Crop genome-wide association study: a harvest of biological relevance

An efficient multi-locus mixed model framework for the detection of small and linked QTLs in F2

(2018) Yang-Jun Wen et al.   BRIEFINGS IN BIOINFORMATICS

Rewiring of the Fruit Metabolome in Tomato Breeding

(2018) Guangtao Zhu et al.   CELL

Genome-Wide Association Studies of Image Traits Reveal Genetic Architecture of Drought Resistance in Rice

(2018) Zilong Guo et al.   Molecular Plant

Resequencing a core collection of upland cotton identifies genomic variation and loci influencing fiber quality and yield

(2018) Zhiying Ma et al.   NATURE GENETICS

Resequencing of 243 diploid cotton accessions based on an updated A genome identifies the genetic basis of key agronomic traits

(2018) Xiongming Du et al.   NATURE GENETICS

Determining the evolutionary forces shaping G  × E

(2018) Emily B. Josephs   NEW PHYTOLOGIST

Genomic and environmental determinants and their interplay underlying phenotypic plasticity

(2018) Xin Li et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Improving genetic prediction by leveraging genetic correlations among human diseases and traits

(2018) Robert M. Maier et al.   Nature Communications

Genome-Wide Association Study of Haploid Male Fertility in Maize (Zea Mays L.)

(2018) Hailin Ma et al.   Frontiers in Plant Science

Ethylene-gibberellin signaling underlies adaptation of rice to periodic flooding

(2018) Takeshi Kuroha et al.   SCIENCE

Deep Learning for Plant Stress Phenotyping: Trends and Future Perspectives

(2018) Asheesh Kumar Singh et al.   TRENDS IN PLANT SCIENCE

Detection of Epistasis for Flowering Time Using Bayesian Multilocus Estimation in a Barley MAGIC Population

(2017) Boby Mathew et al.   GENETICS

The roles of pleiotropy and close linkage as revealed by association mapping of yield and correlated traits of wheat (Triticum aestivum L.)

(2017) Albert W Schulthess et al.   JOURNAL OF EXPERIMENTAL BOTANY

Genotypic variability-based genome-wide association study identifies non-additive loci HLA-C and IL12B for psoriasis

(2017) Wen-Hua Wei et al.   JOURNAL OF HUMAN GENETICS

Genome-wide Association Studies in Maize: Praise and Stargaze

(2017) Yingjie Xiao et al.   Molecular Plant

Genome-wide Targeted Mutagenesis in Rice Using the CRISPR/Cas9 System

(2017) Yuming Lu et al.   Molecular Plant

Construction of a Genome-Wide Mutant Library in Rice Using CRISPR/Cas9

(2017) Xiangbing Meng et al.   Molecular Plant

A quantitative genetic framework highlights the role of epistatic effects for grain-yield heterosis in bread wheat

(2017) Yong Jiang et al.   NATURE GENETICS

Genomic analyses in cotton identify signatures of selection and loci associated with fiber quality and yield traits

(2017) Lei Fang et al.   NATURE GENETICS

A study of allelic diversity underlying flowering-time adaptation in maize landraces

(2017) J Alberto Romero Navarro et al.   NATURE GENETICS

Asymmetric subgenome selection and cis-regulatory divergence during cotton domestication

(2017) Maojun Wang et al.   NATURE GENETICS

A transposon-directed epigenetic change in ZmCCT underlies quantitative resistance to Gibberella stalk rot in maize

(2017) Chao Wang et al.   NEW PHYTOLOGIST

Prioritizing tests of epistasis through hierarchical representation of genomic redundancies

(2017) Tyler Cowman et al.   NUCLEIC ACIDS RESEARCH

ZmCCT9enhances maize adaptation to higher latitudes

(2017) Cheng Huang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A chemical genetic roadmap to improved tomato flavor

(2017) Denise Tieman et al.   SCIENCE

RNA sequencing provides insights into the evolution of lettuce and the regulation of flavonoid biosynthesis

(2017) Lei Zhang et al.   Nature Communications

Statistical methods to detect pleiotropy in human complex traits

(2017) Sophie Hackinger et al.   Open Biology

Genome-Wide Association Study of Major Agronomic Traits Related to Domestication in Peanut

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

Detection of Epistasis for Flowering Time Using Bayesian Multilocus Estimation in a Barley MAGIC Population

(2017) Boby Mathew et al.   GENETICS

Genomic Prediction of Genotypic Effects with Epistasis and Environment Interactions for Yield-Related Traits of Rapeseed (Brassica napus L.)

