A basic helix-loop-helix protein (GhFP1) promotes fibre elongation of cotton (Gossypium hirsutum) by modulating brassinosteroid biosynthesis and signalling

Genes Affecting Cotton Fiber Length: A Systematic Review and Meta-Analysis

Cotton fiber length is an important measurement for application in the textile industry, and researchers are seeking to cultivate cotton plants with longer fibers. In this study, cotton fiber genes were systematically reviewed through meta-analysis in terms of extending and shortening fiber and the use of different research technologies for the first time. PubMed, Web of Science, China National Knowledge Infrastructure (CNKI), and Baidu Xueshu databases were included as literature retrieval sources. A total of 21,467 articles were retrieved, and 45 articles were used in the final analysis. Data analysis was performed using RevMan 5.4 software. To shorten cotton fiber length, clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 technology was superior to virus-induced gene silencing (VIGS) technology and RNA interference (RNAi) technology [p = 0.002, MD = -1.05, 95% CI (-1.73, -0.37), Chi2 = 39.89]. To increase cotton fiber length, CRISPR-Cas9 technology had a similar effect as VIGS technology [p = 0.12, MD = -0.59, 95% CI (-1.33, -0.15), Chi2 = 0.17]. When some genes (GhLAC15, GhALDH7B4, GhMDHAR1A/GhDHAR2A, STTM-miR396b, GhMYB44, GhFP2, GhMYB7, GhKNL1, GhTCP4, GhHDA5, GhGalT1, GhKNOX6, GhXB38D, and GhBZR3) were damaged, cotton fiber length increased. Furthermore, we found that after gene interference, the fiber-shortening genes occurred more frequently than the fiber-elongating genes. Synergistic research on these genes may better promote cotton fiber elongation.

The GhCEWT1-GhCEWT2-GhCes4D/GhCOBL4D module orchestrates plant cell elongation and cell wall thickness

Cell elongation defines cell size and shape, whereas the cell wall supports and protects it. However, the mechanism regulating cell elongation and cell wall thickness remains unknown. Here, taking advantage of a model for both cell elongation and cell wall biogenesis, cotton fiber, we identified a basic-helix-loop-helix (bHLH) factor, GhCEWT1, that contributes to both fiber cell elongation and cell wall thickness. Loss of function of GhCEWT1 reduced the fiber length and cell wall thickness. GhCEWT1 induced transcription of GhCEWT2. We also identified two target genes of GhCEWT2, cellulose synthase 4D (GhCes4D) and COBRA-LIKE 4D (GhCOBL4D). GhCEWT2 enhanced the transcription of GhCes4D and GhCOBL4D. GhCOBL4D overexpression significantly enhanced cotton fiber cell length and cell wall thickness. Our results revealed a GhCEWT1-GhCEWT2-GhCes4D/GhCOBL4D cascade functioning in both fiber cell elongation and cell wall thickness. These findings provide a comprehensive understanding of plant cell elongation and cell wall formation, as well as a theoretical basis for boosting the biomass on Earth.

GhTBL3 is required for fiber secondary cell wall (SCW) formation via maintaining acetylation of xylan in cotton

TBL family proteins containing the domain of unknown function mainly act as xylan O-acetyltransferases, but the specific molecular mechanism of their functions remains unclear in plants (especially in cotton) so far. In this study, we characterized the TBL family proteins containing the conserved GDS and DxxH motifs in cotton (Gossypium hirsutum). Among them, GhTBL3 is highly expressed in fibers at the stage of secondary cell wall (SCW) formation and mainly functions as O-acetyltransferase to maintain acetylation of xylan in fiber SCW development. Overexpression of GhTBL3 in cotton promoted fiber SCW formation, resulting in increased fiber cell wall thickness. In contrast, suppression of GhTBL3 expression in cotton impaired fiber SCW synthesis, leading to the decreased fiber cell wall thickness, compared with wild type (WT). Furthermore, two fiber SCW-related transcription factors GhMYBL1 and GhKNL1 were found to directly bind to the promoter of GhTBL3 in cotton. GhMYBL1 enhanced the transcription activity of GhTBL3, whereas GhKNL1 inhibited the expression of GhTBL3 in fibers. The acetylation level of xylan was remarkably decreased in fibers of GhMYBL1 RNAi transgenic cotton, but the acetylation level of xylan was significantly increased in fibers of GhKNL1 RNAi cotton, relative to WT. Given together, the above results suggested that GhTBL3 may be under the dual control of GhMYBL1 and GhKNL1 to maintain the suitable acetylation level of xylan required for fiber SCW formation in cotton. Thus, our data provide an effective clue for potentially improving fiber quality by genetic manipulation of GhTBL3 in cotton breeding.

