Transcriptomic, Proteomic, Metabolomic and Functional Genomic Approaches for the Study of Abiotic Stress in Vegetable Crops

Genome-wide analysis of the AP2/ERF transcription factor superfamily in Chinese cabbage (Brassica rapa ssp. pekinensis)

(2013) Xiaoming Song et al.   BMC GENOMICS

Metabolic Profiling of Transgenic Potato Tubers Expressing Arabidopsis Dehydration Response Element-Binding Protein 1A (DREB1A)

(2013) Toshio Iwaki et al.   JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY

Comparative transcriptome analysis of pepper (Capsicum annuum) revealed common regulons in multiple stress conditions and hormone treatments

(2013) Sanghyeob Lee et al.   PLANT CELL REPORTS

A Rice OsAP23, Functioning as an AP2/ERF Transcription Factor, Reduces Salt Tolerance in Transgenic Arabidopsis

(2013) Jing Zhuang et al.   PLANT MOLECULAR BIOLOGY REPORTER

Genome-wide Analysis of the Distribution of AP2/ERF Transcription Factors Reveals Duplication and Elucidates their Potential Function in Chinese Cabbage (Brassica rapa ssp. pekinensis)

(2013) Meng-Yao Li et al.   PLANT MOLECULAR BIOLOGY REPORTER

De Novo Assembly, Gene Annotation and Marker Development Using Illumina Paired-End Transcriptome Sequences in Celery (Apium graveolens L.)

(2013) Nan Fu et al.   PLoS One

Identification and QTL mapping of whitefly resistance components in Solanum galapagense

(2013) Syarifin Firdaus et al.   THEORETICAL AND APPLIED GENETICS

Metabolomics of forage plants: a review

(2012) Susanne Rasmussen et al.   ANNALS OF BOTANY

Transcriptome sequencing for SNP discovery across Cucumis melo

(2012) José Blanca et al.   BMC GENOMICS

High-throughput SNP genotyping in Cucurbita pepo for map construction and quantitative trait loci mapping

(2012) Cristina Esteras et al.   BMC GENOMICS

Effects of yeast trehalose-6-phosphate synthase 1 on gene expression and carbohydrate contents of potato leaves under drought stress conditions

(2012) Mihály Kondrák et al.   BMC PLANT BIOLOGY

smRNAome profiling to identify conserved and novel microRNAs in Stevia rebaudiana Bertoni

(2012) Vibha Mandhan et al.   BMC PLANT BIOLOGY

The use of metabolomics to dissect plant responses to abiotic stresses

(2012) Toshihiro Obata et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Salt Tolerance in Selected Vegetable Crops

(2012) M. Shahbaz et al.   CRITICAL REVIEWS IN PLANT SCIENCES

Short Communication Discovery of a large set of SNP and SSR genetic markers by high-throughput sequencing of pepper (Capsicum annuum)

(2012) M. Nicolaï et al.   GENETICS AND MOLECULAR RESEARCH

Recent Progress Using High-throughput Sequencing Technologies in Plant Molecular BreedingF

(2012) Qiang Gao et al.   Journal of Integrative Plant Biology

Proteomic analysis of differentially accumulated proteins during ripening and in response to 1-MCP in papaya fruit

(2012) José Ángel Huerta-Ocampo et al.   Journal of Proteomics

Proteomic analysis of embryonic axis of Pisum sativum seeds during germination and identification of proteins associated with loss of desiccation tolerance

(2012) Wei-Qing Wang et al.   Journal of Proteomics

Differential proteomic analysis of drought stress response in leaves of common bean (Phaseolus vulgaris L.)

