First-generation HapMap inCajanusspp. reveals untapped variations in parental lines of mapping populations

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

(2015) Zhengkui Zhou et al.   NATURE BIOTECHNOLOGY

Genome-wide high-throughput SNP discovery and genotyping for understanding natural (functional) allelic diversity and domestication patterns in wild chickpea

(2015) Deepak Bajaj et al.   Scientific Reports

Genomics-assisted breeding for boosting crop improvement in pigeonpea (Cajanus cajan)

(2015) Lekha Pazhamala et al.   Frontiers in Plant Science

NGS-QCbox and Raspberry for Parallel, Automated and Rapid Quality Control Analysis of Large-Scale Next Generation Sequencing (Illumina) Data

(2015) Mohan A. V. S. K. Katta et al.   PLoS One

A powerful tool for genome analysis in maize: development and evaluation of the high density 600 k SNP genotyping array

(2014) Sandra Unterseer et al.   BMC GENOMICS

SNPhylo: a pipeline to construct a phylogenetic tree from huge SNP data

(2014) Tae-Ho Lee et al.   BMC GENOMICS

Genomic analyses provide insights into the history of tomato breeding

(2014) Tao Lin et al.   NATURE GENETICS

Genetic Diversity and Demographic History of Cajanus spp. Illustrated from Genome-Wide SNPs

(2014) Rachit K. Saxena et al.   PLoS One

Genome-Wide DNA Polymorphisms in Seven Rice Cultivars of Temperate and Tropical Japonica Groups

(2014) Yuko Arai-Kichise et al.   PLoS One

Biparental Resequencing Coupled With SNP Genotyping of a Segregating Population Offers Insights Into the Landscape of Recombination and Fixed Genomic Regions in Elite Soybean

(2014) Ying-hui Li et al.   G3-Genes Genomes Genetics

Understanding how and why the Gene Ontology and its annotations evolve: the GO within UniProt

(2014) Rachael P Huntley et al.   GigaScience

Development of New InDel Marker to Detect Genotypes of Rf-1a Conferring Fertility Restoration of BT-Type Cytoplasmic Male Sterility in Rice

(2014) Tao CHEN et al.   Rice Science

Whole genome resequencing in tomato reveals variation associated with introgression and breeding events

(2013) Mathilde Causse et al.   BMC GENOMICS

A High-Density SNP Genotyping Array for Rice Biology and Molecular Breeding

(2013) Haodong Chen et al.   Molecular Plant

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

(2013) Rajeev K Varshney et al.   NATURE BIOTECHNOLOGY

Development and Evaluation of SoySNP50K, a High-Density Genotyping Array for Soybean

(2013) Qijian Song et al.   PLoS One

Candidate Genes and Genetic Architecture of Symbiotic and Agronomic Traits Revealed by Whole-Genome, Sequence-Based Association Genetics in Medicago truncatula

(2013) John Stanton-Geddes et al.   PLoS One

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

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

The First 50 Plant Genomes

(2013) Todd P. Michael et al.   Plant Genome

Molecular mapping of QTLs for plant type and earliness traits in pigeonpea (Cajanus cajan L. Millsp.)

(2012) Giriraj Kumawat et al.   BMC GENETICS

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

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

Breeding for Earliness in Pigeonpea: Development of New Determinate and Nondeterminate Lines

(2012) M. I. Vales et al.   CROP SCIENCE

Large-Scale Development of Cost-Effective Single-Nucleotide Polymorphism Marker Assays for Genetic Mapping in Pigeonpea and Comparative Mapping in Legumes

(2012) R. K. Saxena et al.   DNA RESEARCH

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff

(2012) Pablo Cingolani et al.   FLY

A Comprehensive Transcriptome Assembly of Pigeonpea (Cajanus cajan L.) using Sanger and Second-Generation Sequencing Platforms

(2012) Himabindu Kudapa et al.   Molecular Plant

A map of rice genome variation reveals the origin of cultivated rice

(2012) Xuehui Huang et al.   NATURE

Comparative population genomics of maize domestication and improvement

(2012) Matthew B Hufford et al.   NATURE GENETICS

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

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

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

Genetic Patterns of Domestication in Pigeonpea (Cajanus cajan (L.) Millsp.) and Wild Cajanus Relatives

(2012) Mulualem T. Kassa et al.   PLoS One

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

(2011) Sutapa Dutta et al.   BMC PLANT BIOLOGY

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

CNVnator: An approach to discover, genotype, and characterize typical and atypical CNVs from family and population genome sequencing

(2011) A. Abyzov et al.   GENOME RESEARCH

The first draft of the pigeonpea genome sequence

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

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

(2011) Rajeev K Varshney et al.   NATURE BIOTECHNOLOGY

Discovery of Genome-Wide DNA Polymorphisms in a Landrace Cultivar of Japonica Rice by Whole-Genome Sequencing

(2011) Yuko Arai-Kichise et al.   PLANT AND CELL PHYSIOLOGY

A Large Maize (Zea mays L.) SNP Genotyping Array: Development and Germplasm Genotyping, and Genetic Mapping to Compare with the B73 Reference Genome

(2011) Martin W. Ganal et al.   PLoS One

Genome-wide patterns of genetic variation in sweet and grain sorghum (Sorghum bicolor)

(2011) Lei-Ying Zheng et al.   GENOME BIOLOGY

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

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

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

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

Pigeonpea genomics initiative (PGI): an international effort to improve crop productivity of pigeonpea (Cajanus cajan L.)

(2009) R. K. Varshney et al.   MOLECULAR BREEDING

Simple sequence repeat-based diversity in elite pigeonpea genotypes for developing mapping populations to map resistance toFusariumwilt and sterility mosaic disease

(2009) R. K. Saxena et al.   PLANT BREEDING

Genomewide SNP variation reveals relationships among landraces and modern varieties of rice

(2009) K. L. McNally et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Next-generation sequencing technologies and their implications for crop genetics and breeding

(2009) Rajeev K. Varshney et al.   TRENDS IN BIOTECHNOLOGY