Brassinosteroids in cotton: orchestrating fiber development

Cotton cultivation spans over 30 million hectares across 85 countries and regions, with more than half participating in the global cotton textile trade. The elongated cotton fiber cell is an ideal model for studying cell elongation and understanding plant growth and development. Brassinosteroids (BRs), recognized for their role in cell elongation, offer the potential for improving cotton fiber quality and yield. Despite extensive research highlighting BR's positive impact on fiber development, a comprehensive review on this topic has been lacking. This review addresses this gap, providing a detailed analysis of the latest advancements in BR signaling and its effects on cotton fiber development. We explore the complex network of BR biosynthesis components, signaling molecules, and regulators, including crosstalk with other pathways and transcriptional control mechanisms. Additionally, we propose molecular strategies and highlight key genetic elements for optimizing BR-related genes to enhance fiber quality and yield. The review emphasizes the importance of BR homeostasis and the hormonal landscape during cotton fiber development, offering insights into targeted manipulation opportunities and challenges. This consolidation offers a comprehensive understanding of BR's multifaceted roles in fiber development, outlining a strategic approach for BR optimization in cotton fiber quality and yield.

Cotton BOP1 mediates SUMOylation of GhBES1 to regulate fibre development and plant architecture

The Arabidopsis BLADE-ON-PETIOLE (BOP) genes are primarily known for their roles in regulating leaf and floral patterning. However, the broader functions of BOPs in regulating plant traits remain largely unexplored. In this study, we investigated the role of the Gossypium hirsutum BOP1 gene in the regulation of fibre length and plant height through the brassinosteroid (BR) signalling pathway. Transgenic cotton plants overexpressing GhBOP1 display shorter fibre lengths and reduced plant height compared to the wild type. Conversely, GhBOP1 knockdown led to increased plant height and longer fibre, indicating a connection with phenotypes influenced by the BR pathway. Our genetic evidence supports the notion that GhBOP1 regulates fibre length and plant height in a GhBES1-dependent manner, with GhBES1 being a major transcription factor in the BR signalling pathway. Yeast two-hybrid, luciferase complementation assay and pull-down assay results demonstrated a direct interaction between GhBOP1 and GhSUMO1, potentially forming protein complexes with GhBES1. In vitro and in vivo SUMOylation analyses revealed that GhBOP1 functions in an E3 ligase-like manner to mediate GhBES1 SUMOylation and subsequent degradation. Therefore, our study not only uncovers a novel mechanism of GhBES1 SUMOylation but also provides significant insights into how GhBOP1 regulates fibre length and plant height by controlling GhBES1 accumulation.

Simultaneous improvement of fiber yield and quality in upland cotton (Gossypium hirsutum L.) by integration of auxin transport and synthesis

Cotton is a widely planted commercial crop in the world. Enhancing fiber yield and quality is a long-term goal for cotton breeders. Our previous work has demonstrated that fine promotion of auxin biosynthesis in ovule epidermis, by overexpressing FBP7pro::iaaM, has a significant improvement on lint yield and fiber fineness. Lately, transgenic cottons overexpressing GhROP6 variants modify mature fiber length by controlling GhPIN3a-mediated polar auxin transport in ovules. Here, this study showed that all these GhROP6-related cottons displayed unsatisfactory agronomic performance in field conditions. Yet extra auxin supply could promote their fiber development, suggesting inadequate auxin supply in the ovules. Thus, these cottons were integrated with enhanced auxin synthesis by crossing with FBP7pro::iaaM cotton. All the transgene-stacked cottons exhibited synergetic effects on cotton yield (seedcotton yield, lint yield, and lint percentage) and quality (length, strength, and micronaire). Notably, comparing to the FBP7pro::iaaM background, the transgene-stacked cotton co-expressing FBP7pro::iaaM and CA-ghrop6 (constitutively active GhROP6) exhibited a 12.6% increase in seedcotton yield and a 19.0% increase in lint yield over a three-year field trial, and simultaneously resulted in further improvement on fiber length, strength, and micronaire. Collectively, our data provide a potential strategy for genetic improvement on cotton fiber yield and quality.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-024-01500-w.