(2017) Xiang Luo et al.   Frontiers in Genetics

Genetic variation in ZmVPP1 contributes to drought tolerance in maize seedlings

(2016) Xianglan Wang 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

Integration of summary data from GWAS and eQTL studies predicts complex trait gene targets

(2016) Zhihong Zhu et al.   NATURE GENETICS

Genome-wide mapping and prediction suggests presence of local epistasis in a vast elite winter wheat populations adapted to Central Europe

(2016) Sang He et al.   THEORETICAL AND APPLIED GENETICS

Genome-wide association study of 12 agronomic traits in peach

(2016) Ke Cao et al.   Nature Communications

Comparative and parallel genome-wide association studies for metabolic and agronomic traits in cereals

(2016) Wei Chen et al.   Nature Communications

PEPIS: A Pipeline for Estimating Epistatic Effects in Quantitative Trait Locus Mapping and Genome-Wide Association Studies

(2016) Wenchao Zhang et al.   PLoS Computational Biology

Multiple alleles at a single locus control seed dormancy in Swedish Arabidopsis

(2016) Envel Kerdaffrec et al.   eLife

A Bayesian model for detection of high-order interactions among genetic variants in genome-wide association studies

(2015) Juexin Wang et al.   BMC GENOMICS

Modelling the genetic architecture of flowering time control in barley through nested association mapping

(2015) Andreas Maurer et al.   BMC GENOMICS

An Efficient Genome-Wide Multilocus Epistasis Search

(2015) H. P. Karkkainen et al.   GENETICS

Genome-wide prediction of maize single-cross performance, considering non-additive genetic effects

(2015) J.P.R. Santos et al.   GENETICS AND MOLECULAR RESEARCH

A rare SNP mutation in Brachytic2 moderately reduces plant height and increases yield potential in maize

(2015) Anqi Xing 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

Genome-wide dissection of the maize ear genetic architecture using multiple populations

(2015) Yingjie Xiao et al.   NEW PHYTOLOGIST

Mapping complex traits as a dynamic system

(2015) Lidan Sun et al.   Physics of Life Reviews

Genome-Wide Mapping of Structural Variations Reveals a Copy Number Variant That Determines Reproductive Morphology in Cucumber

(2015) Zhonghua Zhang et al.   PLANT CELL

Environmental and genetic interactions revealFLOWERING LOCUSCas a modulator of the natural variation for the plasticity of flowering in Arabidopsis

(2015) Belén Méndez-Vigo et al.   PLANT CELL AND ENVIRONMENT

Genome-wide association and epistasis studies unravel the genetic architecture of sudden death syndrome resistance in soybean

(2015) Jiaoping Zhang et al.   PLANT JOURNAL

Combining Quantitative Genetics Approaches with Regulatory Network Analysis to Dissect the Complex Metabolism of the Maize Kernel

(2015) Weiwei Wen et al.   PLANT PHYSIOLOGY

Genome-Wide Association of Carbon and Nitrogen Metabolism in the Maize Nested Association Mapping Population

(2015) Nengyi Zhang et al.   PLANT PHYSIOLOGY

Genomic analysis of hybrid rice varieties reveals numerous superior alleles that contribute to heterosis

(2015) Xuehui Huang et al.   Nature Communications

Genetic discovery for oil production and quality in sesame

(2015) Xin Wei et al.   Nature Communications

gammaMAXT: a fast multiple-testing correction algorithm

(2015) François Van Lishout et al.   BioData Mining

Cloud computing for detecting high-order genome-wide epistatic interaction via dynamic clustering

(2014) Xuan Guo et al.   BMC BIOINFORMATICS

Genome-wide association mapping of quantitative resistance to sudden death syndrome in soybean

(2014) Zixiang Wen et al.   BMC GENOMICS

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

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

Fast detection of high-order epistatic interactions in genome-wide association studies using information theoretic measure

(2014) Sangseob Leem et al.   COMPUTATIONAL BIOLOGY AND CHEMISTRY

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

(2014) Wei Chen et al.   NATURE GENETICS

Genomic analyses provide insights into the history of tomato breeding

(2014) Tao Lin et al.   NATURE GENETICS

Grain Number, Plant Height, and Heading Date7 Is a Central Regulator of Growth, Development, and Stress Response

(2014) X. Weng et al.   PLANT PHYSIOLOGY

Genomewide Association Studies for 50 Agronomic Traits in Peanut Using the ‘Reference Set’ Comprising 300 Genotypes from 48 Countries of the Semi-Arid Tropics of the World

(2014) Manish K. Pandey et al.   PLoS One

Biosynthesis, regulation, and domestication of bitterness in cucumber

(2014) Y. Shang et al.   SCIENCE

Risk of false positive genetic associations in complex traits with underlying population structure: A case study

(2014) Carrie J. Finno et al.   VETERINARY JOURNAL

Metabolome-based genome-wide association study of maize kernel leads to novel biochemical insights

(2014) Weiwei Wen et al.   Nature Communications

Natural Variations and Genome-Wide Association Studies in Crop Plants

(2013) Xuehui Huang et al.   Annual Review of Plant Biology

A QTL model to map the common genetic basis for correlative phenotypic plasticity

(2013) T. Zhou et al.   BRIEFINGS IN BIOINFORMATICS

Plant phenomics and high-throughput phenotyping: accelerating rice functional genomics using multidisciplinary technologies

