Translational genomics for plant breeding with the genome sequence explosion

Genome-wide association analysis of seedling root development in maize (Zea mays L.)

(2015) Jordon Pace et al.   BMC GENOMICS

Genome-wide association study reveals a set of genes associated with resistance to the Mediterranean corn borer (Sesamia nonagrioides L.) in a maize diversity panel

(2015) Luis Samayoa et al.   BMC PLANT BIOLOGY

Genome-wide association mapping of salinity tolerance in rice (Oryza sativa)

(2015) V. Kumar et al.   DNA RESEARCH

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

(2015) Zhengkui Zhou et al.   NATURE BIOTECHNOLOGY

MethylC-seq library preparation for base-resolution whole-genome bisulfite sequencing

(2015) Mark A Urich et al.   Nature Protocols

Association analysis of genes involved in maize (Zea mays L.) root development with seedling and agronomic traits under contrasting nitrogen levels

(2015) Adel H. Abdel-Ghani et al.   PLANT MOLECULAR BIOLOGY

Large effect QTL explain natural phenotypic variation for the developmental timing of vegetative phase change in maize (Zea mays L.)

(2015) Jillian M. Foerster et al.   THEORETICAL AND APPLIED GENETICS

Genome-wide association analysis reveals new targets for carotenoid biofortification in maize

(2015) Willy B. Suwarno et al.   THEORETICAL AND APPLIED GENETICS

Draft genome sequence of adzuki bean, Vigna angularis

(2015) Yang Jae Kang et al.   Scientific Reports

Genomic Selection and Association Mapping in Rice (Oryza sativa): Effect of Trait Genetic Architecture, Training Population Composition, Marker Number and Statistical Model on Accuracy of Rice Genomic Selection in Elite, Tropical Rice Breeding Lines

(2015) Jennifer Spindel et al.   PLoS Genetics

Genome-Wide Association Mapping for Yield and Other Agronomic Traits in an Elite Breeding Population of Tropical Rice (Oryza sativa)

(2015) Hasina Begum et al.   PLoS One

Time-Course Association Mapping of the Grain-Filling Rate in Rice (Oryza sativa L.)

(2015) Erbao Liu et al.   PLoS One

A genome-wide association study of seed protein and oil content in soybean

(2014) Eun-Young Hwang et al.   BMC GENOMICS

Genome-wide association study of blast resistance in indica rice

(2014) Caihong Wang et al.   BMC PLANT BIOLOGY

Genome-wide association study of Fusarium ear rot disease in the U.S.A. maize inbred line collection

(2014) Charles T Zila et al.   BMC PLANT BIOLOGY

Translational Genomics in Agriculture: Some Examples in Grain Legumes

(2014) Rajeev K. Varshney et al.   CRITICAL REVIEWS IN PLANT SCIENCES

Comparison of genomic predictions using genomic relationship matrices built with different weighting factors to account for locus-specific variances

(2014) G. Su et al.   JOURNAL OF DAIRY SCIENCE

Genetic dissection of ozone tolerance in rice (Oryza sativa L.) by a genome-wide association study

(2014) Yoshiaki Ueda et al.   JOURNAL OF EXPERIMENTAL BOTANY

SNP-Seek database of SNPs derived from 3000 rice genomes

(2014) Nickolai Alexandrov et al.   NUCLEIC ACIDS RESEARCH

Genome-Wide Association Studies Identifies Seven Major Regions Responsible for Iron Deficiency Chlorosis in Soybean (Glycine max)

(2014) Sujan Mamidi et al.   PLoS One

Genome-wide association study (GWAS) of carbon isotope ratio (δ13C) in diverse soybean [Glycine max (L.) Merr.] genotypes

(2014) Arun Prabhu Dhanapal et al.   THEORETICAL AND APPLIED GENETICS

Combining high-throughput phenotyping and genome-wide association studies to reveal natural genetic variation in rice

(2014) Wanneng Yang et al.   Nature Communications

Genome sequence of mungbean and insights into evolution within Vigna species

(2014) Yang Jae Kang et al.   Nature Communications

The 3,000 rice genomes project

(2014)   GigaScience

Achievements and prospects of genomics-assisted breeding in three legume crops of the semi-arid tropics

(2013) Rajeev K. Varshney et al.   BIOTECHNOLOGY ADVANCES

Plant genome sequencing — applications for crop improvement

(2013) Marie E Bolger et al.   CURRENT OPINION IN BIOTECHNOLOGY

Population Structure and Domestication Revealed by High-Depth Resequencing of Korean Cultivated and Wild Soybean Genomes

(2013) W.-H. Chung et al.   DNA RESEARCH

Determination of the genetic architecture of seed size and shape via linkage and association analysis in soybean (Glycine max L. Merr.)

