Association mapping in rice: basic concepts and perspectives for molecular breeding

Genome-wide association study of cold tolerance of Chinese indica rice varieties at the bud burst stage

(2018) Mengchen Zhang et al.   PLANT CELL REPORTS

Dynamic monitoring of NDVI in wheat agronomy and breeding trials using an unmanned aerial vehicle

(2017) T. Duan et al.   FIELD CROPS RESEARCH

The advantages of functional phenotyping in pre-field screening for drought-tolerant crops

(2017) Boaz Negin et al.   FUNCTIONAL PLANT BIOLOGY

Crop-model assisted phenomics and genome-wide association study for climate adaptation of indica rice. 1. Phenology

(2017) Michael Dingkuhn et al.   JOURNAL OF EXPERIMENTAL BOTANY

Crop-model assisted phenomics and genome-wide association study for climate adaptation of indica rice. 2. Thermal stress and spikelet sterility

(2017) Michael Dingkuhn et al.   JOURNAL OF EXPERIMENTAL BOTANY

Genome-wide association mapping for phenotypic plasticity in rice

(2017) Shinji Kikuchi et al.   PLANT CELL AND ENVIRONMENT

Association Mapping of Yield and Yield-related Traits Under Reproductive Stage Drought Stress in Rice (Oryza sativa L.)

(2017) B. P. Mallikarjuna Swamy et al.   Rice

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

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

Genome-wide association mapping for root cone angle in rice

(2017) Mathilde Bettembourg et al.   Rice

Genetic Architecture of Natural Variation in Rice Nonphotochemical Quenching Capacity Revealed by Genome-Wide Association Study

(2017) Quanxiu Wang et al.   Frontiers in Plant Science

High-Throughput Phenotyping of Sorghum Plant Height Using an Unmanned Aerial Vehicle and Its Application to Genomic Prediction Modeling

(2017) Kakeru Watanabe et al.   Frontiers in Plant Science

Association Mapping Reveals Novel Genetic Loci Contributing to Flooding Tolerance during Germination in Indica Rice

(2017) Mengchen Zhang et al.   Frontiers in Plant Science

Genetic architecture of cold tolerance in rice (Oryza sativa) determined through high resolution genome-wide analysis

(2017) Ehsan Shakiba et al.   PLoS One

Genome wide association analysis of cold tolerance at germination in temperate japonica rice (Oryza sativa L.) varieties

(2017) Ester Sales et al.   PLoS One

Ror2 signaling regulates Golgi structure and transport through IFT20 for tumor invasiveness

(2017) Michiru Nishita et al.   Scientific Reports

Whole genome sequencing-based association study to unravel genetic architecture of cooked grain width and length traits in rice

(2017) Gopal Misra et al.   Scientific Reports

Genome-wide and gene-based association mapping for rice eating and cooking characteristics and protein content

(2017) Xiaoqian Wang et al.   Scientific Reports

Identification of QTLs associated with agronomic performance under nitrogen-deficient conditions using chromosome segment substitution lines of a wild rice relative, Oryza rufipogon

(2016) Satoshi Ogawa et al.   ACTA PHYSIOLOGIAE PLANTARUM

Genome-wide prediction models that incorporate de novo GWAS are a powerful new tool for tropical rice improvement

(2016) J E Spindel et al.   HEREDITY

Genome-wide association study using whole-genome sequencing rapidly identifies new genes influencing agronomic traits in rice

(2016) Kenji Yano et al.   NATURE GENETICS

From QTL to variety-harnessing the benefits of QTLs for drought, flood and salt tolerance in mega rice varieties of India through a multi-institutional network

(2016) Renu Singh et al.   PLANT SCIENCE

A Genome-Wide Association Study of Field Resistance to Magnaporthe Oryzae in Rice

(2016) Dan Zhu et al.   Rice

Association mapping of resistance to rice blast in upland field conditions

(2016) Louis-Marie Raboin et al.   Rice

GAPIT Version 2: An Enhanced Integrated Tool for Genomic Association and Prediction

(2016) You Tang et al.   Plant Genome

Genome-Wide Association Study for Traits Related to Plant and Grain Morphology, and Root Architecture in Temperate Rice Accessions

(2016) Filippo Biscarini et al.   PLoS One

Uncovering the novel characteristics of Asian honey bee, Apis cerana, by whole genome sequencing

(2015) Doori Park et al.   BMC GENOMICS

Genome-wide indel markers shared by diverse Asian rice cultivars compared to Japanese rice cultivar ‘Koshihikari’

(2015) Jun-ichi Yonemaru et al.   BREEDING SCIENCE

From association to prediction: statistical methods for the dissection and selection of complex traits in plants

(2015) Alexander E Lipka et al.   CURRENT OPINION IN PLANT BIOLOGY

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

(2015) V. Kumar et al.   DNA RESEARCH

Genome-wide association study of rice (Oryza sativaL.) leaf traits with a high-throughput leaf scorer

(2015) Wanneng Yang et al.   JOURNAL OF EXPERIMENTAL BOTANY

Genetic Architecture of Natural Variation in Rice Chlorophyll Content Revealed by a Genome-Wide Association Study

(2015) Quanxiu Wang et al.   Molecular Plant

Automated characterization of flowering dynamics in rice using field-acquired time-series RGB images

(2015) Wei Guo et al.   Plant Methods

Selective impairment of methylation maintenance is the major cause of DNA methylation reprogramming in the early embryo

(2015) Julia Arand et al.   Epigenetics & Chromatin

Genome-Wide Association Studies Reveal New Genetic Targets for Five Panicle Traits of International Rice Varieties