Tea green leafhopper infestations affect tea plant growth by altering the synthesis of brassinolide

Tea green leafhoppers are insects widely distributed in major tea-growing areas. At present, less attention has been paid to the study on effect of tea green leafhopper infestation on tea growth phenotype. In this study, tea green leafhoppers were used to treat tea branches in laboratory and co-treated with brassinolide (BL), the highest bioactivity of brassinosteroids (BRs), in tea garden. The results showed that the expression of genes related to BRs synthesis was inhibited and BL content was reduced in tea shoots after infestation by tea green leafhoppers. In addition, area of each leaf position, length and diameter of internodes, and the biomass of the tender shoots of tea plant were decreased after infestation by tea green leafhoppers. The number of trichomes, leaf thickness, palisade tissue thickness and cuticle thickness of tea shoots were increased after tea green leafhoppers infestation. BL spraying could partially recover the phenotypic changes of tea branches caused by tea green leafhoppers infestation. Further studies showed that tea green leafhoppers infestation may regulate the expression of CsDWF4 (a key gene for BL synthesis) through transcription factors CsFP1 and CsTCP1a, which finally affect the BL content. Moreover, BL was applied to inhibit the tea green leafhoppers infestation on tea shoots. In conclusion, our study revealed the effect of plant hormone BL-mediated tea green leafhoppers infestation on the growth phenotype of tea plants.

Sphingolipid inhibitor response gene GhMYB86 controls fiber elongation by regulating microtubule arrangement

Although the cell membrane and cytoskeleton play essential roles in cellular morphogenesis, the interaction between the membrane and cytoskeleton is poorly understood. Cotton fibers are extremely elongated single cells, which makes them an ideal model for studying cell development. Here, we used the sphingolipid biosynthesis inhibitor, fumonisin B1 (FB1), and found that it effectively suppressed the myeloblastosis (MYB) transcription factor GhMYB86, thereby negatively affecting fiber elongation. A direct target of GhMYB86 is GhTUB7, which encodes the tubulin protein, the major component of the microtubule cytoskeleton. Interestingly, both the overexpression of GhMYB86 and GhTUB7 caused an ectopic microtubule arrangement at the fiber tips, and then leading to shortened fibers. Moreover, we found that GhMBE2 interacted with GhMYB86 and that FB1 and reactive oxygen species induced its transport into the nucleus, thereby enhancing the promotion of GhTUB7 by GhMYB86. Overall, we established a GhMBE2-GhMYB86-GhTUB7 regulation module for fiber elongation and revealed that membrane sphingolipids affect fiber elongation by altering microtubule arrangement.

Co-Expression Network Analysis and Introgressive Gene Identification for Fiber Length and Strength Reveal Transcriptional Differences in 15 Cotton Chromosome Substitution Segment Lines and Their Upland and Sea Island Parents

