A comprehensive overview of cotton genomics, biotechnology and molecular biological studies

Science China Life Sciences, Journal Year: 2023, Volume and Issue: 66(10), P. 2214 - 2256

Published: March 6, 2023

Language: Английский

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CRISPR/Cas genome editing for cotton precision breeding: mechanisms, advances, and prospects

Journal of Cotton Research, Journal Year: 2025, Volume and Issue: 8(1)

Published: Feb. 3, 2025

Abstract Cotton ( Gossypium hirsutum L.) is one of the most important global crops that supports textile industry and provides a living for millions farmers. The constantly increasing demand needs significant rise in cotton production. Genome editing technology, specifically with clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein (Cas) tools, has opened new possibilities trait development cotton. It allows precise efficient manipulation within genome when compared other genetic engineering tools. Current developments CRISPR/Cas including prime editing, base multiplexing have expanded scope traits breeding can be targeted. been employed to generate effectively CRISPRized plants enhanced agronomic traits, fiber yield quality, oil improvement, stress resistance, nutrition. Here we summarized various target genes which successfully altered However, some challenges remain, tetraploid having redundant gene sets homologs making editing. To ensure specificity avoiding off-target effects, need optimize parameters such as site, guide RNA design, choosing right Cas variants. We outline future prospects breeding, suggesting areas further research innovation. A combination speed might useful fastening potentials create customized cultivars meet higher demands agriculture industry.

Language: Английский

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Polyploidization leads to salt stress resilience via ethylene signaling in citrus plants

New Phytologist, Journal Year: 2025, Volume and Issue: unknown

Published: Feb. 19, 2025

Polyploidization is a common occurrence in the evolutionary history of flowering plants, significantly contributing to their adaptability and diversity. However, molecular mechanisms behind these adaptive advantages are not well understood. Through comprehensive phenotyping diploid tetraploid clones from Citrus Poncirus genera, we discovered that genome doubling enhances salt stress resilience. Epigenetic transcriptomic analyses revealed increased ethylene production roots plants was associated with hypomethylation enhanced chromatin accessibility ACO1 gene. This activates transcription reactive oxygen species scavenging genes stress-related hormone biosynthesis genes. Consequently, exhibited superior root functionality under stress, maintaining improved cytosolic K+/Na+ homeostasis. To genetically validate link between resilience expression, generated overexpression knockout lines, confirming central role expression regulation following Our work elucidates underlying We also highlight importance dynamics fine-tuning gene activating pathways, offering valuable insights into plant adaptation crop evolution.

Language: Английский

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Dynamics of cis -regulatory sequences and transcriptional divergence of duplicated genes in soybean

Proceedings of the National Academy of Sciences, Journal Year: 2023, Volume and Issue: 120(44)

Published: Oct. 23, 2023

Transcriptional divergence of duplicated genes after whole genome duplication (WGD) has been described in many plant lineages and is often associated with subgenome dominance, a genome-wide mechanism. However, it unknown what underlies the transcriptional polyploid species that lack dominance. Soybean paleotetraploid WGD occurred 5 to 13 Mya. Approximately 50% retained from this exhibit divergence. We developed accessible chromatin region (ACR) datasets leaf, flower, seed tissues using MNase-hypersensitivity sequencing. validated enhancer function several ACRs known CRISPR/Cas9-mediated editing. The ACR were used examine correlate patterns 17,111 pairs different tissues. demonstrate dynamics are correlated both expression level tissue specificity individual gene pairs. Gain or loss flanking mutation cis -regulatory elements (CREs) within can change balance and/or genes. Analysis DNA sequences revealed extensive sequence rearrangement reshaped CRE landscape, which appears play key role soybean. This may represent general mechanism for polyploids

Language: Английский

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Evolutionary Dynamics of Chromatin Structure and Duplicate Gene Expression in Diploid and Allopolyploid Cotton

Molecular Biology and Evolution, Journal Year: 2024, Volume and Issue: 41(5)

