNA polymerases IV and V: purveyors of non-coding RNA for plant gene silencing

Jeremy R. Haag et al.

NATURE REVIEWS MOLECULAR CELL BIOLOGY (2011)

Article Multidisciplinary Sciences

On the Evolutionary Origin of Eukaryotic DNA Methyltransferases and Dnmt2

Tomasz P. Jurkowski et al.

PLOS ONE (2011)

Review Biochemistry & Molecular Biology

The role of chromosomal HMGB proteins in plants

Dorthe S. Pedersen et al.

BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS (2010)

Article Biochemistry & Molecular Biology

H2A.Z-Containing Nucleosomes Mediate the Thermosensory Response in Arabidopsis

S. Vinod Kumar et al.

Review Biochemistry & Molecular Biology

Histone3 variants in plants

Mathieu Ingouff et al.

CHROMOSOMA (2010)

Review Plant Sciences

Evolution of halophytes: multiple origins of salt tolerance in land plants

Timothy J. Flowers et al.

FUNCTIONAL PLANT BIOLOGY (2010)

Letter Oncology

Ductal Carcinoma in Situ: Dilemma or Denouement Reply

Jay R. Harris et al.

JOURNAL OF CLINICAL ONCOLOGY (2010)

Review Biochemistry & Molecular Biology

Plant Immunity Triggered by Microbial Molecular Signatures

Jie Zhang et al.

MOLECULAR PLANT (2010)

Article Multidisciplinary Sciences

Conserved role of intragenic DNA methylation in regulating alternative promoters

Alika K. Maunakea et al.

NATURE (2010)

Article Plant Sciences

Stress-induced DNA methylation changes and their heritability in asexual dandelions

Koen J. F. Verhoeven et al.

NEW PHYTOLOGIST (2010)

Article Biochemistry & Molecular Biology

Global Epigenetic and Transcriptional Trends among Two Rice Subspecies and Their Reciprocal Hybrids

Guangming He et al.

PLANT CELL (2010)

Article Multidisciplinary Sciences

Conservation and divergence of methylation patterning in plants and animals

Suhua Feng et al.

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2010)

Review Plant Sciences

The biosynthetic pathways and biological scopes of plant small RNAs

Franck Vazquez et al.

TRENDS IN PLANT SCIENCE (2010)

Review Genetics & Heredity

Genome-scale DNA methylation analysis

Shaun D. Fouse et al.

EPIGENOMICS (2010)

Article Plant Sciences

Differential expression of miRNAs in response to salt stress in maize roots

Dong Ding et al.

ANNALS OF BOTANY (2009)

Review Plant Sciences

Roles of Plant Small RNAs in Biotic Stress Responses

Virginia Ruiz-Ferrer et al.

ANNUAL REVIEW OF PLANT BIOLOGY (2009)

Review Plant Sciences

Epigenetic regulation of stress responses in plants

Viswanathan Chinnusamy et al.

CURRENT OPINION IN PLANT BIOLOGY (2009)

Article Cell Biology

An operational definition of epigenetics

Shelley L. Berger et al.

GENES & DEVELOPMENT (2009)

Article Multidisciplinary Sciences

Altered circadian rhythms regulate growth vigour in hybrids and allopolyploids

Zhongfu Ni et al.

NATURE (2009)

Article Multidisciplinary Sciences

A Role for RNAi in the Selective Correction of DNA Methylation Defects

Felipe Karam Teixeira et al.

SCIENCE (2009)

Article Multidisciplinary Sciences

Histone H2A.Z and DNA methylation are mutually antagonistic chromatin marks

Daniel Zilberman et al.

NATURE (2008)

Article Plant Sciences

A gene expression atlas of the model legume Medicago truncatula

Vagner A. Benedito et al.

PLANT JOURNAL (2008)

Review Ecology

Origins and evolution of eukaryotic RNA interference

Svetlana A. Shabalina et al.

TRENDS IN ECOLOGY & EVOLUTION (2008)

Review Plant Sciences

Plant ARGONAUTES

Herve Vaucheret

TRENDS IN PLANT SCIENCE (2008)

Review Biochemistry & Molecular Biology

Stressful memories of plants: Evidence and possible mechanisms

Toby J. A. Bruce et al.

PLANT SCIENCE (2007)

Article Biochemical Research Methods

Comparative proteomics analysis of differentially expressed proteins in chickpea extracellular matrix during dehydration stress

Deepti Bhushan et al.

MOLECULAR & CELLULAR PROTEOMICS (2007)

Review Genetics & Heredity

Specialization and evolution of endogenous small RNA pathways

Elisabeth J. Chapman et al.

NATURE REVIEWS GENETICS (2007)

Review Biochemistry & Molecular Biology

SWI/SNF chromatin remodeling and linker histones in plants

Andrzej Jerzmanowski

BIOCHIMICA ET BIOPHYSICA ACTA-GENE STRUCTURE AND EXPRESSION (2007)

Article Biochemistry & Molecular Biology

Identification of drought-induced microRNAs in rice

Botao Zhao et al.

BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS (2007)

Review Biochemistry & Molecular Biology

The epigenomics of cancer

Peter A. Jones et al.

Article Agronomy

Hydro- and osmopriming improve chickpea germination

Erdal Elkoca et al.

ACTA AGRICULTURAE SCANDINAVICA SECTION B-SOIL AND PLANT SCIENCE (2007)

Article Biochemistry & Molecular Biology

A multistep process gave rise to RNA polymerase IV of land plants

Jie Luo et al.

JOURNAL OF MOLECULAR EVOLUTION (2007)

Article Multidisciplinary Sciences

Transgeneration memory of stress in plants

Jean Molinier et al.

NATURE (2006)

Review Genetics & Heredity

Opinion - Inherited epigenetic variation - revisiting soft inheritance

EJ Richards

NATURE REVIEWS GENETICS (2006)

Review Microbiology

Epigenetic gene regulation in the bacterial world

Josep Casadesus et al.

MICROBIOLOGY AND MOLECULAR BIOLOGY REVIEWS (2006)

Article Biochemistry & Molecular Biology

Arabidopsis RPA2:: A genetic link among transcriptional gene silencing, DNA repair, and DNA replication

T Elmayan et al.

CURRENT BIOLOGY (2005)

Review Biochemistry & Molecular Biology

Pathways through the small RNA world of plants

AJ Herr

FEBS LETTERS (2005)

Review Plant Sciences

The effect of stress on genome regulation and structure

A Madlung et al.

ANNALS OF BOTANY (2004)

Review Plant Sciences

Epi-alleles in plants: Inheritance of epigenetic information over generations

T Kakutani

PLANT AND CELL PHYSIOLOGY (2002)

Review Plant Sciences

Apomixis in agriculture: the quest for clonal seeds

C Spillane et al.

SEXUAL PLANT REPRODUCTION (2001)

Article Biochemistry & Molecular Biology

Epigenetic aspects of somaclonal variation in plants

SM Kaeppler et al.

PLANT MOLECULAR BIOLOGY (2000)

Review Biochemistry & Molecular Biology

Plants as bioreactors for protein production: avoiding the problem of transgene silencing

C De Wilde et al.

PLANT MOLECULAR BIOLOGY (2000)

Article Plant Sciences

Enhancement of salt tolerance in soybean with NaCl pretreatment

T Umezawa et al.

PHYSIOLOGIA PLANTARUM (2000)