Genomic resources for breeding crops with enhanced abiotic stress tolerance

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

(2013) Rajeev K Varshney et al.   NATURE BIOTECHNOLOGY

A draft genome sequence of the pulse crop chickpea (Cicer arietinum L.)

(2013) Mukesh Jain et al.   PLANT JOURNAL

Resequencing rice genomes: an emerging new era of rice genomics

(2013) Xuehui Huang et al.   TRENDS IN GENETICS

A new RNASeq-based reference transcriptome for sugar beet and its application in transcriptome-scale analysis of vernalization and gibberellin responses

(2012) Effie S Mutasa-Göttgens et al.   BMC GENOMICS

Genome wide expression profiling of two accession of G. herbaceum L. in response to drought

(2012) Alok Ranjan et al.   BMC GENOMICS

De novo sequencing and characterization of Picrorhiza kurrooa transcriptome at two temperatures showed major transcriptome adjustments

(2012) Parul Gahlan et al.   BMC GENOMICS

De novo sequencing and analysis of root transcriptome using 454 pyrosequencing to discover putative genes associated with drought tolerance in Ammopiptanthus mongolicus

(2012) Yijun Zhou et al.   BMC GENOMICS

Identification of wounding and topping responsive small RNAs in tobacco (Nicotiana tabacum)

(2012) She Tang et al.   BMC PLANT BIOLOGY

Generation and analysis of blueberry transcriptome sequences from leaves, developing fruit, and flower buds from cold acclimation through deacclimation

(2012) Lisa J Rowland et al.   BMC PLANT BIOLOGY

Identification of novel and conserved Populus tomentosa microRNA as components of a response to water stress

(2012) Yuanyuan Ren et al.   FUNCTIONAL & INTEGRATIVE GENOMICS

Genome-wide identification and expression analysis of heat-responsive and novel microRNAs in Populus tomentosa

(2012) Lei Chen et al.   GENE

Identification of differentially expressed genes in cucumber (Cucumis sativus L.) root under waterlogging stress by digital gene expression profile

(2012) Xiao-Hua Qi et al.   GENOMICS

Molecular dissection of atrazine-responsive transcriptome and gene networks in rice by high-throughput sequencing

(2012) Jia Jun Zhang et al.   JOURNAL OF HAZARDOUS MATERIALS

Identification of SNP Mutations in DREB1, HKT1, and WRKY1 Genes Involved in Drought and Salt Stress Tolerance in Durum Wheat (Triticum turgidum L. var durum)

(2012) Linda Mondini et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

New Insights in the Sugarcane Transcriptome Responding to Drought Stress as Revealed by Supersage

(2012) Éderson Akio Kido et al.   TheScientificWorldJOURNAL

Genome-wide identification of cold-responsive and new microRNAs in Populus tomentosa by high-throughput sequencing

(2011) Lei Chen et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

HTPheno: An image analysis pipeline for high-throughput plant phenotyping

(2011) Anja Hartmann et al.   BMC BIOINFORMATICS

Functional annotation of the transcriptome of Sorghum bicolor in response to osmotic stress and abscisic acid

(2011) Diana V Dugas et al.   BMC GENOMICS

Identification of genes associated with nitrogen-use efficiency by genome-wide transcriptional analysis of two soybean genotypes

(2011) Qing N Hao et al.   BMC GENOMICS

Annotation-based genome-wide SNP discovery in the large and complex Aegilops tauschii genome using next-generation sequencing without a reference genome sequence

(2011) Frank M You et al.   BMC GENOMICS

Identification of drought-responsive microRNAs in Medicago truncatula by genome-wide high-throughput sequencing

(2011) Tianzuo Wang et al.   BMC GENOMICS

Exome-wide DNA capture and next generation sequencing in domestic and wild species

(2011) Ted Cosart et al.   BMC GENOMICS

High levels of nucleotide diversity and fast decline of linkage disequilibrium in rye (Secale cereale L.) genes involved in frost response

(2011) Yongle Li et al.   BMC PLANT BIOLOGY

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

(2011) Carlos Molina et al.   BMC PLANT BIOLOGY

Association analysis of frost tolerance in rye using candidate genes and phenotypic data from controlled, semi-controlled, and field phenotyping platforms

(2011) Yongle Li et al.   BMC PLANT BIOLOGY

Adaptation of barley to mild winters: A role for PPDH2

(2011) M Cristina Casao et al.   BMC PLANT BIOLOGY

Allele mining and haplotype discovery in barley candidate genes for drought tolerance

(2011) András Cseri et al.   EUPHYTICA

An abiotic stress response gene TaSnRK2.7-B in wheat accessions: Genetic diversity analysis and gene mapping based on SNPs

(2011) Hongying Zhang et al.   GENE

Genetic diversity analysis of abiotic stress response gene TaSnRK2.7-A in common wheat

(2011) Hongying Zhang et al.   GENETICA

An analysis of the polymorphisms in a gene for being involved in drought tolerance in maize

(2011) Liang Li et al.   GENETICA

Multiplexed shotgun genotyping for rapid and efficient genetic mapping

(2011) P. Andolfatto et al.   GENOME RESEARCH

Microarray-based analysis of cadmium-responsive microRNAs in rice (Oryza sativa)

(2011) Yanfei Ding et al.   JOURNAL OF EXPERIMENTAL BOTANY

OsWRKY45 alleles play different roles in abscisic acid signalling and salt stress tolerance but similar roles in drought and cold tolerance in rice

(2011) Zeng Tao et al.   JOURNAL OF EXPERIMENTAL BOTANY

Association of an SNP in a novel DREB2-like gene SiDREB2 with stress tolerance in foxtail millet [Setaria italica (L.)]

