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

Rewiring of the Fruit Metabolome in Tomato Breeding

(2018) Guangtao Zhu et al.   CELL

Genome-wide Analysis of Transcriptional Variability in a Large Maize-Teosinte Population

(2018) Xufeng Wang et al.   Molecular Plant

Leveraging molecular quantitative trait loci to understand the genetic architecture of diseases and complex traits

(2018) Farhad Hormozdiari et al.   NATURE GENETICS

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

Dysregulation of expression correlates with rare-allele burden and fitness loss in maize

(2018) Karl A. G. Kremling et al.   NATURE

GWAS Analysis and QTL Identification of Fiber Quality Traits and Yield Components in Upland Cotton Using Enriched High-Density SNP Markers

(2018) Ruixian Liu et al.   Frontiers in Plant Science

Reference genome sequences of two cultivated allotetraploid cottons, Gossypium hirsutum and Gossypium barbadense

(2018) Maojun Wang et al.   NATURE GENETICS

Whole genome sequencing of a MAGIC population identified genomic loci and candidate genes for major fiber quality traits in upland cotton (Gossypium hirsutum L.)

(2018) Gregory N. Thyssen et al.   THEORETICAL AND APPLIED GENETICS

Two maize Kip-related proteins differentially interact with, inhibit and are phosphorylated by cyclin D–cyclin-dependent kinase complexes

(2017) Silvia K. Godínez-Palma et al.   JOURNAL OF EXPERIMENTAL BOTANY

Distant eQTLs and Non-coding Sequences Play Critical Roles in Regulating Gene Expression and Quantitative Trait Variation in Maize

(2017) Haijun Liu et al.   Molecular Plant

Genetic effects on gene expression across human tissues

(2017) François Aguet et al.   NATURE

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

(2017) Lei Fang et al.   NATURE GENETICS

Asymmetric subgenome selection and cis-regulatory divergence during cotton domestication

(2017) Maojun Wang et al.   NATURE GENETICS

agriGO v2.0: a GO analysis toolkit for the agricultural community, 2017 update

(2017) Tian Tian et al.   NUCLEIC ACIDS RESEARCH

Population structure and genetic basis of the agronomic traits of upland cotton in China revealed by a genome-wide association study using high-density SNPs

(2017) Cong Huang et al.   PLANT BIOTECHNOLOGY JOURNAL

Suppressing a Putative Sterol Carrier Gene Reduces Plasmodesmal Permeability and Activates Sucrose Transporter Genes during Cotton Fiber Elongation

(2017) Zhiyuan Zhang et al.   PLANT CELL

RETINOBLASTOMA RELATED1 mediates germline entry in Arabidopsis

(2017) Xin’Ai Zhao 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

Fibre elongation requires normal redox homeostasis modulated by cytosolic ascorbate peroxidase in cotton (Gossypium hirsutum)

(2016) Kai Guo et al.   JOURNAL OF EXPERIMENTAL BOTANY

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

(2016) Zhihong Zhu et al.   NATURE GENETICS

Integrative approaches for large-scale transcriptome-wide association studies

(2016) Alexander Gusev et al.   NATURE GENETICS

Metabolomic and transcriptomic insights into how cotton fiber transitions to secondary wall synthesis, represses lignification, and prolongs elongation

(2015) John R. Tuttle et al.   BMC GENOMICS

StringTie enables improved reconstruction of a transcriptome from RNA-seq reads

(2015) Mihaela Pertea et al.   NATURE BIOTECHNOLOGY

Sequencing of allotetraploid cotton (Gossypium hirsutum L. acc. TM-1) provides a resource for fiber improvement

(2015) Tianzhen Zhang et al.   NATURE BIOTECHNOLOGY

HISAT: a fast spliced aligner with low memory requirements

(2015) Daehwan Kim et al.   NATURE METHODS

GbEXPATR, a species-specific expansin, enhances cotton fibre elongation through cell wall restructuring

