Genome- and transcriptome-wide association studies provide insights into the genetic basis of natural variation of seed oil content in Brassica napus

Combined GWAS and eQTL analysis uncovers a genetic regulatory network orchestrating the initiation of secondary cell wall development in cotton

(2020) Zhonghua Li et al.   NEW PHYTOLOGIST

Two novel plastid fatty acid exporters contribute to seed oil accumulation in Arabidopsis

(2020) Nannan Li et al.   PLANT PHYSIOLOGY

MYB–bHLH–TTG1 Regulates Arabidopsis Seed Coat Biosynthesis Pathways Directly and Indirectly via Multiple Tiers of Transcription Factors

(2020) Song Feng Li et al.   PLANT AND CELL PHYSIOLOGY

SEIPIN Isoforms Interact with the Membrane-tethering Protein VAP27-1 for Lipid Droplet Formation

(2020) Michael Scott Greer et al.   PLANT CELL

Transcriptional regulation of seed oil accumulation in Arabidopsis thaliana: role of transcription factors and chromatin remodelers

(2020) Naveen Kumar et al.   JOURNAL OF PLANT BIOCHEMISTRY AND BIOTECHNOLOGY

Whole-genome resequencing reveals Brassica napus origin and genetic loci involved in its improvement

(2019) Kun Lu et al.   Nature Communications

A Novel Chimeric Mitochondrial Gene Confers Cytoplasmic Effects on Seed Oil Content in Polyploid Rapeseed (Brassica napus)

(2019) Jun Liu et al.   Molecular Plant

Recent advances in enhancement of oil content in oilseed crops

(2019) Sundus Zafar et al.   JOURNAL OF BIOTECHNOLOGY

Plant Regulomics: A Data‐driven Interface for Retrieving Upstream Regulators from Plant Multi‐omics Data

(2019) Xiaojuan Ran et al.   PLANT JOURNAL

Targeted mutagenesis of BnTT8 homologs controls yellow seed coat development for effective oil production in Brassica napus L.

(2019) Yungu Zhai et al.   PLANT BIOTECHNOLOGY JOURNAL

Transcriptome-wide association study of schizophrenia and chromatin activity yields mechanistic disease insights

(2018) Alexander Gusev et al.   NATURE GENETICS

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

Dissection of the genetic architecture of three seed-quality traits and consequences for breeding in Brassica napus

(2018) Bo Wang et al.   PLANT BIOTECHNOLOGY JOURNAL

Spatial analysis of lipid metabolites and expressed genes reveals tissue-specific heterogeneity of lipid metabolism in high- and low-oil Brassica napus L. seeds

(2018) Shaoping Lu et al.   PLANT JOURNAL

A transcriptome-wide association study identifies PALMD as a susceptibility gene for calcific aortic valve stenosis

(2018) Sébastien Thériault et al.   Nature Communications

Changes in production potentials of rapeseed in the Yangtze River Basin of China under climate change: A multi-model ensemble approach

(2018) Zhan Tian et al.   Journal of Geographical Sciences

Large-scale transcriptome-wide association study identifies new prostate cancer risk regions

(2018) Nicholas Mancuso et al.   Nature Communications

Whole-Genome Resequencing of a Worldwide Collection of Rapeseed Accessions Reveals the Genetic Basis of Ecotype Divergence

(2018) Dezhi Wu et al.   Molecular Plant

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

(2017) Lei Fang et al.   NATURE GENETICS

Salmon provides fast and bias-aware quantification of transcript expression

(2017) Rob Patro et al.   NATURE METHODS

LEC1 sequentially regulates the transcription of genes involved in diverse developmental processes during seed development

(2017) Julie M. Pelletier et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Incorporating pleiotropic quantitative trait loci in dissection of complex traits: seed yield in rapeseed as an example

(2017) Ziliang Luo et al.   THEORETICAL AND APPLIED GENETICS

Multiple regulatory roles of AP2/ERF transcription factor in angiosperm

(2017) Chao Gu et al.   Botanical Studies

MultiQC: summarize analysis results for multiple tools and samples in a single report

(2016) Philip Ewels et al.   BIOINFORMATICS

Analysis of QTL for seed oil content in Brassica napus by association mapping and QTL mapping

(2016) Ying Fu et al.   EUPHYTICA

Subgenome parallel selection is associated with morphotype diversification and convergent crop domestication in Brassica rapa and Brassica oleracea

(2016) Feng Cheng 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

Integrative approaches for large-scale transcriptome-wide association studies

(2016) Alexander Gusev et al.   NATURE GENETICS

Potential targets of VIVIPAROUS1/ABI3-LIKE1 (VAL1) repression in developingArabidopsis thalianaembryos

(2016) Andrew Schneider et al.   PLANT JOURNAL

Identification of stable QTLs for seed oil content by combined linkage and association mapping in Brassica napus

(2016) Fengming Sun et al.   PLANT SCIENCE

A genome-wide association study reveals novel elite allelic variations in seed oil content of Brassica napus

(2016) Sheng Liu et al.   THEORETICAL AND APPLIED GENETICS

WRKY Transcription Factors: Molecular Regulation and Stress Responses in Plants

(2016) Ujjal J. Phukan et al.   Frontiers in Plant Science

Resequencing 302 wild and cultivated accessions identifies genes related to domestication and improvement in soybean

(2015) Zhengkui Zhou et al.   NATURE BIOTECHNOLOGY

SIFT missense predictions for genomes

(2015) Robert Vaser et al.   Nature Protocols

limma powers differential expression analyses for RNA-sequencing and microarray studies

(2015) Matthew E. Ritchie et al.   NUCLEIC ACIDS RESEARCH

Phospholipase Dε enhancesBraasca napusgrowth and seed production in response to nitrogen availability

(2015) Shaoping Lu et al.   PLANT BIOTECHNOLOGY JOURNAL

A CRISPR/Cas9 toolkit for multiplex genome editing in plants

(2014) Hui-Li Xing et al.   BMC PLANT BIOLOGY

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

Cell-by-Cell Developmental Transition from Embryo to Post-Germination Phase Revealed by Heterochronic Gene Expression and ER-Body Formation in Arabidopsis leafy cotyledon Mutants

(2014) Akiko Yamamoto et al.   PLANT AND CELL PHYSIOLOGY

Quantitative trait loci that control the oil content variation of rapeseed (Brassica napus L.)

(2014) Congcong Jiang et al.   THEORETICAL AND APPLIED GENETICS

Further Improvements to Linear Mixed Models for Genome-Wide Association Studies

(2014) Christian Widmer et al.   Scientific Reports

Modular construction of plasmids by parallel assembly of linear vector components

(2013) XinZheng Gao et al.   ANALYTICAL BIOCHEMISTRY

A genomic variation map provides insights into the genetic basis of cucumber domestication and diversity

(2013) Jianjian Qi et al.   NATURE GENETICS

A local regulatory network around three NAC transcription factors in stress responses and senescence in Arabidopsis leaves

(2013) Richard Hickman et al.   PLANT JOURNAL

Identification of Direct Targets of FUSCA3, a Key Regulator of Arabidopsis Seed Development

(2013) F. Wang et al.   PLANT PHYSIOLOGY

RSeQC: quality control of RNA-seq experiments

(2012) Liguo Wang et al.   BIOINFORMATICS

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff

(2012) Pablo Cingolani et al.   FLY

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

(2012) Xuehui Huang et al.   NATURE

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

(2012) Hui Li et al.   NATURE GENETICS

Comparative population genomics of maize domestication and improvement

(2012) Matthew B Hufford et al.   NATURE GENETICS

Evaluating the effective numbers of independent tests and significant p-value thresholds in commercial genotyping arrays and public imputation reference datasets

(2011) Miao-Xin Li et al.   HUMAN GENETICS

Compartmentation of Triacylglycerol Accumulation in Plants

(2011) Kent D. Chapman et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

BnMs3 is required for tapetal differentiation and degradation, microspore separation, and pollen-wall biosynthesis in Brassica napus

(2011) Zhengfu Zhou et al.   JOURNAL OF EXPERIMENTAL BOTANY

Arabidopsis TT19 Functions as a Carrier to Transport Anthocyanin from the Cytosol to Tonoplasts

(2011) Yi Sun et al.   Molecular Plant

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

Integrating Genome-Wide Genetic Variations and Monocyte Expression Data Reveals Trans-Regulated Gene Modules in Humans

(2011) Maxime Rotival et al.   PLoS Genetics

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

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

(2010) Xuehui Huang et al.   NATURE GENETICS

Resequencing of 31 wild and cultivated soybean genomes identifies patterns of genetic diversity and selection

(2010) Hon-Ming Lam et al.   NATURE GENETICS

A method and server for predicting damaging missense mutations

(2010) Ivan A Adzhubei et al.   NATURE METHODS

Physiological and developmental regulation of seed oil production

(2010) Sébastien Baud et al.   PROGRESS IN LIPID RESEARCH

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast model-based estimation of ancestry in unrelated individuals

(2009) D. H. Alexander et al.   GENOME RESEARCH

Arabidopsis NAC Transcription Factor, ANAC078, Regulates Flavonoid Biosynthesis under High-light

(2009) Teruyuki Morishita et al.   PLANT AND CELL PHYSIOLOGY

A unified approach to false discovery rate estimation

(2008) Korbinian Strimmer   BMC BIOINFORMATICS