Fiber length (FL) and strength (FS) are the core indicators for evaluating cotton fiber quality. The corresponding stages of fiber elongation and secondary wall thickening are of great significance in determining FL and FS formation, respectively. QTL mapping and high-throughput sequencing technology have been applied to dissect the molecular mechanism of fiber development. In this study, 15 cotton chromosome segment substitution lines (CSSLs) with significant differences in FL and FS, together with their recurrent parental Gossypium hirsutum line CCRI45 and donor parent G. barbadense line Hai1, were chosen to conduct RNA-seq on developing fiber samples at 10 days post anthesis (DPA) and 20 DPA. Differentially expressed genes (DEGs) were obtained via pairwise comparisons among all 24 samples (each one with three biological repeats). A total of 969 DEGs related to FL-high, 1285 DEGs to FS-high, and 997 DEGs to FQ-high were identified. The functional enrichment analyses of them indicated that the GO terms of cell wall structure and ROS, carbohydrate, and phenylpropanoid metabolism were significantly enriched, while the GO terms of glucose and polysaccharide biosynthesis, and brassinosteroid and glycosylphosphatidylinositol metabolism could make great contributions to FL and FS formation, respectively. Weighted gene co-expressed network analyses (WGCNA) were separately conducted for analyzing FL and FS traits, and their corresponding hub DEGs were screened in significantly correlated expression modules, such as EXPA8, XTH, and HMA in the fiber elongation and WRKY, TDT, and RAC-like 2 during secondary wall thickening. An integrated analysis of these hub DEGs with previous QTL identification results successfully identified a total of 33 candidate introgressive DEGs with non-synonymous mutations between the Gh and Gb species. A common DEG encoding receptor-like protein kinase 1 was reported to likely participate in fiber secondary cell thickening regulation by brassionsteroid signaling. Such valuable information was conducive to enlightening the developing mechanism of cotton fiber and also provided an abundant gene pool for further molecular breeding.

Phosphatidic acid interacts with an HD-ZIP transcription factor GhHOX4 to influence its function in fiber elongation of cotton (Gossypium hirsutum)

Upland cotton, the mainly cultivated cotton species in the world, provides over 90% of natural raw materials (fibers) for the textile industry. The development of cotton fibers that are unicellular and highly elongated trichomes on seeds is a delicate and complex process. However, the regulatory mechanism of fiber development is still largely unclear in detail. In this study, we report that a homeodomain-leucine zipper (HD-ZIP) IV transcription factor, GhHOX4, plays an important role in fiber elongation. Overexpression of GhHOX4 in cotton resulted in longer fibers, while GhHOX4-silenced transgenic cotton displayed a "shorter fiber" phenotype compared with wild type. GhHOX4 directly activates two target genes, GhEXLB1D and GhXTH2D, for promoting fiber elongation. On the other hand, phosphatidic acid (PA), which is associated with cell signaling and metabolism, interacts with GhHOX4 to hinder fiber elongation. The basic amino acids KR-R-R in START domain of GhHOX4 protein are essential for its binding to PA that could alter the nuclear localization of GhHOX4 protein, thereby suppressing the transcriptional regulation of GhHOX4 to downstream genes in the transition from fiber elongation to secondary cell wall (SCW) thickening during fiber development. Thus, our data revealed that GhHOX4 positively regulates fiber elongation, while PA may function in the phase transition from fiber elongation to SCW formation by negatively modulating GhHOX4 in cotton.

Active oxygen generation induced by the glucose sensor TaHXK7-1A decreased the drought resistance of transgenic Arabidopsis and wheat (Triticum aestivum L.)

Improving wheat drought resistance is of great significance for grain production and food security. Hexokinases (HXKs) play a role in sugar signal transduction and are involved in abiotic stress responses in wheat. To clarify the relationship between HXKs and drought stress in wheat, we used the rice active oxygen induction gene OsHXK1 as a reference sequence and the homologously cloned wheat TaHXK7-1A gene. TaHXK7-1A was localized in the nucleus and cell membrane. Under drought stress, over-expression of TaHXK7-1A increased the contents of O2·－ and malondialdehyde (MDA) and significantly up-regulated the respiratory burst oxidative homologue (RBOHs) genes in transgenic Arabidopsis. In addition, the over-expression of TaHXK7-1A inhibited the growth of Arabidopsis seedlings and increased ROS accumulation under 6 % exogenous glucose treatment. Gene silencing of TaHXK7-1 decreased the contents of O2·－ and MDA in wheat leaves under drought stress, and the RBOHs was significantly down-regulated, which improved the drought resistance of wheat. The results of yeast one-hybrid, EMSA, and dual-luciferase assays showed that TabHLH148-5A bound to the E-box motif of the TaHXK7-1A promoter and inhibited the expression of TaHXK7-1A. In addition, yeast two-hybrid and luciferase complementation imaging assays showed that TaHXK7-1A interacted with TaGRF3-4A. These results indicate that the glucose sensor TaHXK7-1A was negatively regulated by TabHLH148-5A, interacted with TaGRF3-4A, and negatively regulated wheat drought resistance by regulating RBOHs expression and inducing ROS production, thus providing a theoretical basis for revealing the molecular mechanism of wheat drought resistance.