(2015) ZHANG Ya-fang et al.   Rice Science

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

Characterization of a panel of Vietnamese rice varieties using DArT and SNP markers for association mapping purposes

(2014) Nhung Thi Phuong Phung et al.   BMC PLANT BIOLOGY

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

Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolism

(2014) Wei Chen et al.   NATURE GENETICS

SNP-Seek database of SNPs derived from 3000 rice genomes

(2014) Nickolai Alexandrov et al.   NUCLEIC ACIDS RESEARCH

Genome Wide Association Mapping of Grain Arsenic, Copper, Molybdenum and Zinc in Rice (Oryza sativa L.) Grown at Four International Field Sites

(2014) Gareth J. Norton et al.   PLoS One

A SUPER Powerful Method for Genome Wide Association Study

(2014) Qishan Wang et al.   PLoS One

Laying a solid foundation for Manhattan – ‘setting the functional basis for the post-GWAS era’

(2014) Xiaoyang Zhang et al.   TRENDS IN GENETICS

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

(2014) Wanneng Yang et al.   Nature Communications

The 3,000 rice genomes project

(2014)   GigaScience

Single nucleotide polymorphism genotyping using Kompetitive Allele Specific PCR (KASP): overview of the technology and its application in crop improvement

(2013) Kassa Semagn et al.   MOLECULAR BREEDING

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

(2013) Haodong Chen et al.   Molecular Plant

HapRice, an SNP Haplotype Database and a Web Tool for Rice

(2013) Jun-ichi Yonemaru et al.   PLANT AND CELL PHYSIOLOGY

The advantages and limitations of trait analysis with GWAS: a review

(2013) Arthur Korte et al.   Plant Methods

Genome-Wide Association Mapping of Root Traits in a Japonica Rice Panel

(2013) Brigitte Courtois et al.   PLoS One

Next-generation phenotyping: requirements and strategies for enhancing our understanding of genotype–phenotype relationships and its relevance to crop improvement

(2013) Joshua N. Cobb et al.   THEORETICAL AND APPLIED GENETICS

GAPIT: genome association and prediction integrated tool

(2012) Alexander E. Lipka et al.   BIOINFORMATICS

Phenotyping for drought tolerance in grain crops: when is it useful to breeders?

(2012) J. B. Passioura   FUNCTIONAL PLANT BIOLOGY

Novel Genomic Tools and Modern Genetic and Breeding Approaches for Crop Improvement

(2012) Rajeev K. Varshney et al.   JOURNAL OF PLANT BIOCHEMISTRY AND BIOTECHNOLOGY

An efficient multi-locus mixed-model approach for genome-wide association studies in structured populations

(2012) Vincent Segura et al.   NATURE GENETICS

Accessing complex crop genomes with next-generation sequencing

(2012) David Edwards et al.   THEORETICAL AND APPLIED GENETICS

Development of genome-wide SNP assays for rice

(2011) Susan R. McCouch et al.   BREEDING SCIENCE

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

Crop genomics: advances and applications

(2011) Peter L. Morrell et al.   NATURE REVIEWS GENETICS

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

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

Population genetics of genomics-based crop improvement methods

(2011) Martha T. Hamblin et al.   TRENDS IN GENETICS

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

(2011) Keyan Zhao et al.   Nature Communications

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

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

Association genetics in crop improvement

(2010) J Antoni Rafalski   CURRENT OPINION IN PLANT BIOLOGY

The genetic dissection of quantitative traits in crops

(2010) Kassa Semagn et al.   ELECTRONIC JOURNAL OF BIOTECHNOLOGY

Conditions Under Which Genome-Wide Association Studies Will be Positively Misleading

(2010) A. Platt et al.   GENETICS

Association mapping for yield and grain quality traits in rice (Oryza sativa L.)

(2010) Tereza Cristina de Oliveira Borba et al.   GENETICS AND MOLECULAR BIOLOGY

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

(2010) Susanna Atwell et al.   NATURE

Mixed linear model approach adapted for genome-wide association studies

(2010) Zhiwu Zhang et al.   NATURE GENETICS

Variance component model to account for sample structure in genome-wide association studies

(2010) Hyun Min Kang et al.   NATURE GENETICS

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

(2010) Xuehui Huang et al.   NATURE GENETICS

Association genetics of complex traits in plants

(2010) Pär K. Ingvarsson et al.   NEW PHYTOLOGIST

In the Eye of the Beholder: The Effect of Rater Variability and Different Rating Scales on QTL Mapping

(2010) Jesse A. Poland et al.   PHYTOPATHOLOGY

The genetics of quantitative traits: challenges and prospects

(2009) Trudy F. C. Mackay et al.   NATURE REVIEWS GENETICS

Association Mapping: Critical Considerations Shift from Genotyping to Experimental Design

(2009) S. Myles et al.   PLANT CELL

Why are There Indica Type and Japonica Type in Rice? — History of the Studies and a View for Origin of Two Types

(2009) Hiroshi IKEHASHI   Rice Science

Efficient Control of Population Structure in Model Organism Association Mapping

(2008) H. M. Kang et al.   GENETICS

Linkage disequilibrium — understanding the evolutionary past and mapping the medical future

(2008) Montgomery Slatkin   NATURE REVIEWS GENETICS

Status and Prospects of Association Mapping in Plants

(2008) Chengsong Zhu et al.   Plant Genome

Marker-assisted selection: an approach for precision plant breeding in the twenty-first century

(2007) B. C.Y Collard et al.   PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES