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

Iterative sure independence screening EM-Bayesian LASSO algorithm for multi-locus genome-wide association studies

(2017) Cox Lwaka Tamba et al.   PLoS Computational Biology

New Candidate Genes Affecting Rice Grain Appearance and Milling Quality Detected by Genome-Wide and Gene-Based Association Analyses

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

Indica rice genome assembly, annotation and mining of blast disease resistance genes

(2016) H. B. Mahesh et al.   BMC GENOMICS

OsSPL13 controls grain size in cultivated rice

(2016) Lizhen Si et al.   NATURE GENETICS

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

(2016) Kenji Yano et al.   NATURE GENETICS

Systems Genetics Identifies a Novel Regulatory Domain of Amylose Synthesis

(2016) Vito M. Butardo et al.   PLANT PHYSIOLOGY

Extensive sequence divergence between the reference genomes of two eliteindicarice varieties Zhenshan 97 and Minghui 63

(2016) Jianwei Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

SMALL GRAIN 11 Controls Grain Size, Grain Number and Grain Yield in Rice

(2016) Na Fang et al.   Rice

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

Three Rice NAC Transcription Factors Heteromerize and Are Associated with Seed Size

(2016) Iny Elizebeth Mathew et al.   Frontiers in Plant Science

Improving power and accuracy of genome-wide association studies via a multi-locus mixed linear model methodology

(2016) Shi-Bo Wang et al.   Scientific Reports

Copy number variation at the GL7 locus contributes to grain size diversity in rice

(2015) Yuexing Wang et al.   NATURE GENETICS

QTL analysis for cooking traits of super rice with a high-density SNP genetic map and fine mapping of a novel boiled grain length locus

(2015) Yuanyuan Li et al.   PLANT BREEDING

Prospects of breeding high-quality rice using post-genomic tools

(2015) Roslen Anacleto et al.   THEORETICAL AND APPLIED GENETICS

Second-generation PLINK: rising to the challenge of larger and richer datasets

(2015) Christopher C Chang et al.   GigaScience

SNP-Seek database of SNPs derived from 3000 rice genomes

(2014) Nickolai Alexandrov et al.   NUCLEIC ACIDS RESEARCH

DNA-binding specificities of plant transcription factors and their potential to define target genes

(2014) José M. Franco-Zorrilla et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Warped linear mixed models for the genetic analysis of transformed phenotypes

(2014) Nicolo Fusi et al.   Nature Communications

Ubiquitin-mediated control of seed size in plants

(2014) Na Li et al.   Frontiers in Plant Science

The 3,000 rice genomes project

(2014)   GigaScience

Resequencing rice genomes: an emerging new era of rice genomics

(2013) Xuehui Huang et al.   TRENDS IN GENETICS

A high-performance computing toolset for relatedness and principal component analysis of SNP data

(2012) X. Zheng et al.   BIOINFORMATICS

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

(2012) Xuehui Huang et al.   NATURE

Control of grain size, shape and quality by OsSPL16 in rice

(2012) Shaokui Wang et al.   NATURE GENETICS

MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity

(2012) Y. Wang et al.   NUCLEIC ACIDS RESEARCH

Plant Proteins Containing High Mobility Group Box DNA-Binding Domains Modulate Different Nuclear Processes

(2012) M. Antosch et al.   PLANT PHYSIOLOGY

Genetic bases of rice grain shape: so many genes, so little known

(2012) Rongyu Huang et al.   TRENDS IN PLANT SCIENCE

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

Comprehensive analysis of AHL homologous genes encoding AT-hook motif nuclear localized protein in rice

(2011) Ho-Bang Kim et al.   BMB Reports

A Rice Diversity Panel Evaluated for Genetic and Agro-Morphological Diversity between Subpopulations and its Geographic Distribution

(2011) M. Liakat Ali et al.   CROP 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

Molecular evidence for a single evolutionary origin of domesticated rice

(2011) J. Molina et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Identification of Quantitative Trait Loci for Grain Traits in Japonica Rice

(2010) Mao-mao LI et al.   Agricultural Sciences in China

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

Linking differential domain functions of the GS3 protein to natural variation of grain size in rice

(2010) H. Mao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

(2009) Noriko Takano-Kai et al.   GENETICS

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

Isolation and initial characterization of GW5, a major QTL associated with rice grain width and weight

(2008) Jianfeng Weng et al.   CELL RESEARCH

Deletion in a gene associated with grain size increased yields during rice domestication

(2008) Ayahiko Shomura et al.   NATURE GENETICS

Dynamic Evolution of Oryza Genomes Is Revealed by Comparative Genomic Analysis of a Genus-Wide Vertical Data Set

(2008) J. S.S. Ammiraju et al.   PLANT CELL

Genome-Wide Analysis of Transposon Insertion Polymorphisms Reveals Intraspecific Variation in Cultivated Rice

(2008) X. Huang et al.   PLANT PHYSIOLOGY