(2012) Tanja Zadražnik et al.   Journal of Proteomics

Expression and Function of a Modified AP2/ERF Transcription Factor from Brassica napus Enhances Cold Tolerance in Transgenic Arabidopsis

(2012) Ai-Sheng Xiong et al.   MOLECULAR BIOTECHNOLOGY

Transcriptome analysis of rin mutant fruit and in silico analysis of promoters of differentially regulated genes provides insight into LeMADS-RIN-regulated ethylene-dependent as well as ethylene-independent aspects of ripening in tomato

(2012) Rahul Kumar et al.   MOLECULAR GENETICS AND GENOMICS

The tomato genome sequence provides insights into fleshy fruit evolution

(2012)   NATURE

Why We Should Stop Inferring Simple Correlations Between Antioxidants and Plant Stress Resistance: Towards the Antioxidomic Era

(2012) F. Vanessa Loiacono et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

Relevance of Proteomic Investigations in Plant Abiotic Stress Physiology

(2012) Khalid Rehman Hakeem et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

Proteome Changes in Tomato Fruits Prior to Visible Symptoms of Chilling Injury are Linked to Defensive Mechanisms, Uncoupling of Photosynthetic Processes and Protein Degradation Machinery

(2012) Paloma Sanchez-Bel et al.   PLANT AND CELL PHYSIOLOGY

Proteomic changes associated with freeze-thaw injury and post-thaw recovery in onion (Allium cepaL.) scales

(2012) KETING CHEN et al.   PLANT CELL AND ENVIRONMENT

Metabolite analyses of single cells

(2012) Akira Oikawa et al.   PLANT JOURNAL

Use of mass spectrometry for imaging metabolites in plants

(2012) Young Jin Lee et al.   PLANT JOURNAL

High-resolution plant metabolomics: from mass spectral features to metabolites and from whole-cell analysis to subcellular metabolite distributions

(2012) Stephan Kueger et al.   PLANT JOURNAL

Towards a synthetic view of potato cold and salt stress response by transcriptomic and proteomic analyses

(2012) D. Evers et al.   PLANT MOLECULAR BIOLOGY

Genome-wide characterization of the CBF/DREB1 gene family in Brassica rapa

(2012) Sang-Choon Lee et al.   PLANT PHYSIOLOGY AND BIOCHEMISTRY

Identification of heat-sensitive QTL derived from common wild rice (Oryza rufipogon Griff.)

(2012) Dongyang Lei et al.   PLANT SCIENCE

Digital Gene Expression Analysis Based on Integrated De Novo Transcriptome Assembly of Sweet Potato [Ipomoea batatas (L.) Lam.]

(2012) Xiang Tao et al.   PLoS One

QTL Analysis of Na+ and K+ Concentrations in Roots and Shoots under Different Levels of NaCl Stress in Rice (Oryza sativa L.)

(2012) Zhoufei Wang et al.   PLoS One

Arabidopsis proline-rich protein important for development and abiotic stress tolerance is involved in microRNA biogenesis

(2012) X. Zhan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Enabling proteomic studies with RNA-Seq: The proteome of tomato pollen as a test case

(2012) Gloria Lopez-Casado et al.   PROTEOMICS

The Oviduct: Functional Genomic and Proteomic Approach

(2012) I Mondéjar et al.   REPRODUCTION IN DOMESTIC ANIMALS

Functions of microRNAs in plant stress responses

(2012) Ramanjulu Sunkar et al.   TRENDS IN PLANT SCIENCE

Proteome-wide prediction of protein-protein interactions from high-throughput data

(2012) Zhi-Ping Liu et al.   Protein & Cell

AP2/ERF family transcription factors in plant abiotic stress responses

(2011) Junya Mizoi et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

Expression of dehydration responsive element-binding protein-3 (DREB3) under different abiotic stresses in tomato

(2011) Mohammad Saiful Islam et al.   BMB Reports

Comprehensive transcriptome analysis of the highly complex Pisum sativum genome using next generation sequencing

(2011) Susanne U Franssen et al.   BMC GENOMICS

Transcriptome characterization and high throughput SSRs and SNPs discovery in Cucurbita pepo (Cucurbitaceae)

(2011) José Blanca et al.   BMC GENOMICS

The salt-responsive transcriptome of chickpea roots and nodules via deepSuperSAGE

