Genome‐wide association coupled gene to gene interaction studies unveil novel epistatic targets among major effect loci impacting rice grain chalkiness

Genome-wide association and epistatic interactions of flowering time in soybean cultivar

(2020) Kyoung Hyoun Kim et al.   PLoS One

Dissecting the genome wide genetic variants of milling and appearance quality traits in rice

(2019) Gopal Misra et al.   JOURNAL OF EXPERIMENTAL BOTANY

Genome-wide associations and epistatic interactions for internode number, plant height, seed weight and seed yield in soybean

(2019) Teshale Assefa et al.   BMC GENOMICS

Genome-Wide Association Study Using Historical Breeding Populations Discovers Genomic Regions Involved in High-Quality Rice

(2018) Gastón Quero et al.   Plant Genome

Identification of a G2-like transcription factor, OsPHL3, functions as a negative regulator of flowering in rice by co-expression and reverse genetic analysis

(2018) Liping Zeng et al.   BMC PLANT BIOLOGY

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

(2018) Wensheng Wang et al.   NATURE

Laser microdissection-based tissue specific transcriptome analyses reveals novel regulatory network of genes involved in heat-induced grain chalk in rice endosperm

(2018) Tsutomu Ishimaru et al.   PLANT AND CELL PHYSIOLOGY

Integrating a genome‐wide association study with a large‐scale transcriptome analysis to predict genetic regions influencing the glycaemic index and texture in rice

(2018) Roslen Anacleto et al.   PLANT BIOTECHNOLOGY JOURNAL

Deciphering the Genetic Architecture of Cooked Rice Texture

(2018) Gopal Misra et al.   Frontiers in Plant Science

Maintenance of phosphate homeostasis and root development are coordinately regulated by MYB1, an R2R3-type MYB transcription factor in rice

(2017) Mian Gu et al.   JOURNAL OF EXPERIMENTAL BOTANY

Dissecting the Genetic Basis of Grain Shape and Chalkiness Traits in Hybrid Rice Using Multiple Collaborative Populations

(2017) Junyi Gong et al.   Molecular Plant

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

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

Systems Genetics Identifies a Novel Regulatory Domain of Amylose Synthesis

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

Proteomic and Glycomic Characterization of Rice Chalky Grains Produced Under Moderate and High-temperature Conditions in Field System

(2016) Kentaro Kaneko et al.   Rice

High-resolution QTL mapping for grain appearance traits and co-localization of chalkiness-associated differentially expressed candidate genes in rice

(2016) Likai Chen et al.   Rice

Designing climate-resilient rice with ideal grain quality suited for high-temperature stress

(2015) Nese Sreenivasulu et al.   JOURNAL OF EXPERIMENTAL BOTANY

Identification of stable QTLs causing chalk in rice grains in nine environments

(2015) Xiangqian Zhao et al.   THEORETICAL AND APPLIED GENETICS

The Usefulness of Known Genes/Qtls for Grain Quality Traits in an Indica Population of Diverse Breeding Lines Tested using Association Analysis

(2015) Xiangqian Zhao et al.   Rice

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

(2015) Christopher C Chang et al.   GigaScience

Farmers’ Preference for Rice Traits: Insights from Farm Surveys in Central Luzon, Philippines, 1966-2012

(2015) Alice G. Laborte et al.   PLoS One

Marker-Based Estimation of Heritability in Immortal Populations

(2014) Willem Kruijer et al.   GENETICS

Chalk5 encodes a vacuolar H+-translocating pyrophosphatase influencing grain chalkiness in rice

(2014) Yibo Li et al.   NATURE GENETICS

Beyond the single gene: How epistasis and gene-by-environment effects influence crop domestication

(2014) A. N. Doust 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

The 3,000 rice genomes project

(2014)   GigaScience

Epistasis and quantitative traits: using model organisms to study gene–gene interactions

(2013) Trudy F. C. Mackay   NATURE REVIEWS GENETICS

Impacts of Preharvest Factors During Kernel Development on Rice Quality and Functionality

(2013) Terry J. Siebenmorgen et al.   Annual Review of Food Science and Technology

Improved Heritability Estimation from Genome-wide SNPs

(2012) Doug Speed et al.   AMERICAN JOURNAL OF HUMAN GENETICS

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

(2012) X. Zheng et al.   BIOINFORMATICS

The use of weighted multiple linear regression to estimate QTL-by-QTL epistatic effects

(2012) Jan Bocianowski   GENETICS AND MOLECULAR BIOLOGY

The mystery of missing heritability: Genetic interactions create phantom heritability

(2012) O. Zuk et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Uniform ripening Encodes a Golden 2-like Transcription Factor Regulating Tomato Fruit Chloroplast Development

(2012) A. L. T. Powell et al.   SCIENCE

Effects of Phosphorus on Grain Quality of Upland and Paddy Rice under Different Cultivation

(2012) Ya-jie ZHANG et al.   Rice Science

Transcriptome analysis of grain-filling caryopses reveals involvement of multiple regulatory pathways in chalky grain formation in rice

(2011) Xiaolu Liu et al.   BMC GENOMICS

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

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

(2010) Hyun Min Kang et al.   NATURE GENETICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Circos: An information aesthetic for comparative genomics

(2009) M. Krzywinski et al.   GENOME RESEARCH

Not just a grain of rice: the quest for quality

(2009) Melissa A. Fitzgerald et al.   TRENDS IN PLANT SCIENCE

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS

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