Genomic and GWAS analyses demonstrate phylogenomic relationships of Gossypium barbadense in China and selection for fibre length, lint percentage and Fusarium wilt resistance

Divergent improvement of two cultivated allotetraploid cotton species

(2021) Lei Fang et al.   PLANT BIOTECHNOLOGY JOURNAL

A Single‐Nucleotide Mutation in a GLUTAMATE RECEPTOR‐LIKE Gene Confers Resistance to Fusarium Wilt in Gossypium hirsutum

(2021) Shiming Liu et al.   Advanced Science

Parallel and Intertwining Threads of Domestication in Allopolyploid Cotton

(2021) Daojun Yuan et al.   Advanced Science

Whole-genome resequencing of 240 Gossypium barbadense accessions reveals genetic variation and genes associated with fiber strength and lint percentage

(2021) Jingwen Yu et al.   THEORETICAL AND APPLIED GENETICS

The Gossypium longicalyx Genome as a Resource for Cotton Breeding and Evolution

(2020) Corrinne E. Grover et al.   G3-Genes Genomes Genetics

Genome sequence of Gossypium herbaceum and genome updates of Gossypium arboreum and Gossypium hirsutum provide insights into cotton A-genome evolution

(2020) Gai Huang et al.   NATURE GENETICS

Genomic diversifications of five Gossypium allopolyploid species and their impact on cotton improvement

(2020) Z. Jeffrey Chen et al.   NATURE GENETICS

Dual Activities of Receptor-like Kinase OsWAKL21.2 Induce Immune Responses

(2020) Kamal Kumar Malukani et al.   PLANT PHYSIOLOGY

CsWAKL08, a pathogen-induced wall-associated receptor-like kinase in sweet orange, confers resistance to citrus bacterial canker via ROS control and JA signaling

(2020) Qiang Li et al.   Horticulture Research

Genome-wide association analysis reveals loci and candidate genes involved in fiber quality traits in sea island cotton (Gossypium barbadense)

(2020) Xiujuan Su et al.   BMC PLANT BIOLOGY

Identifying Functional Genes Influencing Gossypium hirsutum Fiber Quality

(2019) Chengguang Dong et al.   Frontiers in Plant Science

A Pivotal Role of Hormones in Regulating Cotton Fiber Development

(2019) Guanghui Xiao et al.   Frontiers in Plant Science

The susceptibility of sea-island cotton recombinant inbred lines to Fusarium oxysporum f. sp. vasinfectum infection is characterized by altered expression of long noncoding RNAs

(2019) Zhengpei Yao et al.   Scientific Reports

Gossypium barbadense and Gossypium hirsutum genomes provide insights into the origin and evolution of allotetraploid cotton

(2019) Yan Hu et al.   NATURE GENETICS

Extensive intraspecific gene order and gene structural variations in upland cotton cultivars

(2019) Zhaoen Yang et al.   Nature Communications

De Novo Genome Sequence Assemblies of Gossypium raimondii and Gossypium turneri

(2019) Joshua A. Udall et al.   G3-Genes Genomes Genetics

A high-density genetic map of extra-long staple cotton (Gossypium barbadense) constructed using genotyping-by-sequencing based single nucleotide polymorphic markers and identification of fiber traits-related QTL in a recombinant inbred line population

(2018) Liping Fan et al.   BMC GENOMICS

GhHUB2, a ubiquitin ligase, is involved in cotton fiber development

(2018) Hao Feng et al.   JOURNAL OF EXPERIMENTAL BOTANY

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

Resequencing core accessions of a pedigree identifies derivation of genomic segments and key agronomic trait loci during cotton improvement

(2018) Xiongfeng Ma et al.   PLANT BIOTECHNOLOGY JOURNAL

Multi-Locus Genome-Wide Association Studies of Fiber-Quality Related Traits in Chinese Early-Maturity Upland Cotton

(2018) Junji Su et al.   Frontiers in Plant Science

Single-Locus and Multi-Locus Genome-Wide Association Studies in the Genetic Dissection of Fiber Quality Traits in Upland Cotton (Gossypium hirsutum L.)

(2018) Chengqi Li et al.   Frontiers in Plant Science

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

Genetic variation of dynamic fiber elongation and developmental quantitative trait locus mapping of fiber length in upland cotton (Gossypium hirsutum L.)

(2018) Jianjiang Ma et al.   BMC GENOMICS

Insights into the Evolution of the New World Diploid Cottons (Gossypium, Subgenus Houzingenia) Based on Genome Sequencing

(2018) Corrinne E Grover et al.   Genome Biology and Evolution

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

(2018) Maojun Wang 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

Asymmetric subgenome selection and cis-regulatory divergence during cotton domestication

(2017) Maojun Wang et al.   NATURE GENETICS

Genome-wide association study discovered genetic variation and candidate genes of fibre quality traits in Gossypium hirsutum L.

