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

Genotyping by sequencing for genomic prediction in a soybean breeding population

(2014) Diego Jarquín et al.   BMC GENOMICS

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 evaluation of genotyping by sequencing (GBS) to map the Breviaristatum-e (ari-e) locus in cultivated barley

(2014) Hui Liu 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

Efficient Imputation of Missing Markers in Low-Coverage Genotyping-by-Sequencing Data from Multiparental Crosses

(2014) B. Emma Huang et al.   GENETICS

An efficient and cost-effective approach for genic microsatellite marker-based large-scale trait association mapping: identification of candidate genes for seed weight in chickpea

(2014) Alice Kujur et al.   MOLECULAR BREEDING

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

A chromosomal genomics approach to assess and validate thedesiandkabulidraft chickpea genome assemblies

(2014) Pradeep Ruperao et al.   PLANT BIOTECHNOLOGY JOURNAL

Identification of loci governing eight agronomic traits using a GBS-GWAS approach and validation by QTL mapping in soya bean

(2014) Humira Sonah et al.   PLANT BIOTECHNOLOGY JOURNAL

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

Natural Allelic Diversity, Genetic Structure and Linkage Disequilibrium Pattern in Wild Chickpea

(2014) Maneesha S. Saxena et al.   PLoS One

Polymorphism Identification and Improved Genome Annotation of Brassica rapa Through Deep RNA Sequencing

(2014) Upendra Kumar Devisetty et al.   G3-Genes Genomes Genetics

Rapid Identification of Alleles at the Soybean Maturity Gene E3 using genotyping by Sequencing and a Haplotype-Based Approach

(2014) Aurélie Tardivel et al.   Plant Genome

Genome Wide Association Mapping of Resistance in Soybean with a Genotyping-by-Sequencing Approach

(2014) Maxime Bastien et al.   Plant Genome

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

Genotyping-by-sequencing (GBS), an ultimate marker-assisted selection (MAS) tool to accelerate plant breeding

(2014) Jiangfeng He et al.   Frontiers in Plant Science

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

Marker Density and Read Depth for Genotyping Populations Using Genotyping-by-Sequencing

(2013) T. M. Beissinger et al.   GENETICS

A Central Role for Thiols in Plant Tolerance to Abiotic Stress

(2013) Lyuben Zagorchev et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Genetic marker discovery, intraspecific linkage map construction and quantitative trait locus analysis of ascochyta blight resistance in chickpea (Cicer arietinum L.)

(2013) Amber Stephens et al.   MOLECULAR BREEDING

Stacks: an analysis tool set for population genomics

(2013) Julian Catchen et al.   MOLECULAR ECOLOGY

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

(2013) Rajeev K Varshney et al.   NATURE BIOTECHNOLOGY

Genomewide discovery of DNA polymorphisms in rice cultivars with contrasting drought and salinity stress response and their functional relevance

(2013) Mukesh Jain et al.   PLANT BIOTECHNOLOGY JOURNAL

Barley whole exome capture: a tool for genomic research in the genusHordeumand beyond

(2013) Martin Mascher et al.   PLANT JOURNAL

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

(2013) Mukesh Jain et al.   PLANT JOURNAL

Identification of Genes Involved in the Response of Arabidopsis to Simultaneous Biotic and Abiotic Stresses

(2013) N. J. Atkinson et al.   PLANT PHYSIOLOGY

Genome Wide Allele Frequency Fingerprints (GWAFFs) of Populations via Genotyping by Sequencing

(2013) Stephen Byrne et al.   PLoS One

An Improved Genotyping by Sequencing (GBS) Approach Offering Increased Versatility and Efficiency of SNP Discovery and Genotyping

(2013) Humira Sonah et al.   PLoS One

A Next-Generation Sequencing Method for Genotyping-by-Sequencing of Highly Heterozygous Autotetraploid Potato

(2013) Jan G. A. M. L. Uitdewilligen et al.   PLoS One

Bridging the genotyping gap: using genotyping by sequencing (GBS) to add high-density SNP markers and new value to traditional bi-parental mapping and breeding populations

(2013) Jennifer Spindel et al.   THEORETICAL AND APPLIED GENETICS

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

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

Genomic Prediction in Maize Breeding Populations with Genotyping-by-Sequencing

(2013) José Crossa et al.   G3-Genes Genomes Genetics

Single Nucleotide Polymorphism Genotyping for Breeding and Genetics Applications in Chickpea and Pigeonpea using the BeadXpress Platform

(2013) Manish Roorkiwal et al.   Plant Genome

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

Coverage-based consensus calling (CbCC) of short sequence reads and comparison of CbCC results to identify SNPs in chickpea (Cicer arietinum ; Fabaceae), a crop species without a reference genome

(2012) Sarwar Azam et al.   AMERICAN JOURNAL OF BOTANY

SNPs in stress-responsive rice genes: validation, genotyping, functional relevance and population structure

(2012) Swarup K Parida et al.   BMC GENOMICS

Current state-of-art of sequencing technologies for plant genomics research

(2012) M. Thudi et al.   Briefings in Functional Genomics

High-Throughput SNP Discovery and Genotyping for Constructing a Saturated Linkage Map of Chickpea (Cicer arietinum L.)