(2015) Yang Li et al.   PLANT BIOTECHNOLOGY JOURNAL

The genome sequence of Sea-Island cotton (Gossypium barbadense) provides insights into the allopolyploidization and development of superior spinnable fibres

(2015) Daojun Yuan et al.   Scientific Reports

Identification of chromosomal translocation hotspots via scan statistics

(2014) Israel T. Silva et al.   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

An expression quantitative trait loci-guided co-expression analysis for constructing regulatory network using a rice recombinant inbred line population

(2014) Jia Wang et al.   JOURNAL OF EXPERIMENTAL BOTANY

An Arabidopsis gene regulatory network for secondary cell wall synthesis

(2014) M. Taylor-Teeples et al.   NATURE

Control of cotton fibre elongation by a homeodomain transcription factor GhHOX3

(2014) Chun-Min Shan et al.   Nature Communications

Interplay between cell growth and cell cycle in plants

(2013) Robert Sablowski et al.   JOURNAL OF EXPERIMENTAL BOTANY

Transcriptome and genome sequencing uncovers functional variation in humans

(2013) Tuuli Lappalainen et al.   NATURE

The Dual Functions of WLIM1a in Cell Elongation and Secondary Wall Formation in Developing Cotton Fibers

(2013) L.-B. Han et al.   PLANT CELL

Expression Quantitative Trait Locus Mapping across Water Availability Environments Reveals Contrasting Associations with Genomic Features in Arabidopsis

(2013) D. B. Lowry et al.   PLANT CELL

Multiple Functions of Kip-Related Protein5 Connect Endoreduplication and Cell Elongation

(2013) T. Jegu et al.   PLANT PHYSIOLOGY

A Genetic and Metabolic Analysis Revealed that Cotton Fiber Cell Development Was Retarded by Flavonoid Naringenin

(2013) J. Tan et al.   PLANT PHYSIOLOGY

RNA sequencing reveals the complex regulatory network in the maize kernel

(2013) Junjie Fu et al.   Nature Communications

MYB46 directly regulates the gene expression of secondary wall-associated cellulose synthases in Arabidopsis

(2012) Won-Chan Kim et al.   PLANT JOURNAL

Cotton fiber: a powerful single-cell model for cell wall and cellulose research

(2012) Candace H. Haigler et al.   Frontiers in Plant Science

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

Genetic architecture of regulatory variation in Arabidopsis thaliana

(2011) X. Zhang et al.   GENOME RESEARCH

FaST linear mixed models for genome-wide association studies

(2011) Christoph Lippert et al.   NATURE METHODS

GCTA: A Tool for Genome-wide Complex Trait Analysis

(2010) Jian Yang et al.   AMERICAN JOURNAL OF HUMAN GENETICS

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

(2010) A. McKenna et al.   GENOME RESEARCH

ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data

(2010) K. Wang et al.   NUCLEIC ACIDS RESEARCH

Fasciclin-like arabinogalactan proteins: specialization for stem biomechanics and cell wall architecture in Arabidopsis and Eucalyptus

(2010) Colleen P. MacMillan et al.   PLANT JOURNAL

A global analysis of QTLs for expression variations in rice shoots at the early seedling stage

(2010) Jia Wang et al.   PLANT JOURNAL

TRICHOME BIREFRINGENCE and Its Homolog AT5G01360 Encode Plant-Specific DUF231 Proteins Required for Cellulose Biosynthesis in Arabidopsis

(2010) V. Bischoff et al.   PLANT PHYSIOLOGY

Differential expression analysis for sequence count data

(2010) Simon Anders et al.   GENOME BIOLOGY

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Genetics of human gene expression: mapping DNA variants that influence gene expression

(2009) Vivian G. Cheung et al.   NATURE REVIEWS GENETICS

Mapping complex disease traits with global gene expression

(2009) William Cookson et al.   NATURE REVIEWS GENETICS

Partitioned expression of duplicated genes during development and evolution of a single cell in a polyploid plant

(2008) R. Hovav et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA