Upland cotton (Gossypium hirsutum) is the most important natural fiber crop in the world. The overall genetic diversity among cultivated species of cotton and the genetic changes that occurred during their improvement are poorly understood. Here we report a comprehensive genomic assessment of modern improved upland cotton based on the genome-wide resequencing of 318 landraces and modern improved cultivars or lines. We detected more associated loci for lint yield than for fiber quality, which suggests that lint yield has stronger selection signatures than other traits. We found that two ethylene-pathway-related genes were associated with increased lint yield in improved cultivars. We evaluated the population frequency of each elite allele in historically released cultivar groups and found that 54.8% of the elite genome-wide association study (GWAS) alleles detected were transferred from three founder landraces: Deltapine 15, Stoneville 2B and Uganda Mian. Our results provide a genomic basis for improving cotton cultivars and for further evolutionary analysis of polyploid crops.
Activation of the ethylene gas response pathway in Arabidopsis by the nuclear protein ETHYLENE-INSENSITIVE3 and related proteins
Transcriptome profiling, molecular biological, and physiological studies reveal a major role for ethylene in cotton fiber cell elongation
The Arabidopsis histidine phosphotransfer proteins are redundant positive regulators of cytokinin signaling
QTL mapping in A-genome diploid Asiatic cotton and their congruence analysis with AD-genome tetraploid cotton in genus Gossypium
A unified approach to genotype imputation and haplotype-phase inference for large data sets of trios and unrelated individuals
Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation
Class XI myosins are required for development, cell expansion, and F-Actin organization in Arabidopsis
The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data
Evaluating the effective numbers of independent tests and significant p-value thresholds in commercial genotyping arrays and public imputation reference datasets.
Genome-wide comparative diversity uncovers multiple targets of selection for improvement in hexaploid wheat landraces and cultivars
A haplotype map of genomic variations and genome-wide association studies of agronomic traits in foxtail millet (Setaria italica)
The distribution of Gossypium hirsutum chromatin in G. barbadense germ plasm: molecular analysis of introgressive plant breeding
De novo assembly of soybean wild relatives for pan-genome analysis of diversity and agronomic traits
Resequencing 302 wild and cultivated accessions identifies genes related to domestication and improvement in soybean
Moderately enhancing cytokinin level by down-regulation of GhCKX expression in cotton concurrently increases fiber and seed yield.
Sequencing of allotetraploid cotton (Gossypium hirsutum L. acc. TM-1) provides a resource for fiber improvement
Monopodial and sympodial branching architecture in cotton is differentially regulated by the Gossypium hirsutum SINGLE FLOWER TRUSS and SELF-PRUNING orthologs
Genome-wide association study using whole-genome sequencing rapidly identifies new genes influencing agronomic traits in rice
Core cis-element variation confers subgenome-biased expression of a transcription factor that functions in cotton fiber elongation
Exploration of miRNAs and target genes of cytoplasmic male sterility line in cotton during flower bud development
QTLs Analysis and Validation for Fiber Quality Traits Using Maternal Backcross Population in Upland Cotton
QTL delineation for five fiber quality traits based on an intra-specific Gossypium hirsutum L. recombinant inbred line population
Genome-wide association study identified genetic variations and candidate genes for plant architecture component traits in Chinese upland cotton
Resequencing core accessions of a pedigree identifies derivation of genomic segments and key agronomic trait loci during cotton improvement
Comparative population genomics identified genomic regions and candidate genes associated with fruit domestication traits in peach
Deep Transcriptome Analysis Reveals Reactive Oxygen Species (ROS) Network Evolution, Response to Abiotic Stress, and Regulation of Fiber Development in Cotton
Meta-analysis of genome-wide association studies for loin muscle area and loin muscle depth in two Duroc pig populations
A high density SLAF-seq SNP genetic map and QTL for seed size, oil and protein content in upland cotton
Gene-set association and epistatic analyses reveal complex gene interaction networks affecting flowering time in a worldwide barley collection
Natural variation in a CENTRORADIALIS homolog contributed to cluster fruiting and early maturity in cotton
Dissection of soybean populations according to selection signatures based on whole-genome sequences.
Investigation of the EIL/EIN3 Transcription Factor Gene Family Members and Their Expression Levels in the Early Stage of Cotton Fiber Development
Genomic signatures and candidate genes of lint yield and fibre quality improvement in Upland cotton in Xinjiang
Combined GWAS and eQTL analysis uncovers a genetic regulatory network orchestrating the initiation of secondary cell wall development in cotton
Genomic analyses reveal the genetic basis of early maturity and identification of loci and candidate genes in upland cotton (Gossypium hirsutum L.).
Conservation and Divergence in Duplicated Fiber Coexpression Networks Accompanying Domestication of the Polyploid Gossypium hirsutum L
An RTM-GWAS procedure reveals the QTL alleles and candidate genes for three yield-related traits in upland cotton.
A high-density genetic map and multiple environmental tests reveal novel quantitative trait loci and candidate genes for fibre quality and yield in cotton.
The cotton HD-Zip transcription factor GhHB12 regulates flowering time and plant architecture via the GhmiR157-GhSPL pathway
Genetic basis of heterosis for yield and yield components explored by QTL mapping across four genetic populations in upland cotton
Global status of 47 major wheat loci controlling yield, quality, adaptation and stress resistance selected over the last century
Resequencing of 429 chickpea accessions from 45 countries provides insights into genome diversity, domestication and agronomic traits
Whole Genome Sequencing of the Giant Grouper (Epinephelus lanceolatus ) and High-Throughput Screening of Putative Antimicrobial Peptide Genes
Genome-wide association analysis of nutrient traits in the oyster Crassostrea gigas: genetic effect and interaction network
Genetic dissection of yield-related traits via genome-wide association analysis across multiple environments in wild soybean (Glycine soja Sieb. and Zucc.)