(2011) Charu Lata et al.   JOURNAL OF EXPERIMENTAL BOTANY

Identification of Functional Genetic Variations Underlying Drought Tolerance in Maize Using SNP Markers

(2011) Zhuanfang Hao et al.   Journal of Integrative Plant Biology

The first draft of the pigeonpea genome sequence

(2011) Nagendra K. Singh et al.   JOURNAL OF PLANT BIOCHEMISTRY AND BIOTECHNOLOGY

SNP discovery in black cottonwood (Populus trichocarpa) by population transcriptome resequencing

(2011) ARMANDO GERALDES et al.   Molecular Ecology Resources

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

(2011) Rajeev K Varshney et al.   NATURE BIOTECHNOLOGY

Whole-genome sequencing of multiple Arabidopsis thaliana populations

(2011) Jun Cao et al.   NATURE GENETICS

Genome-wide genetic marker discovery and genotyping using next-generation sequencing

(2011) John W. Davey et al.   NATURE REVIEWS GENETICS

Physiological and molecular analysis of polyethylene glycol-induced reduction of aluminium accumulation in the root tips of common bean (Phaseolus vulgaris)

(2011) Zhong-Bao Yang et al.   NEW PHYTOLOGIST

Analysis of Leaf and Root Transcriptomes of Soil-Grown Avena barbata Plants

(2011) Stéphanie M. Swarbreck et al.   PLANT AND CELL PHYSIOLOGY

Characterisation and natural variation of a dehydrin gene in Quercus petraea (Matt.) Liebl.

(2011) B. Vornam et al.   PLANT BIOLOGY

Large-scale transcriptome analysis in chickpea (Cicer arietinum L.), an orphan legume crop of the semi-arid tropics of Asia and Africa

(2011) Pavana J. Hiremath et al.   PLANT BIOTECHNOLOGY JOURNAL

Regulation of miR319 during cold stress in sugarcane

(2011) FLÁVIA THIEBAUT et al.   PLANT CELL AND ENVIRONMENT

Use of EcoTILLING to identify natural allelic variants of rice candidate genes involved in salinity tolerance

(2011) S. Negrão et al.   Plant Genetic Resources-Characterization and Utilization

A Robust, Simple Genotyping-by-Sequencing (GBS) Approach for High Diversity Species

(2011) Robert J. Elshire et al.   PLoS One

Linkage Mapping and Comparative Genomics Using Next-Generation RAD Sequencing of a Non-Model Organism

(2011) Simon W. Baxter et al.   PLoS One

Genome-Wide Identification of MicroRNAs in Response to Low Nitrate Availability in Maize Leaves and Roots

(2011) Zhenhua Xu et al.   PLoS One

Targeted enrichment of ancient pathogens yielding the pPCP1 plasmid of Yersinia pestis from victims of the Black Death

(2011) V. J. Schuenemann et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genome-wide association mapping reveals a rich genetic architecture of complex traits in Oryza sativa

(2011) Keyan Zhao et al.   Nature Communications

Two Evolutionary Histories in the Genome of Rice: the Roles of Domestication Genes

(2011) Ziwen He et al.   PLoS Genetics

Allele mining in crops: Prospects and potentials

(2010) G. Ram Kumar et al.   BIOTECHNOLOGY ADVANCES

Massive parallel sequencing of mRNA in identification of unannotated salinity stress-inducible transcripts in rice (Oryza sativa L.)

(2010) Hiroshi Mizuno et al.   BMC GENOMICS

Using association mapping to dissect the genetic basis of complex traits in plants

(2010) D. Hall et al.   Briefings in Functional Genomics

Association genetics in crop improvement

(2010) J Antoni Rafalski   CURRENT OPINION IN PLANT BIOLOGY

Accessing genetic diversity for crop improvement

(2010) JC Glaszmann et al.   CURRENT OPINION IN PLANT BIOLOGY

Glutenin allelic variation and 1AL.1RS effects on dough mixing properties of wheat grown in irrigated and rainfed environments

(2010) Shusong Zheng et al.   EUPHYTICA

Accurate detection and genotyping of SNPs utilizing population sequencing data

(2010) V. Bansal et al.   GENOME RESEARCH

Population genetic inference from genomic sequence variation

(2010) J. E. Pool et al.   GENOME RESEARCH

Characterization of a common wheat (Triticum aestivum L.) TaSnRK2.7 gene involved in abiotic stress responses