The transcription factor ERF108 interacts with AUXIN RESPONSE FACTORs to mediate cotton fiber secondary cell wall biosynthesis

Phytohormones play indispensable roles in plant growth and development. However, the molecular mechanisms underlying phytohormone-mediated regulation of fiber secondary cell wall (SCW) formation in cotton (Gossypium hirsutum) remain largely underexplored. Here, we provide mechanistic evidence for functional interplay between the APETALA2/ethylene response factor (AP2/ERF) transcription factor GhERF108 and auxin response factors GhARF7-1 and GhARF7-2 in dictating the ethylene-auxin signaling crosstalk that regulates fiber SCW biosynthesis. Specifically, in vitro cotton ovule culture revealed that ethylene and auxin promote fiber SCW deposition. GhERF108 RNA interference (RNAi) cotton displayed remarkably reduced cell wall thickness compared with controls. GhERF108 interacted with GhARF7-1 and GhARF7-2 to enhance the activation of the MYB transcription factor gene GhMYBL1 (MYB domain-like protein 1) in fibers. GhARF7-1 and GhARF7-2 respond to auxin signals that promote fiber SCW thickening. GhMYBL1 RNAi and GhARF7-1 and GhARF7-2 virus-induced gene silencing (VIGS) cotton displayed similar defects in fiber SCW formation as GhERF108 RNAi cotton. Moreover, the ethylene and auxin responses were reduced in GhMYBL1 RNAi plants. GhMYBL1 directly binds to the promoters of GhCesA4-1, GhCesA4-2, and GhCesA8-1 and activates their expression to promote cellulose biosynthesis, thereby boosting fiber SCW formation. Collectively, our findings demonstrate that the collaboration between GhERF108 and GhARF7-1 or GhARF7-2 establishes ethylene-auxin signaling crosstalk to activate GhMYBL1, ultimately leading to the activation of fiber SCW biosynthesis.

LIPID TRANSFER PROTEIN4 regulates cotton ceramide content and activates fiber cell elongation

Cell elongation is a fundamental process for plant growth and development. Studies have shown lipid metabolism plays important role in cell elongation; however, the related functional mechanisms remain largely unknown. Here, we report that cotton (Gossypium hirsutum) LIPID TRANSFER PROTEIN4 (GhLTP4) promotes fiber cell elongation via elevating ceramides (Cers) content and activating auxin-responsive pathways. GhLTP4 was preferentially expressed in elongating fibers. Over-expression and down-regulation of GhLTP4 led to longer and shorter fiber cells, respectively. Cers were greatly enriched in GhLTP4-overexpressing lines and decreased dramatically in GhLTP4 down-regulating lines. Moreover, auxin content and transcript levels of indole-3-acetic acid (IAA)-responsive genes were significantly increased in GhLTP4-overexpressing cotton fibers. Exogenous application of Cers promoted fiber elongation, while NPA (N-1-naphthalic acid, a polar auxin transport inhibitor) counteracted the promoting effect, suggesting that IAA functions downstream of Cers in regulating fiber elongation. Furthermore, we identified a basic helix-loop-helix transcription factor, GhbHLH105, that binds to the E-box element in the GhLTP4 promoter region and promotes the expression of GhLTP4. Suppression of GhbHLH105 in cotton reduced the transcripts level of GhLTP4, resulting in smaller cotton bolls and decreased fiber length. These results provide insights into the complex interactions between lipids and auxin-signaling pathways to promote plant cell elongation.

