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

Science China Life Sciences, Год журнала: 2023, Номер 66(10), С. 2214 - 2256

Опубликована: Март 6, 2023

Язык: Английский

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

Journal of Cotton Research, Год журнала: 2025, Номер 8(1)

Опубликована: Фев. 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.

Язык: Английский

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

New Phytologist, Год журнала: 2025, Номер unknown

Опубликована: Фев. 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.

Язык: 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, Год журнала: 2023, Номер 120(44)

Опубликована: Окт. 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

Язык: Английский

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Cis-regulatory dynamics in plant domestication

Trends in Genetics, Год журнала: 2025, Номер unknown

Опубликована: Март 1, 2025

Язык: Английский

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

Molecular Biology and Evolution, Год журнала: 2024, Номер 41(5)

Опубликована: Май 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

Язык: Английский

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

Nature Protocols, Год журнала: 2024, Номер 19(11), С. 3389 - 3425

Опубликована: Июнь 28, 2024

Язык: Английский

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Characterization of polyploidy in cancer: Current status and future perspectives

International Journal of Biological Macromolecules, Год журнала: 2024, Номер 268, С. 131706 - 131706

Опубликована: Апрель 21, 2024

Язык: 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), Год журнала: 2025, Номер 160(2)

Опубликована: Янв. 22, 2025

Язык: Английский

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

Nature Communications, Год журнала: 2025, Номер 16(1)

Опубликована: Март 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.

Язык: Английский

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