(2011) Carlos Molina et al.   BMC PLANT BIOLOGY

Development of genic-SSR markers by deep transcriptome sequencing in pigeonpea [Cajanus cajan (L.) Millspaugh]

(2011) Sutapa Dutta et al.   BMC PLANT BIOLOGY

Transcriptome analysis of ectopic chloroplast development in green curd cauliflower (Brassica oleracea L. var. botrytis)

(2011) Xiangjun Zhou et al.   BMC PLANT BIOLOGY

Cell Wall Modifying Proteins Mediate Plant Acclimatization to Biotic and Abiotic Stresses

(2011) Rashmi Sasidharan et al.   CRITICAL REVIEWS IN PLANT SCIENCES

Recent Updates on Salinity Stress in Rice: From Physiological to Molecular Responses

(2011) S. Negrão et al.   CRITICAL REVIEWS IN PLANT SCIENCES

TransgenicPopulusTrees for Forest Products, Bioenergy, and Functional Genomics

(2011) Xia Ye et al.   CRITICAL REVIEWS IN PLANT SCIENCES

Gene Expression Profiling of Plants under Salt Stress

(2011) A. Jamil et al.   CRITICAL REVIEWS IN PLANT SCIENCES

Defining the Transcriptome Assembly and Its Use for Genome Dynamics and Transcriptome Profiling Studies in Pigeonpea (Cajanus cajan L.)

(2011) A. Dubey et al.   DNA RESEARCH

Genome-wide identification and phylogenetic analysis of the ERF gene family in cucumbers

(2011) Lifang Hu et al.   GENETICS AND MOLECULAR BIOLOGY

Assessment of Prunus persica fruit softening using a proteomics approach

(2011) Ricardo Nilo P. et al.   Journal of Proteomics

Proteomic analysis of papaya fruit ripening using 2DE-DIGE

(2011) Silvia Beserra Nogueira et al.   Journal of Proteomics

Floral reversion mechanism in longan (Dimocarpus longan Lour.) revealed by proteomic and anatomic analyses

(2011) Xiangrong You et al.   Journal of Proteomics

A novel cold-inducible gene from Pak-choi (Brassica campestris ssp. chinensis), BcWRKY46, enhances the cold, salt and dehydration stress tolerance in transgenic tobacco

(2011) Feng Wang et al.   MOLECULAR BIOLOGY REPORTS

Identification of miRNAs and Their Target Genes Using Deep Sequencing and Degradome Analysis in Trifoliate Orange [Poncirus trifoliate (L.) Raf]

(2011) Jin-Zhi Zhang et al.   MOLECULAR BIOTECHNOLOGY

Genome sequence and analysis of the tuber crop potato

(2011) Xun Xu et al.   NATURE

Draft genome sequence of pigeonpea (Cajanus cajan), an orphan legume crop of resource-poor farmers

(2011) Rajeev K Varshney et al.   NATURE BIOTECHNOLOGY

The genome of the mesopolyploid crop species Brassica rapa

(2011) Xiaowu Wang et al.   NATURE GENETICS

Salt stress induces the formation of a novel type of ‘pressure wood’ in two Populus species

(2011) Dennis Janz et al.   NEW PHYTOLOGIST

Arabidopsis Seed Germination Under Abiotic Stress as a Concert of Action of Phytohormones

(2011) Agata Daszkowska-Golec   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

Transcription Regulation of Abiotic Stress Responses in Rice: A Combined Action of Transcription Factors and Epigenetic Mechanisms

(2011) Ana Paula Santos et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

An Omics Approach to Understand the Plant Abiotic Stress

(2011) Mousumi Debnath et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

Salt-Stress Induced Physiological and Proteomic Changes in Tomato (Solanum lycopersicum) Seedlings

(2011) Arafet Manaa et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

Proteomic analysis of peach endocarp and mesocarp during early fruit development

(2011) Hao Hu et al.   PHYSIOLOGIA PLANTARUM

An ethylene response factor (ERF5) promoting adaptation to drought and salt tolerance in tomato