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

Cotton is an irreplaceable economic crop currently domesticated in the human world for its extremely elongated fiber cells specialized in seed epidermis, which makes it of high research and application value. To date, numerous research on cotton has navigated various aspects, from multi-genome assembly, genome editing, mechanism of fiber development, metabolite biosynthesis, and analysis to genetic breeding. Genomic and 3D genomic studies reveal the origin of cotton species and the spatiotemporal asymmetric chromatin structure in fibers. Mature multiple genome editing systems, such as CRISPR/Cas9, Cas12 (Cpf1) and cytidine base editing (CBE), have been widely used in the study of candidate genes affecting fiber development. Based on this, the cotton fiber cell development network has been preliminarily drawn. Among them, the MYB-bHLH-WDR (MBW) transcription factor complex and IAA and BR signaling pathway regulate the initiation; various plant hormones, including ethylene, mediated regulatory network and membrane protein overlap fine-regulate elongation. Multistage transcription factors targeting CesA 4, 7, and 8 specifically dominate the whole process of secondary cell wall thickening. And fluorescently labeled cytoskeletal proteins can observe real-time dynamic changes in fiber development. Furthermore, research on the synthesis of cotton secondary metabolite gossypol, resistance to diseases and insect pests, plant architecture regulation, and seed oil utilization are all conducive to finding more high-quality breeding-related genes and subsequently facilitating the cultivation of better cotton varieties. This review summarizes the paramount research achievements in cotton molecular biology over the last few decades from the above aspects, thereby enabling us to conduct a status review on the current studies of cotton and provide strong theoretical support for the future direction.

Brassinosteroids regulate cotton fiber elongation by modulating very-long-chain fatty acid biosynthesis

Brassinosteroid (BR), a growth-promoting phytohormone, regulates many plant growth processes including cell development. However, the mechanism by which BR regulates fiber growth is poorly understood. Cotton (Gossypium hirsutum) fibers are an ideal single-cell model in which to study cell elongation due to their length. Here we report that BR controls cotton fiber elongation by modulating very-long-chain fatty acid (VLCFA) biosynthesis. BR deficiency reduces the expression of 3-ketoacyl-CoA synthases (GhKCSs), the rate-limiting enzymes involved in VLCFA biosynthesis, leading to lower saturated VLCFA contents in pagoda1 (pag1) mutant fibers. In vitro ovule culture experiments show that BR acts upstream of VLCFAs. Silencing of BRI1-EMS-SUPPRESOR 1.4 (GhBES1.4), encoding a master transcription factor of the BR signaling pathway, significantly reduces fiber length, whereas GhBES1.4 overexpression produces longer fibers. GhBES1.4 regulates endogenous VLCFA contents and directly binds to BR RESPONSE ELEMENTS (BRREs) in the GhKCS10_At promoter region, which in turn regulates GhKCS10_At expression to increase endogenous VLCFA contents. GhKCS10_At overexpression promotes cotton fiber elongation, whereas GhKCS10_At silencing inhibits cotton fiber growth, supporting a positive regulatory role for GhKCS10_At in fiber elongation. Overall, these results uncover a mechanism of fiber elongation through crosstalk between BR and VLCFAs at the single-cell level.

A conserved brassinosteroid-mediated BES1-CERP-EXPA3 signaling cascade controls plant cell elongation

Continuous plant growth is achieved by cell division and cell elongation. Brassinosteroids control cell elongation and differentiation throughout plant life. However, signaling cascades underlying BR-mediated cell elongation are unknown. In this study, we introduce cotton fiber, one of the most representative single-celled tissues, to decipher cell-specific BR signaling. We find that gain of function of GhBES1, a key transcriptional activator in BR signaling, enhances fiber elongation. The chromatin immunoprecipitation sequencing analysis identifies a cell-elongation-related protein, GhCERP, whose transcription is directly activated by GhBES1. GhCERP, a downstream target of GhBES1, transmits the GhBES1-mediated BR signaling to its target gene, GhEXPA3-1. Ultimately, GhEXPA3-1 promotes fiber cell elongation. In addition, inter-species functional analysis of the BR-mediated BES1-CERP-EXPA3 signaling cascade also promotes Arabidopsis root and hypocotyl growth. We propose that the BES1-CERP-EXPA3 module may be a broad-spectrum pathway that is universally exploited by diverse plant species to regulate BR-promoted cell elongation.