High-density genetic variation maps reveal the correlation between asymmetric interspecific introgressions and improvement of agronomic traits in Upland and Pima cotton varieties developed in Xinjiang, China.
Resequencing of 243 diploid cotton accessions based on an updated A genome identifies the genetic basis of key agronomic traits
Identification of Introgressed Alleles Conferring High Fiber Quality Derived From Gossypium barbadense L. in Secondary Mapping Populations of G. hirsutum L
Cumulative and different genetic effects contributed to yield heterosis using maternal and paternal backcross populations in Upland cotton
Genome-wide quantitative trait loci reveal the genetic basis of cotton fibre quality and yield-related traits in a Gossypium hirsutum recombinant inbred line population
Dissection of the genetic variation and candidate genes of lint percentage by a genome-wide association study in upland cotton
Open-Bud Duplicate Loci Are Identified as MML10s , Orthologs of MIXTA-Like Genes on Homologous Chromosomes of Allotetraploid Cotton
Genetic Basis of Fiber Improvement and Decreased Stress Tolerance in Cultivated Versus Semi-Domesticated Upland Cotton
Genome sequence of Gossypium herbaceum and genome updates of Gossypium arboreum and Gossypium hirsutum provide insights into cotton A-genome evolution.
QTL analysis for yield and fibre quality traits using three sets of introgression lines developed from three Gossypium hirsutum race stocks
Genome-Wide Association Study Identifies Candidate Genes Related to Seed Oil Composition and Protein Content in Gossypium hirsutum L
Genome-wide analysis of genetic variations between dominant and recessive NILs of glanded and glandless cottons
Identification and characterization analysis of sulfotransferases (SOTs) gene family in cotton (Gossypium) and its involvement in fiber development
Genome-wide identification and characterization of TALE superfamily genes in cotton reveals their functions in regulating secondary cell wall biosynthesis
A Genome-Wide Association Study Revealed Key SNPs/Genes Associated With Salinity Stress Tolerance In Upland Cotton
Up-regulation of GhPAP1A results in moderate anthocyanin accumulation and pigmentation in sub-red cotton
Fiber Quality Improvement in Upland Cotton (Gossypium hirsutum L.): Quantitative Trait Loci Mapping and Marker Assisted Selection Application
Identification of SNPs and Candidate Genes Associated With Salt Tolerance at the Seedling Stage in Cotton (Gossypium hirsutum L.)
Genetic variation of dynamic fiber elongation and developmental quantitative trait locus mapping of fiber length in upland cotton (Gossypium hirsutum L.)
Multi-Locus Genome-Wide Association Studies of Fiber-Quality Related Traits in Chinese Early-Maturity Upland Cotton
Genome-Wide Association Studies Reveal Genetic Variation and Candidate Genes of Drought Stress Related Traits in Cotton (Gossypium hirsutum L.)
Evaluation and Recommendations for Routine Genotyping Using Skim Whole Genome Re-sequencing in Canola
Genome-wide association reveals genetic variation of lint yield components under salty field conditions in cotton (Gossypium hirsutum L.)
Genetic regulatory networks for salt-alkali stress in Gossypium hirsutum with differing morphological characteristics
Genome-wide association study reveals the genetic basis of fiber quality traits in upland cotton (Gossypium hirsutum L.).
GhCIPK6a increases salt tolerance in transgenic upland cotton by involving in ROS scavenging and MAPK signaling pathways.
Resequencing a core collection of upland cotton identifies genomic variation and loci influencing fiber quality and yield
Whole genome sequencing of a MAGIC population identified genomic loci and candidate genes for major fiber quality traits in upland cotton (Gossypium hirsutum L.)
Genetic Detection of Lint Percentage Applying Single-Locus and Multi-Locus Genome-Wide Association Studies in Chinese Early-Maturity Upland Cotton
Genetic dissection of an allotetraploid interspecific CSSLs guides interspecific genetics and breeding in cotton.
Extensive haplotypes are associated with population differentiation and environmental adaptability in Upland cotton (Gossypium hirsutum).
Identification of candidate genes for key fibre-related QTLs and derivation of favourable alleles in Gossypium hirsutum recombinant inbred lines with G. barbadense introgressions
Genome-wide dissection of hybridization for fiber quality- and yield-related traits in upland cotton
Genome- and transcriptome-wide association studies provide insights into the genetic basis of natural variation of seed oil content in Brassica napus.
The cellulose synthase (CesA) gene family in four Gossypium species: phylogenetics, sequence variation and gene expression in relation to fiber quality in Upland cotton.
Genome-wide association analysis reveals genetic variations and candidate genes associated with salt tolerance related traits in Gossypium hirsutum.
Whole genome variants across 57 pig breeds enable comprehensive identification of genetic signatures that underlie breed features
The cotton HD-Zip transcription factor GhHB12 regulates flowering time and plant architecture via the GhmiR157-GhSPL pathway
Fine-mapping and candidate gene analysis of qFS-Chr. D02, a QTL for fibre strength introgressed from a semi-wild cotton into Gossypium hirsutum.
Evaluation and genome-wide association study of resistance to bacterial blight race 18 in U.S. Upland cotton germplasm.
Full-length annotation with multistrategy RNA-seq uncovers transcriptional regulation of lncRNAs in cotton.
Identification and functional analysis of 9-cis-epoxy carotenoid dioxygenase (NCED) homologs in G. hirsutum.
Genome-wide association and transcriptome analysis of root color-related genes in Gossypium arboreum L.
Genome-wide association analysis reveals quantitative trait loci and candidate genes involved in yield components under multiple field environments in cotton (Gossypium hirsutum).
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