(2011) Yu Pan et al.   PLANT CELL REPORTS

MicroRNAs and their diverse functions in plants

(2011) Guiling Sun   PLANT MOLECULAR BIOLOGY

Ubiquitin/proteasome-mediated proteolysis is involved in the response to flooding stress in soybean roots, independent of oxygen limitation

(2011) Yuki Yanagawa et al.   PLANT SCIENCE

Transcriptome Analysis of Potato Leaves Expressing the Trehalose-6-Phosphate Synthase 1 Gene of Yeast

(2011) Mihály Kondrák et al.   PLoS One

Identification and Characterization of microRNAs from Peanut (Arachis hypogaea L.) by High-Throughput Sequencing

(2011) Xiaoyuan Chi et al.   PLoS One

MALDI-imaging mass spectrometry - An emerging technique in plant biology

(2011) Stephanie Kaspar et al.   PROTEOMICS

Diverse set of microRNAs are responsive to powdery mildew infection and heat stress in wheat (Triticum aestivum L.)

(2010) Mingming Xin et al.   BMC PLANT BIOLOGY

‘Omics’ analyses of regulatory networks in plant abiotic stress responses

(2010) Kaoru Urano et al.   CURRENT OPINION IN PLANT BIOLOGY

Identification of drought-responsive compounds in potato through a combined transcriptomic and targeted metabolite approach

(2010) Danièle Evers et al.   JOURNAL OF EXPERIMENTAL BOTANY

Molecular Mechanisms Regulating Rapid Stress Signaling Networks inArabidopsis

(2010) Justin W. Walley et al.   Journal of Integrative Plant Biology

Isolation and characterization of an AP2/ERF-RAV transcription factor BnaRAV-1-HY15 in Brassica napus L. HuYou15

(2010) Jing Zhuang et al.   MOLECULAR BIOLOGY REPORTS

Identification, phylogeny, and transcript profiling of ERF family genes during development and abiotic stress treatments in tomato

(2010) Manoj K. Sharma et al.   MOLECULAR GENETICS AND GENOMICS

Quantitative analysis of major plant hormones in crude plant extracts by high-performance liquid chromatography–mass spectrometry

(2010) Xiangqing Pan et al.   Nature Protocols

PlantTFDB 2.0: update and improvement of the comprehensive plant transcription factor database

(2010) He Zhang et al.   NUCLEIC ACIDS RESEARCH

Metabolomics for plant stress response

(2010) Vladimir Shulaev et al.   PHYSIOLOGIA PLANTARUM

The role of abscisic acid and auxin in the response of poplar to abiotic stress

(2010) J. Popko et al.   PLANT BIOLOGY

Identification and validation of conserved microRNAs along with their differential expression in roots of Vigna unguiculata grown under salt stress

(2010) Sujay Paul et al.   PLANT CELL TISSUE AND ORGAN CULTURE

Evolutionary and comparative analysis of MYB and bHLH plant transcription factors

(2010) Antje Feller et al.   PLANT JOURNAL

Components of the Arabidopsis CBF Cold-Response Pathway Are Conserved in Non-heading Chinese Cabbage

(2010) Fangling Jiang et al.   PLANT MOLECULAR BIOLOGY REPORTER

DREB2C Interacts with ABF2, a bZIP Protein Regulating Abscisic Acid-Responsive Gene Expression, and Its Overexpression Affects Abscisic Acid Sensitivity

(2010) S.-j. Lee et al.   PLANT PHYSIOLOGY

A proteomic approach to decipher chilling response from cold acclimation in pea (Pisum sativum L.)

