1k-RiCA (1K-Rice Custom Amplicon) a novel genotyping amplicon-based SNP assay for genetics and breeding applications in rice

Criteria for evaluating molecular markers: Comprehensive quality metrics to improve marker-assisted selection

(2019) John Damien Platten et al.   PLoS One

Multienvironment Models Increase Prediction Accuracy of Complex Traits in Advanced Breeding Lines of Rice

(2018) Eliana Monteverde et al.   CROP SCIENCE

HiMAP: Robust phylogenomics from highly multiplexed amplicon sequencing

(2018) Julian R. Dupuis et al.   Molecular Ecology Resources

When less can be better: How can we make genomic selection more cost-effective and accurate in barley?

(2018) Amina Abed et al.   THEORETICAL AND APPLIED GENETICS

Effective Genomic Selection in a Narrow-Genepool Crop with Low-Density Markers: Asian Rapeseed as an Example

(2018) Christian R. Werner et al.   Plant Genome

Multiplex PCR Targeted Amplicon Sequencing (MTA-Seq): Simple, Flexible, and Versatile SNP Genotyping by Highly Multiplexed PCR Amplicon Sequencing

(2018) Yoshihiko Onda et al.   Frontiers in Plant Science

Genomic variation in 3,010 diverse accessions of Asian cultivated rice

(2018) Wensheng Wang et al.   NATURE

Using markers with large effect in genetic and genomic predictions1

(2017) M. S. Lopes et al.   JOURNAL OF ANIMAL SCIENCE

Crop Breeding Chips and Genotyping Platforms: Progress, Challenges, and Perspectives

(2017) Awais Rasheed et al.   Molecular Plant

Genome-wide Association Analysis Tracks Bacterial Leaf Blight Resistance Loci In Rice Diverse Germplasm

(2017) Christine Jade Dilla-Ermita et al.   Rice

Large-scale deployment of a rice 6 K SNP array for genetics and breeding applications

(2017) Michael J. Thomson et al.   Rice

Genetic Architecture of a Rice Nested Association Mapping Population

(2017) Christopher A. Fragoso et al.   G3-Genes Genomes Genetics

Genotype Imputation To Improve the Cost-Efficiency of Genomic Selection in Farmed Atlantic Salmon

(2017) Hsin-Yuan Tsai et al.   G3-Genes Genomes Genetics

Application of Targeted Next-generation Sequencing, TruSeq Custom Amplicon Assay for Molecular Pathology Diagnostics on Formalin-fixed and Paraffin-embedded Samples

(2017) Erzsébet Csernák et al.   APPLIED IMMUNOHISTOCHEMISTRY & MOLECULAR MORPHOLOGY

Optimizing Training Population Size and Genotyping Strategy for Genomic Prediction Using Association Study Results and Pedigree Information. A Case of Study in Advanced Wheat Breeding Lines

(2017) Fabio Cericola et al.   PLoS One

Comparison of Next-Generation Sequencing Panels and Platforms for Detection and Verification of Somatic Tumor Variants for Clinical Diagnostics

(2016) Maksym Misyura et al.   JOURNAL OF MOLECULAR DIAGNOSTICS

Crystalline, thermal and swelling properties of starches from single-segment substitution lines with different Wx alleles in rice (Oryza sativa L.)

(2016) Bin Teng et al.   JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE

Harnessing the power of RADseq for ecological and evolutionary genomics

(2016) Kimberly R. Andrews et al.   NATURE REVIEWS GENETICS

Rice SNP-seek database update: new SNPs, indels, and queries

(2016) Locedie Mansueto et al.   NUCLEIC ACIDS RESEARCH

Construction of a versatile SNP array for pyramiding useful genes of rice

(2016) Yusuke Kurokawa et al.   PLANT SCIENCE

Genomic Prediction of Seed Quality Traits Using Advanced Barley Breeding Lines

(2016) Nanna Hellum Nielsen et al.   PLoS One

The Development of Quality Control Genotyping Approaches: A Case Study Using Elite Maize Lines

(2016) Jiafa Chen et al.   PLoS One

Genome-wide association and high-resolution phenotyping link Oryza sativa panicle traits to numerous trait-specific QTL clusters

(2016) Samuel Crowell et al.   Nature Communications

Open access resources for genome-wide association mapping in rice

(2016) Susan R. McCouch et al.   Nature Communications

Validation of a Next-Generation–Sequencing Cancer Panel for Use in the Clinical Laboratory

(2015) Birgitte B. Simen et al.   ARCHIVES OF PATHOLOGY & LABORATORY MEDICINE

Targeted next-generation sequencing (NGS) of nine candidate genes with custom AmpliSeq in patients and a cardiomyopathy risk group

(2015) Andrey S. Glotov et al.   CLINICA CHIMICA ACTA

Fitting Linear Mixed-Effects Models Usinglme4

(2015) Douglas Bates et al.   Journal of Statistical Software

Development of maizeSNP3072, a high-throughput compatible SNP array, for DNA fingerprinting identification of Chinese maize varieties

(2015) Hong-Li Tian et al.   MOLECULAR BREEDING

Development and validation of SNP-based functional codominant markers for two major disease resistance genes in rice (O. sativa L.)

(2015) G. Ramkumar et al.   MOLECULAR BREEDING

Development and GBS-genotyping of introgression lines (ILs) using two wild species of rice, O. meridionalis and O. rufipogon, in a common recurrent parent, O. sativa cv. Curinga

(2015) Juan D. Arbelaez et al.   MOLECULAR BREEDING

XA23 Is an Executor R Protein and Confers Broad-Spectrum Disease Resistance in Rice

(2015) Chunlian Wang et al.   Molecular Plant

Accuracy of Genomic Selection in a Rice Synthetic Population Developed for Recurrent Selection Breeding

(2015) Cécile Grenier et al.   PLoS One

Whole Genome Sequencing of Elite Rice Cultivars as a Comprehensive Information Resource for Marker Assisted Selection

(2015) Jorge Duitama et al.   PLoS One

Single-copy gene based 50 K SNP chip for genetic studies and molecular breeding in rice

(2015) Nisha Singh et al.   Scientific Reports

Rice Xa21 primed genes and pathways that are critical for combating bacterial blight infection

(2015) Hai Peng et al.   Scientific Reports

LinkImpute: Fast and Accurate Genotype Imputation for Nonmodel Organisms

(2015) Daniel Money et al.   G3-Genes Genomes Genetics

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

Next-Generation Sampling: Pairing Genomics with Herbarium Specimens Provides Species-Level Signal inSolidago(Asteraceae)

(2015) James B. Beck et al.   Applications in Plant Sciences

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

Genomic Selection for Quantitative Adult Plant Stem Rust Resistance in Wheat

(2015) Jessica E. Rutkoski et al.   Plant Genome

Genome-Wide Regression and Prediction with the BGLR Statistical Package

(2014) P. Perez et al.   GENETICS

Ward’s Hierarchical Agglomerative Clustering Method: Which Algorithms Implement Ward’s Criterion?

(2014) Fionn Murtagh et al.   JOURNAL OF CLASSIFICATION

SNP-Seek database of SNPs derived from 3000 rice genomes

(2014) Nickolai Alexandrov et al.   NUCLEIC ACIDS RESEARCH

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

(2013) Haodong Chen et al.   Molecular Plant

A whole-genome SNP array (RICE6K) for genomic breeding in rice

(2013) Huihui Yu et al.   PLANT BIOTECHNOLOGY JOURNAL

Yield Trends Are Insufficient to Double Global Crop Production by 2050

(2013) Deepak K. Ray 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

Imputation of Unordered Markers and the Impact on Genomic Selection Accuracy

(2013) Jessica E. Rutkoski et al.   G3-Genes Genomes Genetics

Design of a Bovine Low-Density SNP Array Optimized for Imputation

(2012) Didier Boichard et al.   PLoS One

Crops that feed the world 7: Rice

(2012) Papa Abdoulaye Seck et al.   Food Security

Extension of the bayesian alphabet for genomic selection

(2011) David Habier et al.   BMC BIOINFORMATICS

Genomic selection in plant breeding: from theory to practice

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

Genomic Selection in Plant Breeding: A Comparison of Models

(2011) Nicolas Heslot et al.   CROP SCIENCE

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

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

Development and application of a set of breeder-friendly SNP markers for genetic analyses and molecular breeding of rice (Oryza sativa L.)

(2011) Haodong Chen 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

Ridge Regression and Other Kernels for Genomic Selection with R Package rrBLUP

(2011) Jeffrey B. Endelman   Plant Genome

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

Augmented p-rep designs

(2010) Emlyn Williams et al.   BIOMETRICAL JOURNAL

Polymorphism in the GBSS gene affects amylose content in US and European rice germplasm

(2010) Macaire Dobo et al.   JOURNAL OF CEREAL SCIENCE

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

(2010) Xuehui Huang et al.   NATURE GENETICS

Genomic Diversity and Introgression in O. sativa Reveal the Impact of Domestication and Breeding on the Rice Genome

(2010) Keyan Zhao et al.   PLoS One

Genomic-Enabled Prediction Based on Molecular Markers and Pedigree Using the Bayesian Linear Regression Package in R

(2010) Paulino Pérez et al.   Plant Genome

Evolutionary History of GS3 , a Gene Conferring Grain Length in Rice

(2009) Noriko Takano-Kai et al.   GENETICS

Genomic Selection Using Low-Density Marker Panels

(2009) D. Habier et al.   GENETICS

Single Nucleotide Polymorphisms in a Gene for Translation Initiation Factor (eIF4G) of Rice (Oryza sativa) Associated with Resistance toRice tungro spherical virus

(2009) Jong-Hee Lee et al.   MOLECULAR PLANT-MICROBE INTERACTIONS

A single plant resistance gene promoter engineered to recognize multiple TAL effectors from disparate pathogens

(2009) P. Romer et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Development of submergence-tolerant rice cultivars: the Sub1 locus and beyond

(2008) Endang M. Septiningsih et al.   ANNALS OF BOTANY

The Bayesian Lasso

(2008) Trevor Park et al.   JOURNAL OF THE AMERICAN STATISTICAL ASSOCIATION