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

Sequencing-based genome-wide association study in rice

(2013) Bin Han et al.   CURRENT OPINION IN PLANT BIOLOGY

Resequencing rice genomes: an emerging new era of rice genomics

(2013) Xuehui Huang et al.   TRENDS IN GENETICS

Resolving candidate genes of mouse skeletal muscle QTL via RNA-Seq and expression network analyses

(2012) Arimantas Lionikas et al.   BMC GENOMICS

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

(2012) Swarup K Parida et al.   BMC GENOMICS

Water uptake dynamics under progressive drought stress in diverse accessions of the OryzaSNP panel of rice (Oryza sativa)

(2012) Veeresh R. P. Gowda et al.   FUNCTIONAL PLANT BIOLOGY

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

(2012) Xuehui Huang et al.   NATURE

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

NGS QC Toolkit: A Toolkit for Quality Control of Next Generation Sequencing Data

(2012) Ravi K. Patel 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

Identification of QTLs with main, epistatic and QTL × environment interaction effects for salt tolerance in rice seedlings under different salinity conditions

(2012) Zhoufei Wang et al.   THEORETICAL AND APPLIED GENETICS

Fine mapping of QTLs for rice grain yield under drought reveals sub-QTLs conferring a response to variable drought severities

(2012) Shalabh Dixit et al.   THEORETICAL AND APPLIED GENETICS

Meta-analysis of grain yield QTL identified during agricultural drought in grasses showed consensus

(2011) BP Mallikarjuna Swamy et al.   BMC GENOMICS

Core single-nucleotide polymorphisms—a tool for genetic analysis of the Japanese rice population

(2011) Hideki Nagasaki et al.   BREEDING SCIENCE

Genetic architecture of regulatory variation in Arabidopsis thaliana

(2011) X. Zhang et al.   GENOME RESEARCH

Genetic Analysis and Fine Mapping of a Novel Semidominant Dwarfing Gene LB4D in Rice

(2011) Fei Liang et al.   Journal of Integrative Plant Biology

Genome-wide association study of flowering time and grain yield traits in a worldwide collection of rice germplasm

(2011) Xuehui Huang et al.   NATURE GENETICS

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

Differential gene expression and associated QTL mapping for cotton yield based on a cDNA-AFLP transcriptome map in an immortalized F2

(2011) Renzhong Liu 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

Fine definition of the pedigree haplotypes of closely related rice cultivars by means of genome-wide discovery of single-nucleotide polymorphisms

(2010) Toshio Yamamoto et al.   BMC GENOMICS

Genome-Wide Survey and Expression Analysis Suggest Diverse Roles of Glutaredoxin Gene Family Members During Development and Response to Various Stimuli in Rice

(2010) R. Garg et al.   DNA RESEARCH

Variation in root system architecture and drought response in rice (Oryza sativa): Phenotyping of the OryzaSNP panel in rainfed lowland fields

(2010) Amelia Henry et al.   FIELD CROPS RESEARCH

Combining QTL mapping and transcriptome profiling of bulked RILs for identification of functional polymorphism for salt tolerance genes in rice (Oryza sativa L.)

(2010) Awadhesh Pandit et al.   MOLECULAR GENETICS AND GENOMICS

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

(2010) Xuehui Huang 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

Towards the Understanding of Complex Traits in Rice: Substantially or Superficially?

(2009) T. Yamamoto et al.   DNA RESEARCH

Identification of a Cis-Acting Regulatory Polymorphism in a Eucalypt COBRA-Like Gene Affecting Cellulose Content

(2009) B. R. Thumma et al.   GENETICS

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

SNP deserts of Asian cultivated rice: genomic regions under domestication

(2009) L. WANG et al.   JOURNAL OF EVOLUTIONARY BIOLOGY

Expression quantitative trait loci analysis in plants

(2009) Arnis Druka et al.   PLANT BIOTECHNOLOGY JOURNAL

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

Quantitative Genomics: Analyzing Intraspecific Variation Using Global Gene Expression Polymorphisms or eQTLs

(2008) Dan Kliebenstein   Annual Review of Plant Biology

Development of genomic resources for Citrus clementina: characterization of three deep-coverage BAC libraries and analysis of 46,000 BAC end sequences

(2008) Javier Terol et al.   BMC GENOMICS

Phenotypic and genotypic analysis of drought-resistance traits for development of rice cultivars adapted to rainfed environments

(2008) Akihiko Kamoshita et al.   FIELD CROPS RESEARCH

Transcriptome map for seedling stage specific salinity stress response indicates a specific set of genes as candidate for saline tolerance in Oryza sativa L.

(2008) Sumita Kumari et al.   FUNCTIONAL & INTEGRATIVE GENOMICS

The Receptor-Like Cytoplasmic Kinase (OsRLCK) Gene Family in Rice: Organization, Phylogenetic Relationship, and Expression during Development and Stress

(2008) Shubha Vij et al.   Molecular Plant

Regulatory changes underlying expression differences within and between Drosophila species

(2008) Patricia J Wittkopp et al.   NATURE GENETICS