(2010) Estelle Dumont et al.   PLANT SCIENCE

MYB transcription factors in Arabidopsis

(2010) Christian Dubos et al.   TRENDS IN PLANT SCIENCE

Metabolomics for Functional Genomics, Systems Biology, and Biotechnology

(2009) Kazuki Saito et al.   Annual Review of Plant Biology

Deep sequencing of Brachypodium small RNAs at the global genome level identifies microRNAs involved in cold stress response

(2009) Jingyu Zhang et al.   BMC GENOMICS

Expression profiling of microRNAs by deep sequencing

(2009) C. J. Creighton et al.   BRIEFINGS IN BIOINFORMATICS

Origins and Mechanisms of miRNAs and siRNAs

(2009) Richard W. Carthew et al.   CELL

Mass spectrometry based metabolomics and enzymatic assays for functional genomics

(2009) Richard Baran et al.   CURRENT OPINION IN MICROBIOLOGY

Proteome changes induced by aluminium stress in tomato roots

(2009) S. Zhou et al.   JOURNAL OF EXPERIMENTAL BOTANY

Proteomic analysis of salt-stressed tomato (Solanum lycopersicum) seedlings: effect of genotype and exogenous application of glycinebetaine

(2009) Songbi Chen et al.   JOURNAL OF EXPERIMENTAL BOTANY

Metabolic changes in Agrobacterium tumefaciens-infected Brassica rapa

(2009) Sanimah Simoh et al.   JOURNAL OF PLANT PHYSIOLOGY

Analysis of Brassica rapa ESTs: gene discovery and expression patterns of AP2/ERF family genes

(2009) Jing Zhuang et al.   MOLECULAR BIOLOGY REPORTS

The genome of the cucumber, Cucumis sativus L.

(2009) Sanwen Huang et al.   NATURE GENETICS

Metabolomic analysis of host plant resistance to thrips in wild and cultivated tomatoes

(2009) Mohammad Mirnezhad et al.   PHYTOCHEMICAL ANALYSIS

Application of NMR in plant metabolomics: techniques, problems and prospects

(2009) Jan Schripsema   PHYTOCHEMICAL ANALYSIS

Metabolic response of tomato leaves upon different plant–pathogen interactions

(2009) M. Pilar López-Gresa et al.   PHYTOCHEMICAL ANALYSIS

Functional Analysis of Transcription Factors in Arabidopsis

(2009) Nobutaka Mitsuda et al.   PLANT AND CELL PHYSIOLOGY

Transcriptional Regulatory Networks in Response to Abiotic Stresses in Arabidopsis and Grasses

(2009) K. Nakashima et al.   PLANT PHYSIOLOGY

Proteomics reveal tissue-specific features of the cress (Lepidium sativumL.) endosperm cap proteome and its hormone-induced changes during seed germination

(2009) Kerstin Müller et al.   PROTEOMICS

Genome-wide analysis of the putative AP2/ERF family genes in Vitis vinifera

(2009) Jing Zhuang et al.   SCIENTIA HORTICULTURAE

Genome-wide analysis of the AP2/ERF gene family in Populus trichocarpa

(2008) Jing Zhuang et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

Two-dimensional polyacrylamide gel electrophoresis (2D-PAGE): advances and perspectives

(2008) Haleem J. Issaq et al.   BIOTECHNIQUES

Water-deficit stress-induced anatomical changes in higher plants

(2008) Hong-Bo Shao et al.   COMPTES RENDUS BIOLOGIES

Deep sequencing of tomato short RNAs identifies microRNAs targeting genes involved in fruit ripening

(2008) S. Moxon et al.   GENOME RESEARCH

Metal ion-inducing metabolite accumulation in Brassica rapa

(2008) Muhammad Jahangir et al.   JOURNAL OF PLANT PHYSIOLOGY

Proteome Analysis of Potato under Salt Stress

(2008) Keyvan Aghaei et al.   JOURNAL OF PROTEOME RESEARCH

Differential expression of proteins in the wild type and 7B-1 male-sterile mutant anthers of tomato (Solanum lycopersicum): A proteomic analysis

(2008) Inder S. Sheoran et al.   Journal of Proteomics

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS

Proteomic analysis of somatic embryogenesis in Valencia sweet orange (Citrus sinensis Osbeck)

(2008) Zhiyong Pan et al.   PLANT CELL REPORTS