(2013) Zhenbin Hu et al.   GENETICA

Epigenome-wide inheritance of cytosine methylation variants in a recombinant inbred population

(2013) R. J. Schmitz et al.   GENOME RESEARCH

21st Century natural product research and drug development and traditional medicines

(2013) Linh T. Ngo et al.   NATURAL PRODUCT REPORTS

RNA interference in the nucleus: roles for small RNAs in transcription, epigenetics and beyond

(2013) Stephane E. Castel et al.   NATURE REVIEWS GENETICS

Sequence assembly demystified

(2013) Niranjan Nagarajan et al.   NATURE REVIEWS GENETICS

Soybean knowledge base (SoyKB): a web resource for integration of soybean translational genomics and molecular breeding

(2013) Trupti Joshi et al.   NUCLEIC ACIDS RESEARCH

Gramene 2013: comparative plant genomics resources

(2013) Marcela K. Monaco et al.   NUCLEIC ACIDS RESEARCH

The NHGRI GWAS Catalog, a curated resource of SNP-trait associations

(2013) Danielle Welter et al.   NUCLEIC ACIDS RESEARCH

Pfam: the protein families database

(2013) Robert D. Finn et al.   NUCLEIC ACIDS RESEARCH

Plant Genome DataBase Japan (PGDBj): A Portal Website for the Integration of Plant Genome-Related Databases

(2013) Erika Asamizu et al.   PLANT AND CELL PHYSIOLOGY

Comparison of SSR and SNP Markers in Estimation of Genetic Diversity and Population Structure of Indian Rice Varieties

(2013) Nivedita Singh et al.   PLoS One

CerealsDB 2.0: an integrated resource for plant breeders and scientists

(2012) Paul A Wilkinson et al.   BMC BIOINFORMATICS

Application of next-generation sequencing for rapid marker development in molecular plant breeding: a case study on anthracnose disease resistance in Lupinus angustifolius L.

(2012) Huaan Yang et al.   BMC GENOMICS

Functions of DNA methylation: islands, start sites, gene bodies and beyond

(2012) Peter A. Jones   NATURE REVIEWS GENETICS

Patterns and processes in crop domestication: an historical review and quantitative analysis of 203 global food crops

(2012) Rachel S. Meyer et al.   NEW PHYTOLOGIST

RiceXPro Version 3.0: expanding the informatics resource for rice transcriptome

(2012) Yutaka Sato et al.   NUCLEIC ACIDS RESEARCH

Genome-wide association study (GWAS) of resistance to head smut in maize

(2012) Ming Wang et al.   PLANT SCIENCE

Genome-wide association study of leaf architecture in the maize nested association mapping population

(2011) Feng Tian et al.   NATURE GENETICS

Phytozome: a comparative platform for green plant genomics

(2011) David M. Goodstein et al.   NUCLEIC ACIDS RESEARCH

GWASdb: a database for human genetic variants identified by genome-wide association studies

(2011) Mulin Jun Li et al.   NUCLEIC ACIDS RESEARCH

PLEXdb: gene expression resources for plants and plant pathogens

(2011) S. Dash et al.   NUCLEIC ACIDS RESEARCH

InterPro in 2011: new developments in the family and domain prediction database

(2011) S. Hunter et al.   NUCLEIC ACIDS RESEARCH

Reorganizing the protein space at the Universal Protein Resource (UniProt)

(2011)   NUCLEIC ACIDS RESEARCH

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

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

Identification of single nucleotide polymorphisms and haplotypes associated with yield and yield components in soybean (Glycine max) landraces across multiple environments

(2011) Derong Hao et al.   THEORETICAL AND APPLIED GENETICS

Genetic Architecture of Aluminum Tolerance in Rice (Oryza sativa) Determined through Genome-Wide Association Analysis and QTL Mapping

(2011) Adam N. Famoso et al.   PLoS Genetics

Insights from the Comparison of Plant Genome Sequences

(2010) Andrew H. Paterson et al.   Annual Review of Plant Biology

Association genetics in crop improvement

(2010) J Antoni Rafalski   CURRENT OPINION IN PLANT BIOLOGY

A review of the antioxidant potential of medicinal plant species

(2010) Duduku Krishnaiah et al.   FOOD AND BIOPRODUCTS PROCESSING

Rational association of genes with traits using a genome-scale gene network for Arabidopsis thaliana

(2010) Insuk Lee et al.   NATURE BIOTECHNOLOGY

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

(2010) Xuehui Huang et al.   NATURE GENETICS

RNA sequencing: advances, challenges and opportunities

(2010) Fatih Ozsolak et al.   NATURE REVIEWS GENETICS

High-quality draft assemblies of mammalian genomes from massively parallel sequence data

(2010) S. Gnerre et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Network Modeling Reveals Prevalent Negative Regulatory Relationships between Signaling Sectors in Arabidopsis Immune Signaling

(2010) Masanao Sato et al.   PLoS Pathogens

Bias in Plant Gene Content Following Different Sorts of Duplication: Tandem, Whole-Genome, Segmental, or by Transposition

(2009) Michael Freeling   Annual Review of Plant Biology

An Open Access Database of Genome-wide Association Results

(2009) Andrew D Johnson et al.   BMC Medical Genetics

JBrowse: A next-generation genome browser

(2009) M. E. Skinner et al.   GENOME RESEARCH

SoyBase, the USDA-ARS soybean genetics and genomics database

(2009) David Grant et al.   NUCLEIC ACIDS RESEARCH

Three Sequenced Legume Genomes and Many Crop Species: Rich Opportunities for Translational Genomics

(2009) S. B. Cannon et al.   PLANT PHYSIOLOGY

Highly Integrated Single-Base Resolution Maps of the Epigenome in Arabidopsis

(2008) Ryan Lister et al.   CELL

Finding and Comparing Syntenic Regions among Arabidopsis and the Outgroups Papaya, Poplar, and Grape: CoGe with Rosids

(2008) E. Lyons et al.   PLANT PHYSIOLOGY

Importance of Lineage-Specific Expansion of Plant Tandem Duplicates in the Adaptive Response to Environmental Stimuli

(2008) K. Hanada et al.   PLANT PHYSIOLOGY