(2012) R. Gaur et al.   DNA RESEARCH

A physical, genetic and functional sequence assembly of the barley genome

(2012)   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

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

(2012) Shalu Jhanwar et al.   PLANT BIOTECHNOLOGY JOURNAL

Genome-wide DNA polymorphisms in eliteindicarice inbreds discovered by whole-genome sequencing

(2012) Gopala K. Subbaiyan et al.   PLANT BIOTECHNOLOGY JOURNAL

Large-scale development of cost-effective SNP marker assays for diversity assessment and genetic mapping in chickpea and comparative mapping in legumes

(2012) Pavana J. Hiremath et al.   PLANT BIOTECHNOLOGY JOURNAL

Development of High-Density Genetic Maps for Barley and Wheat Using a Novel Two-Enzyme Genotyping-by-Sequencing Approach

(2012) Jesse A. Poland et al.   PLoS One

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

Genome-wide association mapping of leaf metabolic profiles for dissecting complex traits in maize

(2012) C. Riedelsheimer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Population genomic and genome-wide association studies of agroclimatic traits in sorghum

(2012) G. P. Morris et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genetic structure and linkage disequilibrium pattern of a rapeseed (Brassica napus L.) association mapping panel revealed by microsatellites

(2012) Yingjie Xiao et al.   THEORETICAL AND APPLIED GENETICS

Patterns of linkage disequilibrium and association mapping in diploid alfalfa (M. sativa L.)

(2012) Muhammet Sakiroglu et al.   THEORETICAL AND APPLIED GENETICS

Genotyping-by-Sequencing for Plant Breeding and Genetics

(2012) Jesse A. Poland et al.   Plant Genome

Genomic Selection in Wheat Breeding using Genotyping-by-Sequencing

(2012) Jesse Poland et al.   Plant Genome

Identification of SNP and SSR markers in eggplant using RAD tag sequencing

(2011) Lorenzo Barchi et al.   BMC GENOMICS

Construction and application for QTL analysis of a Restriction Site Associated DNA (RAD) linkage map in barley

(2011) Yada Chutimanitsakun 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

MEGA5: Molecular Evolutionary Genetics Analysis Using Maximum Likelihood, Evolutionary Distance, and Maximum Parsimony Methods

(2011) K. Tamura et al.   MOLECULAR BIOLOGY AND EVOLUTION

Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes

(2011) Xun Xu et al.   NATURE BIOTECHNOLOGY

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

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

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

Towards marker-assisted selection in pulses: a review

(2011) Jitendra Kumar et al.   PLANT BREEDING

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

(2011) R. Garg et al.   PLANT PHYSIOLOGY

Correction: Gains in QTL Detection Using an Ultra-High Density SNP Map Based on Population Sequencing Relative to Traditional RFLP/SSR Markers

(2011) Huihui Yu et al.   PLoS One

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

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

Whole-genome nucleotide diversity, recombination, and linkage disequilibrium in the model legume Medicago truncatula

(2011) A. Branca et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mapping with RAD (restriction-site associated DNA) markers to rapidly identify QTL for stem rust resistance in Lolium perenne

(2011) W. F. Pfender et al.   THEORETICAL AND APPLIED GENETICS

Development and use of genic molecular markers (GMMs) for construction of a transcript map of chickpea (Cicer arietinum L.)

(2011) Neha Gujaria et al.   THEORETICAL AND APPLIED GENETICS

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

(2011) Keyan Zhao et al.   Nature Communications

Modulation of transcription factor and metabolic pathway genes in response to water-deficit stress in rice

(2010) Swatismita Ray et al.   FUNCTIONAL & INTEGRATIVE GENOMICS

Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines

(2010) Susanna Atwell et al.   NATURE

Genome-wide association studies of 14 agronomic traits in rice landraces

(2010) Xuehui Huang et al.   NATURE GENETICS

Resequencing of 31 wild and cultivated soybean genomes identifies patterns of genetic diversity and selection

(2010) Hon-Ming Lam et al.   NATURE GENETICS

Integration of novel SSR and gene-based SNP marker loci in the chickpea genetic map and establishment of new anchor points with Medicago truncatula genome

(2010) Spurthi N. Nayak et al.   THEORETICAL AND APPLIED GENETICS

Population Genomics of Parallel Adaptation in Threespine Stickleback using Sequenced RAD Tags

(2010) Paul A. Hohenlohe et al.   PLoS Genetics

High-throughput genotyping by whole-genome resequencing

(2009) X. Huang et al.   GENOME RESEARCH

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

Soybean GmPHD-Type Transcription Regulators Improve Stress Tolerance in Transgenic Arabidopsis Plants

(2009) Wei Wei et al.   PLoS One

The B73 Maize Genome: Complexity, Diversity, and Dynamics

(2009) P. S. Schnable et al.   SCIENCE

Molecular insights into the evolution of crop plants

(2008) Jutta C. Burger et al.   AMERICAN JOURNAL OF BOTANY

Genetic structure, diversity, and allelic richness in composite collection and reference set in chickpea (Cicer arietinum L.)

(2008) Hari D Upadhyaya et al.   BMC PLANT BIOLOGY

Discovery and detection of single nucleotide polymorphism (SNP) in coding and genomic sequences in chickpea (Cicer arietinum L.)

(2008) P. N. Rajesh et al.   EUPHYTICA

A note on the evolution of kabuli chickpeas as shown by induced mutations in Cicer reticulatum Ladizinsky

(2008) Cengiz Toker   GENETIC RESOURCES AND CROP EVOLUTION

Identification of genetic variants using bar-coded multiplexed sequencing

(2008) David W Craig et al.   NATURE METHODS

SNP discovery and allele frequency estimation by deep sequencing of reduced representation libraries

(2008) Curtis P Van Tassell et al.   NATURE METHODS

Multiplex sequencing of plant chloroplast genomes using Solexa sequencing-by-synthesis technology

(2008) Richard Cronn et al.   NUCLEIC ACIDS RESEARCH

Rapid SNP Discovery and Genetic Mapping Using Sequenced RAD Markers

(2008) Nathan A. Baird et al.   PLoS One