Current advances in chickpea genomics: applications and future perspectives

Plant vigour QTLs co-map with an earlier reported QTL hotspot for drought tolerance while water saving QTLs map in other regions of the chickpea genome

(2018) Kaliamoorthy Sivasakthi et al.   BMC PLANT BIOLOGY

Identification of QTLs for resistance to Fusarium wilt and Ascochyta blight in a recombinant inbred population of chickpea (Cicer arietinum L.)

(2018) Tosh Garg et al.   EUPHYTICA

Transcriptional regulation of chickpea ferritin CaFer1 influences its role in iron homeostasis and stress response

(2018) Shaista Parveen et al.   JOURNAL OF PLANT PHYSIOLOGY

Investigating Drought Tolerance in Chickpea Using Genome-Wide Association Mapping and Genomic Selection Based on Whole-Genome Resequencing Data

(2018) Yongle Li et al.   Frontiers in Plant Science

Population structure and association analysis of heat stress relevant traits in chickpea (Cicer arietinum L.)

(2018) Uday Chand Jha et al.   3 Biotech

Population structure and association analysis of heat stress relevant traits in chickpea (Cicer arietinum L.)

(2018) Uday Chand Jha et al.   3 Biotech

Genetic dissection of plant growth habit in chickpea

(2017) Hari D. Upadhyaya et al.   FUNCTIONAL & INTEGRATIVE GENOMICS

Genomic innovation for crop improvement

(2017) Michael W. Bevan et al.   NATURE

PLncPRO for prediction of long non-coding RNAs (lncRNAs) in plants and its application for discovery of abiotic stress-responsive lncRNAs in rice and chickpea

(2017) Urminder Singh et al.   NUCLEIC ACIDS RESEARCH

Integrated “omics” approaches to sustain global productivity of major grain legumes under heat stress

(2017) Uday Chand Jha et al.   PLANT BREEDING

Global transcriptome and coexpression network analyses reveal cultivar-specific molecular signatures associated with seed development and seed size/weight determination in chickpea

(2017) Rohini Garg et al.   PLANT JOURNAL

Genomic Selection in Plant Breeding: Methods, Models, and Perspectives

(2017) José Crossa et al.   TRENDS IN PLANT SCIENCE

Molecular Mapping of Flowering Time Major Genes and QTLs in Chickpea (Cicer arietinum L.)

(2017) Bingi P. Mallikarjuna et al.   Frontiers in Plant Science

A Multiple QTL-Seq Strategy Delineates Potential Genomic Loci Governing Flowering Time in Chickpea

(2017) Rishi Srivastava et al.   Frontiers in Plant Science

Genetic Analysis of NBS-LRR Gene Family in Chickpea and Their Expression Profiles in Response to Ascochyta Blight Infection

(2017) Mandeep S. Sagi et al.   Frontiers in Plant Science

Phylogenomic analysis of MKKs and MAPKs from 16 legumes and detection of interacting pairs in chickpea divulge MAPK signalling modules

(2017) Savithri Purayannur et al.   Scientific Reports

A repeat length variation in myo-inositol monophosphatase gene contributes to seed size trait in chickpea

(2017) Vikas Dwivedi et al.   Scientific Reports

Chickpea-Fusarium oxysporum interaction transcriptome reveals differential modulation of plant defense strategies

(2017) Medha L. Upasani et al.   Scientific Reports

Genomic Selection Accuracy using Multifamily Prediction Models in a Wheat Breeding Program

(2017) Elliot L. Heffner et al.   Plant Genome

CicerTransDB 1.0: a resource for expression and functional study of chickpea transcription factors

(2016) Saurabh Gayali et al.   BMC PLANT BIOLOGY

Chromatin-Based Epigenetic Regulation of Plant Abiotic Stress Response

(2016) Garima Pandey et al.   CURRENT GENOMICS

WRKY domain-encoding genes of a crop legume chickpea (Cicer arietinum): comparative analysis withMedicago truncatulaWRKY family and characterization of group-III gene(s)

(2016) Kamal Kumar et al.   DNA RESEARCH

QTL mapping of early flowering and resistance to ascochyta blight in chickpea

(2016) Ketema Daba et al.   GENOME

Multiple post-domestication origins ofkabulichickpea through allelic variation in a diversification-associated transcription factor

(2016) R. Varma Penmetsa et al.   NEW PHYTOLOGIST

QTL-seq for rapid identification of candidate genes for 100-seed weight and root/total plant dry weight ratio under rainfed conditions in chickpea

(2016) Vikas K. Singh et al.   PLANT BIOTECHNOLOGY JOURNAL

Genome-wide development and deployment of informative intron-spanning and intron-length polymorphism markers for genomics-assisted breeding applications in chickpea

(2016) Rishi Srivastava et al.   PLANT SCIENCE

Identification of candidate genes for dissecting complex branch number trait in chickpea

(2016) Deepak Bajaj et al.   PLANT SCIENCE

Defence gene expression profiling to Ascochyta rabiei aggressiveness in chickpea

(2016) Audrey E. Leo et al.   THEORETICAL AND APPLIED GENETICS

Genome-Wide Scans for Delineation of Candidate Genes Regulating Seed-Protein Content in Chickpea

(2016) Hari D. Upadhyaya et al.   Frontiers in Plant Science

EcoTILLING-Based Association Mapping Efficiently Delineates Functionally Relevant Natural Allelic Variants of Candidate Genes Governing Agronomic Traits in Chickpea

(2016) Deepak Bajaj et al.   Frontiers in Plant Science

Identification and Expression Analysis of Candidate Genes Involved in Carotenoid Biosynthesis in Chickpea Seeds

(2016) Mohammad K. Rezaei et al.   Frontiers in Plant Science

Genome-Enabled Prediction Models for Yield Related Traits in Chickpea

(2016) Manish Roorkiwal et al.   Frontiers in Plant Science

Progress in genome sequencing will accelerate molecular breeding in cotton (Gossypium spp.)

(2016) Rong Yan et al.   3 Biotech

Progress in genome sequencing will accelerate molecular breeding in cotton (Gossypium spp.)

(2016) Rong Yan et al.   3 Biotech

Dissecting the Root Nodule Transcriptome of Chickpea (Cicer arietinum L.)

(2016) Chandra Kant et al.   PLoS One

Dynamics of Colonization and Expression of Pathogenicity Related Genes in Fusarium oxysporum f.sp. ciceri during Chickpea Vascular Wilt Disease Progression

(2016) Medha L. Upasani et al.   PLoS One

Transcriptome analyses reveal genotype- and developmental stage-specific molecular responses to drought and salinity stresses in chickpea

(2016) Rohini Garg et al.   Scientific Reports

Identification of candidate genes and natural allelic variants for QTLs governing plant height in chickpea

(2016) Alice Kujur et al.   Scientific Reports

Genetic dissection of seed-iron and zinc concentrations in chickpea

(2016) Hari D. Upadhyaya et al.   Scientific Reports

Transcriptome landscape of perennial wild Cicer microphyllum uncovers functionally relevant molecular tags regulating agronomic traits in chickpea

(2016) Rishi Srivastava et al.   Scientific Reports

Genome-wide analysis of long intergenic non-coding RNAs in chickpea and their potential role in flower development

(2016) Niraj Khemka et al.   Scientific Reports

Recent breeding programs enhanced genetic diversity in both desi and kabuli varieties of chickpea (Cicer arietinum L.)

(2016) Mahendar Thudi et al.   Scientific Reports

The CRISPR/Cas9 system for plant genome editing and beyond

(2015) Luisa Bortesi et al.   BIOTECHNOLOGY ADVANCES

Genome-wide survey and expression analysis of F-box genes in chickpea

(2015) Shefali Gupta et al.   BMC GENOMICS

Two key genomic regions harbour QTLs for salinity tolerance in ICCV 2 × JG 11 derived chickpea (Cicer arietinum L.) recombinant inbred lines

(2015) Raju Pushpavalli et al.   BMC PLANT BIOLOGY

Deploying QTL-seq for rapid delineation of a potential candidate gene underlying major trait-associated QTL in chickpea

(2015) S. Das et al.   DNA RESEARCH

Repeat length variation in the 5ʹUTR ofmyo-inositol monophosphatase gene is related to phytic acid content and contributes to drought tolerance in chickpea (Cicer arietinumL.)

(2015) Archana Joshi-Saha et al.   JOURNAL OF EXPERIMENTAL BOTANY

Marker-trait association study for protein content in chickpea (Cicer arietinum L.)

(2015) A. A. JADHAV et al.   JOURNAL OF GENETICS

Development of molecular map and identification of QTLs linked to Fusarium wilt resistance in chickpea

(2015) PAVANKUMAR JINGADE et al.   JOURNAL OF GENETICS

Development of gene-based markers for use in construction of the chickpea (Cicer arietinum L.) genetic linkage map and identification of QTLs associated with seed weight and plant height

(2015) Shefali Gupta et al.   MOLECULAR BIOLOGY REPORTS

Discovery of molecular markers for Fusarium wilt via transcriptome sequencing of chickpea cultivars

(2015) Mukesh Jain et al.   MOLECULAR BREEDING

Whole-genome resequencing: changing the paradigms of SNP detection, molecular mapping and gene discovery

(2015) Xiangyang Xu et al.   MOLECULAR BREEDING

Resequencing 302 wild and cultivated accessions identifies genes related to domestication and improvement in soybean

(2015) Zhengkui Zhou et al.   NATURE BIOTECHNOLOGY

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

(2015) Parvin Mohammadi et al.   PHYSIOLOGICAL AND MOLECULAR PLANT PATHOLOGY

A genome-scale integrated approach aids in genetic dissection of complex flowering time trait in chickpea

(2015) Hari D. Upadhyaya et al.   PLANT MOLECULAR BIOLOGY

High throughput sequencing of small RNA component of leaves and inflorescence revealed conserved and novel miRNAs as well as phasiRNA loci in chickpea

(2015) Sangeeta Srivastava et al.   PLANT SCIENCE

DNA methylation and physio-biochemical analysis of chickpea in response to cold stress

(2015) Aida Rakei et al.   PROTOPLASMA

Fine mapping for double podding gene in chickpea

(2015) L. Ali et al.   THEORETICAL AND APPLIED GENETICS

A genome-wide SNP scan accelerates trait-regulatory genomic loci identification in chickpea

(2015) Alice Kujur et al.   Scientific Reports

High density linkage mapping of genomic and transcriptomic SNPs for synteny analysis and anchoring the genome sequence of chickpea

(2015) Rashmi Gaur et al.   Scientific Reports

Ultra-high density intra-specific genetic linkage maps accelerate identification of functionally relevant molecular tags governing important agronomic traits in chickpea

(2015) Alice Kujur et al.   Scientific Reports

An advanced draft genome assembly of a desi type chickpea (Cicer arietinum L.)

(2015) Sabiha Parween et al.   Scientific Reports

Prioritization of candidate genes in “QTL-hotspot” region for drought tolerance in chickpea (Cicer arietinum L.)

(2015) Sandip M Kale et al.   Scientific Reports

High-density linkage map construction and mapping of seed trait QTLs in chickpea (Cicer arietinum L.) using Genotyping-by-Sequencing (GBS)

(2015) Subodh Verma et al.   Scientific Reports

Employing genome-wide SNP discovery and genotyping strategy to extrapolate the natural allelic diversity and domestication patterns in chickpea

(2015) Alice Kujur et al.   Frontiers in Plant Science

Genome-Wide Analysis of Homeobox Gene Family in Legumes: Identification, Gene Duplication and Expression Profiling

(2015) Annapurna Bhattacharjee et al.   PLoS One

Development and Integration of Genome-Wide Polymorphic Microsatellite Markers onto a Reference Linkage Map for Constructing a High-Density Genetic Map of Chickpea

(2015) Yash Paul Khajuria et al.   PLoS One

CTDB: An Integrated Chickpea Transcriptome Database for Functional and Applied Genomics

(2015) Mohit Verma et al.   PLoS One

CicArMiSatDB: the chickpea microsatellite database

(2014) Dadakhalandar Doddamani et al.   BMC BIOINFORMATICS

Genome wide SNP identification in chickpea for use in development of a high density genetic map and improvement of chickpea reference genome assembly

(2014) Amit A Deokar et al.   BMC GENOMICS

An Integrated Genomic Approach for Rapid Delineation of Candidate Genes Regulating Agro-Morphological Traits in Chickpea

(2014) Maneesha S. Saxena et al.   DNA RESEARCH

Genetic and physical mapping of the QTLAR3 controlling blight resistance in chickpea (Cicer arietinum L)

(2014) E. Madrid et al.   EUPHYTICA

Allelic relationships of flowering time genes in chickpea

(2014) Pooran M. Gaur et al.   EUPHYTICA

Integrated physical, genetic and genome map of chickpea (Cicer arietinum L.)