(2013) Wanneng Yang et al.   CURRENT OPINION IN PLANT BIOLOGY

FaST-LMM-Select for addressing confounding from spatial structure and rare variants

(2013) Jennifer Listgarten et al.   NATURE GENETICS

Loss of function of the IAA-glucose hydrolase gene TGW6 enhances rice grain weight and increases yield

(2013) Ken Ishimaru et al.   NATURE GENETICS

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

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

Pleiotropy in complex traits: challenges and strategies

(2013) Nadia Solovieff et al.   NATURE REVIEWS GENETICS

A synthetic framework for modeling the genetic basis of phenotypic plasticity and its costs

(2013) Yi Zhai et al.   NEW PHYTOLOGIST

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

(2013) Arthur Korte et al.   Plant Methods

Dominance and epistasis are the main contributors to heterosis for plant height in rice

(2013) Guojing Shen et al.   PLANT SCIENCE

CACTA-like transposable element in ZmCCT attenuated photoperiod sensitivity and accelerated the postdomestication spread of maize

(2013) Q. Yang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

RNA sequencing reveals the complex regulatory network in the maize kernel

(2013) Junjie Fu et al.   Nature Communications

Genome-wide association mapping of flowering time inArabidopsis thalianain nature: genetics for underlying components and reaction norms across two successive years

(2013) Benjamin Brachi et al.   ACTA BOTANICA GALLICA

High-throughput analysis of epistasis in genome-wide association studies with BiForce

(2012) Attila Gyenesei et al.   BIOINFORMATICS

A dynamic framework for quantifying the genetic architecture of phenotypic plasticity

(2012) Z. Wang et al.   BRIEFINGS IN BIOINFORMATICS

Flowering Time in Maize: Linkage and Epistasis at a Major Effect Locus

(2012) E. Durand et al.   GENETICS

Genome-wide association study dissects the genetic architecture of oil biosynthesis in maize kernels

(2012) Hui Li et al.   NATURE GENETICS

Parallel domestication of the Shattering1 genes in cereals

(2012) Zhongwei Lin et al.   NATURE GENETICS

Rare and common variants: twenty arguments

(2012) Greg Gibson   NATURE REVIEWS GENETICS

Evolution and Association Analysis of Ghd7 in Rice

(2012) Li Lu et al.   PLoS One

ZmCCT and the genetic basis of day-length adaptation underlying the postdomestication spread of maize

(2012) H.-Y. Hung et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Rare allele of OsPPKL1 associated with grain length causes extra-large grain and a significant yield increase in rice

(2012) X. Zhang et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Phenotypic plasticity and adaptive evolution contribute to advancing flowering phenology in response to climate change

(2012) J. T. Anderson et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Predicting Signatures of “Synthetic Associations” and “Natural Associations” from Empirical Patterns of Human Genetic Variation

(2012) Diana Chang et al.   PLoS Computational Biology

EpiGPU: exhaustive pairwise epistasis scans parallelized on consumer level graphics cards

(2011) G. Hemani et al.   BIOINFORMATICS

Do Large Effect QTL Fractionate? A Case Study at the Maize Domestication QTLteosinte branched1

(2011) Anthony J. Studer et al.   GENETICS

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

(2011) Feng Tian et al.   NATURE GENETICS

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

Genome-wide association mapping of agronomic traits in sugar beet

(2011) Tobias Würschum et al.   THEORETICAL AND APPLIED GENETICS

Integrating Rare-Variant Testing, Function Prediction, and Gene Network in Composite Resequencing-Based Genome-Wide Association Studies (CR-GWAS)

(2011) Chengsong Zhu et al.   G3-Genes Genomes Genetics

One Hundred Years of Pleiotropy: A Retrospective

(2010) F. W. Stearns   GENETICS

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

(2010) Susanna Atwell et al.   NATURE

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

Plant phenotypic plasticity in a changing climate

(2010) A.B. Nicotra et al.   TRENDS IN PLANT SCIENCE

Rare Variants Create Synthetic Genome-Wide Associations

(2010) Samuel P. Dickson et al.   PLOS BIOLOGY

Simultaneous Genotype Calling and Haplotype Phasing Improves Genotype Accuracy and Reduces False-Positive Associations for Genome-wide Association Studies

(2009) Brian L. Browning et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Epistatic Interactions between Opaque2 Transcriptional Activator and Its Target Gene CyPPDK1 Control Kernel Trait Variation in Maize

(2009) D. Manicacci et al.   PLANT PHYSIOLOGY

The Genetic Architecture of Maize Flowering Time

(2009) E. S. Buckler et al.   SCIENCE

Quantitative Trait Loci Mapping and The Genetic Basis of Heterosis in Maize and Rice

(2008) Antonio Augusto Franco Garcia et al.   GENETICS

Natural variation in Ghd7 is an important regulator of heading date and yield potential in rice

(2008) Weiya Xue et al.   NATURE GENETICS