(2017) Zhengwen Sun et al.   PLANT BIOTECHNOLOGY JOURNAL

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

Transcriptome Analysis Suggests That Chromosome Introgression Fragments from Sea Island Cotton ( Gossypium barbadense ) Increase Fiber Strength in Upland Cotton ( Gossypium hirsutum )

(2017) Quanwei Lu et al.   G3-Genes Genomes Genetics

Developmental and hormonal regulation of fiber quality in two natural-colored cotton cultivars

(2017) Xiang ZHANG et al.   Journal of Integrative Agriculture

iTRAQ-Based Comparative Proteomic Analysis of Seedling Leaves of Two Upland Cotton Genotypes Differing in Salt Tolerance

(2017) Wenfang Gong et al.   Frontiers in Plant Science

Genetic diversity, linkage disequilibrium, and association mapping analyses of Gossypium barbadense L. germplasm

(2017) Alisher A. Abdullaev et al.   PLoS One

A MAGIC population-based genome-wide association study reveals functional association of GhRBB1_A07 gene with superior fiber quality in cotton

(2016) Md Sariful Islam et al.   BMC GENOMICS

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

(2016) Kenji Yano et al.   NATURE GENETICS

EXTRA-LARGE G PROTEINs Interact with E3 Ligases PUB4 and PUB2 and Function in Cytokinin and Developmental Processes

(2016) Yiping Wang et al.   PLANT PHYSIOLOGY

Early pre-Hispanic use of indigo blue in Peru

(2016) J. C. Splitstoser et al.   Science Advances

Two genomic regions associated with fiber quality traits in Chinese upland cotton under apparent breeding selection

(2016) Junji Su et al.   Scientific Reports

A plant U-box protein, PUB4, regulates asymmetric cell division and cell proliferation in the root meristem

(2015) A. Kinoshita et al.   DEVELOPMENT

Genome sequence of cultivated Upland cotton (Gossypium hirsutum TM-1) provides insights into genome evolution

(2015) Fuguang Li et al.   NATURE BIOTECHNOLOGY

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

(2015) Zhengkui Zhou 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

Analyzing serial cDNA libraries revealed reactive oxygen species and gibberellins signaling pathways in the salt response of Upland cotton (Gossypium hirsutum L.)

(2015) Gongyao Shi et al.   PLANT CELL REPORTS

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

HTSeq--a Python framework to work with high-throughput sequencing data

(2014) S. Anders et al.   BIOINFORMATICS

Genetics, Breeding, and Marker-Assisted Selection for Verticillium Wilt Resistance in Cotton

(2014) Jinfa Zhang et al.   CROP SCIENCE

Genome sequence of the cultivated cotton Gossypium arboreum

(2014) Fuguang Li et al.   NATURE GENETICS

A versatile system for functional analysis of genes and microRNAs in cotton

(2014) Zhouhang Gu et al.   PLANT BIOTECHNOLOGY JOURNAL

Genetic Structure, Linkage Disequilibrium and Association Mapping of Verticillium Wilt Resistance in Elite Cotton (Gossypium hirsutum L.) Germplasm Population

(2014) Yunlei Zhao et al.   PLoS One

Natural Variations and Genome-Wide Association Studies in Crop Plants

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

Proteomic and Virus-induced Gene Silencing (VIGS) Analyses Reveal That Gossypol, Brassinosteroids, and Jasmonic acid Contribute to the Resistance of Cotton toVerticillium dahliae

(2013) Wei Gao et al.   MOLECULAR & CELLULAR PROTEOMICS

A haplotype map of genomic variations and genome-wide association studies of agronomic traits in foxtail millet (Setaria italica)

(2013) Guanqing Jia et al.   NATURE GENETICS

Genetic diversity and population structure in the US Upland cotton (Gossypium hirsutum L.)

(2013) Priyanka Tyagi et al.   THEORETICAL AND APPLIED GENETICS

Whole-genome sequencing reveals untapped genetic potential in Africa’s indigenous cereal crop sorghum

(2013) Emma S. Mace et al.   Nature Communications

Repeated polyploidization of Gossypium genomes and the evolution of spinnable cotton fibres

(2012) Andrew H. Paterson et al.   NATURE

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

Genome-wide genetic changes during modern breeding of maize

(2012) Yinping Jiao et al.   NATURE GENETICS

The draft genome of a diploid cotton Gossypium raimondii

(2012) Kunbo Wang et al.   NATURE GENETICS

Genome-wide efficient mixed-model analysis for association studies

(2012) Xiang Zhou et al.   NATURE GENETICS

Mapping quantitative trait loci for lint yield and fiber quality across environments in a Gossypium hirsutum × Gossypium barbadense backcross inbred line population

(2012) Jiwen Yu et al.   THEORETICAL AND APPLIED GENETICS

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

Genome-wide nested association mapping of quantitative resistance to northern leaf blight in maize

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

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

Rice early flowering1, a CKI, phosphorylates DELLA protein SLR1 to negatively regulate gibberellin signalling

(2010) Cheng Dai et al.   EMBO JOURNAL

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

(2010) A. McKenna et al.   GENOME RESEARCH

Characterization and Promoter Analysis of a Cotton RING-Type Ubiquitin Ligase (E3) Gene

(2010) Meng-Hsuan Ho et al.   MOLECULAR BIOTECHNOLOGY

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

(2010) Xuehui Huang et al.   NATURE GENETICS

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

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

Gene ontology analysis for RNA-seq: accounting for selection bias

(2010) Matthew D Young et al.   GENOME BIOLOGY

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

Linkage disequilibrium based association mapping of fiber quality traits in G. hirsutum L. variety germplasm

(2008) Ibrokhim Y. Abdurakhmonov et al.   GENETICA