(2014) Rajeev K. Varshney et al.   FUNCTIONAL & INTEGRATIVE GENOMICS

Genomics-assisted breeding for drought tolerance in chickpea

(2014) Mahendar Thudi et al.   FUNCTIONAL PLANT BIOLOGY

Genetic diversity and association mapping of iron and zinc concentrations in chickpea (Cicer arietinum L.)

(2014) Marwan Diapari et al.   GENOME

Genome-wide conserved non-coding microsatellite (CNMS) marker-based integrative genetical genomics for quantitative dissection of seed weight in chickpea

(2014) Deepak Bajaj et al.   JOURNAL OF EXPERIMENTAL BOTANY

Genome-wide discovery and differential regulation of conserved and novel microRNAs in chickpea via deep sequencing

(2014) Mukesh Jain et al.   JOURNAL OF EXPERIMENTAL BOTANY

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

(2014) Deepa Jaganathan et al.   MOLECULAR GENETICS AND GENOMICS

Heat stress in crop plants: its nature, impacts and integrated breeding strategies to improve heat tolerance

(2014) Uday Chand Jha et al.   PLANT BREEDING

Abiotic stresses, constraints and improvement strategies in chickpea

(2014) Uday C. Jha et al.   PLANT BREEDING

Genome-Scale Transcriptomic Insights into Molecular Aspects of Abiotic Stress Responses in Chickpea

(2014) Rohini Garg et al.   PLANT MOLECULAR BIOLOGY REPORTER

Genomic Survey, Gene Expression Analysis and Structural Modeling Suggest Diverse Roles of DNA Methyltransferases in Legumes

(2014) Rohini Garg et al.   PLoS One

Comprehensive Transcriptome Assembly of Chickpea (Cicer arietinum L.) Using Sanger and Next Generation Sequencing Platforms: Development and Applications

(2014) Himabindu Kudapa et al.   PLoS One

Genetic Dissection of Drought and Heat Tolerance in Chickpea through Genome-Wide and Candidate Gene-Based Association Mapping Approaches

(2014) Mahendar Thudi et al.   PLoS One

Genome-Wide Identification and Expression Analysis of the CaNAC Family Members in Chickpea during Development, Dehydration and ABA Treatments

(2014) Chien Van Ha et al.   PLoS One

Identification and Characterization of Wilt and Salt Stress-Responsive MicroRNAs in Chickpea through High-Throughput Sequencing

(2014) Deshika Kohli et al.   PLoS One

Genome-Wide Identification and Tissue-Specific Expression Analysis of UDP-Glycosyltransferases Genes Confirm Their Abundance in Cicer arietinum (Chickpea) Genome

(2014) Ranu Sharma et al.   PLoS One

Genomic selection: genome-wide prediction in plant improvement

(2014) Zeratsion Abera Desta et al.   TRENDS IN PLANT SCIENCE

Marker-Assisted Backcrossing to Introgress Resistance to Fusarium Wilt Race 1 and Ascochyta Blight in C 214, an Elite Cultivar of Chickpea

(2014) R. K. Varshney et al.   Plant Genome

Global transcriptome analysis of developing chickpea (Cicer arietinum L.) seeds

(2014) Seema Pradhan et al.   Frontiers in Plant Science

Natural Variations and Genome-Wide Association Studies in Crop Plants

(2013) Xuehui Huang et al.   Annual Review of Plant Biology

Functionally Relevant Microsatellite Markers From Chickpea Transcription Factor Genes for Efficient Genotyping Applications and Trait Association Mapping

(2013) A. Kujur et al.   DNA RESEARCH

Molecular mapping of QTLs for resistance to Fusarium wilt (race 1) and Ascochyta blight in chickpea (Cicer arietinum L.)

(2013) Murali Mohan Sabbavarapu et al.   EUPHYTICA

Differentially expressed myo-inositol monophosphatase gene (CaIMP) in chickpea (Cicer arietinum L.) encodes a lithium-sensitive phosphatase enzyme with broad substrate specificity and improves seed germination and seedling growth under abiotic stresses

(2013) Saurabh C. Saxena et al.   JOURNAL OF EXPERIMENTAL BOTANY

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

(2013) Rajeev K Varshney et al.   NATURE BIOTECHNOLOGY

Targeted genome modification of crop plants using a CRISPR-Cas system

(2013) Qiwei Shan et al.   NATURE BIOTECHNOLOGY

A global view of transcriptome dynamics during flower development in chickpea by deep sequencing

(2013) Vikash K. Singh et al.   PLANT BIOTECHNOLOGY JOURNAL

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

(2013) Mukesh Jain et al.   PLANT JOURNAL

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

Identification of Upregulated Genes under Cold Stress in Cold-Tolerant Chickpea Using the cDNA-AFLP Approach

(2013) Ali Dinari et al.   PLoS One

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

(2013) Rajeev K. Varshney et al.   THEORETICAL AND APPLIED GENETICS

Whole-genome sequencing reveals untapped genetic potential in Africa’s indigenous cereal crop sorghum

(2013) Emma S. Mace et al.   Nature Communications

Fast-Track Introgression of “ for Root Traits and Other Drought Tolerance Traits in JG 11, an Elite and Leading Variety of Chickpea

(2013) Rajeev K. Varshney et al.   Plant Genome

Will genomic selection be a practical method for plant breeding?

(2012) Akihiro Nakaya et al.   ANNALS OF BOTANY

Genome-wide genetic changes during modern breeding of maize

(2012) Yinping Jiao et al.   NATURE GENETICS

Transcriptome sequencing of wild chickpea as a rich resource for marker development

(2012) Shalu Jhanwar et al.   PLANT BIOTECHNOLOGY JOURNAL

Characterization and genetic analysis of an EIN4-like sequence (CaETR-1) located in QTLAR1 implicated in ascochyta blight resistance in chickpea

(2012) E. Madrid et al.   PLANT CELL REPORTS

Comparative Analysis of Kabuli Chickpea Transcriptome with Desi and Wild Chickpea Provides a Rich Resource for Development of Functional Markers

(2012) Gaurav Agarwal et al.   PLoS One

Impact of Genomic Technologies on Chickpea Breeding Strategies

(2012) Pooran M. Gaur et al.   Agronomy-Basel

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

(2011) Carlos Molina et al.   BMC PLANT BIOLOGY

Genomic selection in plant breeding: from theory to practice

(2011) J.-L. Jannink et al.   Briefings in Functional Genomics

De Novo Assembly of Chickpea Transcriptome Using Short Reads for Gene Discovery and Marker Identification

(2011) R. Garg et al.   DNA RESEARCH

Genetics and Characterization of an Open Flower Mutant in Chickpea

(2011) Samineni Srinivasan et al.   JOURNAL OF HEREDITY

Tracing the origin and evolutionary history of plant nucleotide-binding site-leucine-rich repeat (NBS-LRR) genes

(2011) Jia-Xing Yue et al.   NEW PHYTOLOGIST

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

Gene Discovery and Tissue-Specific Transcriptome Analysis in Chickpea with Massively Parallel Pyrosequencing and Web Resource Development

(2011) R. Garg et al.   PLANT PHYSIOLOGY

Genome-wide association studies in plants: the missing heritability is in the field

(2011) Benjamin Brachi et al.   GENOME BIOLOGY

Genetics of flowering time in chickpea in a semi-arid environment

(2010) V. S. Hegde   PLANT BREEDING

Primary Metabolism of Chickpea Is the Initial Target of Wound Inducing Early Sensed Fusarium oxysporum f. sp. ciceri Race I

(2010) Sumanti Gupta et al.   PLoS One

A comprehensive resource of drought- and salinity- responsive ESTs for gene discovery and marker development in chickpea (Cicer arietinum L.)

(2009) Rajeev K Varshney et al.   BMC GENOMICS

Mutagenic induction of double-podding trait in different genotypes of chickpea and their characterization by STMS marker

(2009) H. Ali et al.   PLANT BREEDING

SuperSAGE: the drought stress-responsive transcriptome of chickpea roots

(2008) Carlos Molina et al.   BMC GENOMICS