(2010) Hongying Zhang et al.   JOURNAL OF EXPERIMENTAL BOTANY

Association mapping in durum wheat grown across a broad range of water regimes

(2010) Marco Maccaferri et al.   JOURNAL OF EXPERIMENTAL BOTANY

Genetic association mapping identifies single nucleotide polymorphisms in genes that affect abscisic acid levels in maize floral tissues during drought

(2010) Tim L. Setter et al.   JOURNAL OF EXPERIMENTAL BOTANY

Genome-wide identification and analysis of drought-responsive microRNAs in Oryza sativa

(2010) Liguo Zhou et al.   JOURNAL OF EXPERIMENTAL BOTANY

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

(2010) Jinsheng Lai et al.   NATURE GENETICS

Comparative analysis of drought-responsive transcriptome in Indica rice genotypes with contrasting drought tolerance

(2010) Sangram K. Lenka et al.   PLANT BIOTECHNOLOGY JOURNAL

Identification of iron-deficiency responsive microRNA genes and cis-elements in Arabidopsis

(2010) Wei Wei Kong et al.   PLANT PHYSIOLOGY AND BIOCHEMISTRY

Overexpression of a Common Wheat Gene TaSnRK2.8 Enhances Tolerance to Drought, Salt and Low Temperature in Arabidopsis

(2010) Hongying Zhang et al.   PLoS One

Joint linkage-linkage disequilibrium mapping is a powerful approach to detecting quantitative trait loci underlying drought tolerance in maize

(2010) Y. Lu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Rate and Molecular Spectrum of Spontaneous Mutations in Arabidopsis thaliana

(2010) S. Ossowski et al.   SCIENCE

Development of highly polymorphic SNP markers from the complexity reduced portion of maize [Zea mays L.] genome for use in marker-assisted breeding

(2010) Jafar A. Mammadov et al.   THEORETICAL AND APPLIED GENETICS

Effects of ascertainment bias and marker number on estimations of barley diversity from high-throughput SNP genotype data

(2010) M. Moragues et al.   THEORETICAL AND APPLIED GENETICS

Structure, allelic diversity and selection of Asr genes, candidate for drought tolerance, in Oryza sativa L. and wild relatives

(2010) Romain Philippe et al.   THEORETICAL AND APPLIED GENETICS

SNP identification in crop plants

(2009) Martin W Ganal et al.   CURRENT OPINION IN PLANT BIOLOGY

High-throughput genotyping by whole-genome resequencing

(2009) X. Huang et al.   GENOME RESEARCH

Finding the fifth base: Genome-wide sequencing of cytosine methylation

(2009) R. Lister et al.   GENOME RESEARCH

Multilocus sequence data reveal extensive departures from equilibrium in domesticated tomato (Solanum lycopersicum L.)

(2009) J A Labate et al.   HEREDITY

Hypoxia-responsive microRNAs and trans-acting small interfering RNAs in Arabidopsis

(2009) Dov Moldovan et al.   JOURNAL OF EXPERIMENTAL BOTANY

UV-B-responsive microRNAs in Populus tremula

(2009) Xiaoyun Jia et al.   JOURNAL OF PLANT PHYSIOLOGY

The genetics of quantitative traits: challenges and prospects

(2009) Trudy F. C. Mackay et al.   NATURE REVIEWS GENETICS

Copper homeostasis

(2009) Jason L. Burkhead et al.   NEW PHYTOLOGIST

Conserved and novel miRNAs in the legume Phaseolus vulgaris in response to stress

(2009) Catalina Arenas-Huertero et al.   PLANT MOLECULAR BIOLOGY

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

(2009) Inês Trindade et al.   PLANTA

Evolutionary analysis of the Sub1 gene cluster that confers submergence tolerance to domesticated rice

(2008) Takeshi Fukao et al.   ANNALS OF BOTANY

Submergence-responsive MicroRNAs are Potentially Involved in the Regulation of Morphological and Metabolic Adaptations in Maize Root Cells

(2008) Zuxin Zhang et al.   ANNALS OF BOTANY

Identification of cold-inducible microRNAs in plants by transcriptome analysis

(2008) X ZHOU et al.   Biochimica et Biophysica Acta-Gene Regulatory Mechanisms

SuperSAGE: the drought stress-responsive transcriptome of chickpea roots

(2008) Carlos Molina et al.   BMC GENOMICS

Genetic Design and Statistical Power of Nested Association Mapping in Maize

(2008) Jianming Yu et al.   GENETICS

Nucleotide Variation in theNCED3 Region ofArabidopsis thalianaand its Association Study with Abscisic Acid Content under Drought Stress

(2008) Gang-Ping Hao et al.   Journal of Integrative Plant Biology

Stress-responsive microRNAs inPopulus

(2008) Shanfa Lu et al.   PLANT JOURNAL

Sulphur starvation induces the expression of microRNA-395 and one of its target genes but in different cell types

(2008) Cintia Goulart Kawashima et al.   PLANT JOURNAL

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

(2008) H.-H. Liu et al.   RNA

Search for nucleotide diversity patterns of local adaptation in dehydrins and other cold-related candidate genes in Scots pine (Pinus sylvestris L.)

(2008) Witold Wachowiak et al.   Tree Genetics & Genomes