Published: May 1, 2024

Abstract Polyploidy is a prominent mechanism of plant speciation and adaptation, yet the mechanistic understandings duplicated gene regulation remain elusive. Chromatin structure dynamics are suggested to govern regulatory control. Here, we characterized genome-wide nucleosome organization chromatin accessibility in allotetraploid cotton, Gossypium hirsutum (AADD, 2n = 4X 52), relative its two diploid parents (AA or DD genome) their synthetic hybrid (AD), using DNS-seq. The larger A-genome exhibited wider average spacing diploids, this intergenomic difference diminished allopolyploid but not hybrid. Allopolyploidization also increased at promoters synchronized cis-regulatory motifs between subgenomes. A cis-acting control was inferred for demonstrated by transposable element removal from promoters. Linking expression patterns, found distinct effects hybridization later stages, including nuanced establishment homoeolog bias level dominance. Histone coordinated through accessibility. Our study demonstrates capability track high-resolution reveals role evolution landscapes duplicate polyploids, illuminating ties subgenomic asymmetry

Language: Английский

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Spatially resolved epigenome sequencing via Tn5 transposition and deterministic DNA barcoding in tissue

Nature Protocols, Journal Year: 2024, Volume and Issue: 19(11), P. 3389 - 3425

Published: June 28, 2024

Language: Английский

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Genome-wide identification of cis-regulatory elements and transcription factors associated with promoted callus formation in Brachypodium distachyon

Plant Cell Tissue and Organ Culture (PCTOC), Journal Year: 2025, Volume and Issue: 160(2)

Published: Jan. 22, 2025

Language: Английский

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Constraint of accessible chromatins maps regulatory loci involved in maize speciation and domestication

Nature Communications, Journal Year: 2025, Volume and Issue: 16(1)

Published: March 12, 2025

Comparative genomic studies can identify genes under evolutionary constraint or specialized for trait innovation. Growing evidence suggests that also acts on non-coding regulatory sequences, exerting significant impacts fitness-related traits, although it has yet to be thoroughly explored in plants. Using the assay transposase-accessible chromatin by sequencing (ATAC-seq), we profile over 80,000 maize accessible regions (ACRs), revealing ACRs evolve faster than coding genes, with about one-third being maize-specific and regulating associated speciation. We highlight role of transposable elements (TEs) driving intraspecific innovation hundreds candidate potentially involved transcriptional rewiring during domestication. Additionally, demonstrate importance maintaining subgenome dominance controlling complex variations. This study establishes a framework analyzing trajectory plant sequences offers loci downstream exploration application breeding. Intricate regulation gene expression is important execution biology processes. Here, authors generate comprehensive map integrating ATAC-seq data 12 major tissues explore their interspecific constraints multiple Poaceae genomes.

Language: Английский

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Comparative single-cell transcriptomic map reveals divergence in leaves between two cotton species at cell type resolution

Journal of Advanced Research, Journal Year: 2025, Volume and Issue: unknown

Published: April 1, 2025

Language: Английский

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Centromere-size reduction and chromatin state dynamics following intergenomic hybridization in cotton

PLoS Genetics, Journal Year: 2025, Volume and Issue: 21(5), P. e1011689 - e1011689

Published: May 2, 2025

Centromeres are pivotal for accurate chromosome segregation, yet their regulation and evolutionary dynamics remain poorly understood. Here, we investigate centromeres of the diploid species Gossypium anomalum (Ga, B-genome) that were transferred into tetraploid cotton G. hirsutum (Gh, AD-genome) as either an additional or integrated chromosome, well in synthetic allohexaploid (AABBDD) lines. We demonstrate consistent size reduction all Ga Gh background. Histone modification profiling across 10 marks revealed heightened levels both active repressive chromatin within when background, particularly H3K36me2. The centromeric histone perturbation extended pericentromeric regions, with variable CENH3-binding domains consistently exhibiting a more pronounced increase compared to stable centromere highlighting role elevation dynamics. In addition, observed enhanced accessibility presence non-B-form DNA motifs, such A-phased repeats correlated stability. Hi-C analysis reveals reorganized 3D architecture introgression line centromeres, including formation new topologically associating linked H3K36me2 dynamics, emphasizing importance organization. Together, these findings elucidate epigenetic mechanisms underlying composition following intergenomic hybridization allopolyploid formation, offering insights evolution plants its myriad potentially functional dimensions.

Language: Английский

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