A brassinosteroid transcriptional regulatory network participates in regulating fiber elongation in cotton

Brassinosteroids (BRs) participate in the regulation of plant growth and development through BRI1-EMS-SUPPRESSOR1 (BES1)/BRASSINAZOLE-RESISTANT1 (BZR1) family transcription factors. Cotton (Gossypium hirsutum) fibers are highly elongated single cells, and BRs play a vital role in the regulation of fiber elongation. However, the mode of action on how BR is involved in the regulation of cotton fiber elongation remains unexplored. Here, we generated GhBES1.4 over expression lines and found that overexpression of GhBES1.4 promoted fiber elongation, whereas silencing of GhBES1.4 reduced fiber length. DNA affinity purification and sequencing (DAP-seq) identified 1,531 target genes of GhBES1.4, and five recognition motifs of GhBES1.4 were identified by enrichment analysis. Combined analysis of DAP-seq and RNA-seq data of GhBES1.4-OE/RNAi provided mechanistic insights into GhBES1.4-mediated regulation of cotton fiber development. Further, with the integrated approach of GWAS, RNA-seq, and DAP-seq, we identified seven genes related to fiber elongation that were directly regulated by GhBES1.4. Of them, we showed Cytochrome P450 84A1 (GhCYP84A1) and 3-hydroxy-3-methylglutaryl-coenzyme A reductase 1 (GhHMG1) promote cotton fiber elongation. Overall, the present study established the role of GhBES1.4-mediated gene regulation and laid the foundation for further understanding the mechanism of BR participation in regulating fiber development.

Epi-Brassinolide Regulates ZmC4 NADP-ME Expression through the Transcription Factors ZmbHLH157 and ZmNF-YC2

Maize is a main food and feed crop with great production potential and high economic benefits. Improving its photosynthesis efficiency is crucial for increasing yield. Maize photosynthesis occurs mainly through the C4 pathway, and NADP-ME (NADP-malic enzyme) is a key enzyme in the photosynthetic carbon assimilation pathway of C4 plants. ZmC4-NADP-ME catalyzes the release of CO₂ from oxaloacetate into the Calvin cycle in the maize bundle sheath. Brassinosteroid (BL) can improve photosynthesis; however, its molecular mechanism of action remains unclear. In this study, transcriptome sequencing of maize seedlings treated with epi-brassinolide (EBL) showed that differentially expressed genes (DEGs) were significantly enriched in photosynthetic antenna proteins, porphyrin and chlorophyll metabolism, and photosynthesis pathways. The DEGs of C4-NADP-ME and pyruvate phosphate dikinase in the C4 pathway were significantly enriched in EBL treatment. Co-expression analysis showed that the transcription level of ZmNF-YC2 and ZmbHLH157 transcription factors was increased under EBL treatment and moderately positively correlated with ZmC4-NADP-ME. Transient overexpression of protoplasts revealed that ZmNF-YC2 and ZmbHLH157 activate C4-NADP-ME promoters. Further experiments showed ZmNF-YC2 and ZmbHLH157 transcription factor binding sites on the -1616 bp and -1118 bp ZmC4 NADP-ME promoter. ZmNF-YC2 and ZmbHLH157 were screened as candidate transcription factors mediating brassinosteroid hormone regulation of the ZmC4 NADP-ME gene. The results provide a theoretical basis for improving maize yield using BR hormones.

Identification of bHLH family genes in Agaricus bisporus and transcriptional regulation of arginine catabolism-related genes by AbbHLH1 after harvest

Basic helix-loop-helix (bHLH) transcription factors (TFs) are widely distributed in eukaryotes and play an important role in biological growth and development. The identification and functional analyses of bHLH genes/proteins in edible mushrooms (Agaricus bisporus) have yet to be reported. In the present study, we identified 10 putative bHLH members carrying the conserved bHLH domains. Phylogenetic analyses revealed that the 10 AbbHLHs were the closest to sequences of species belonging to 7 different fungal subgroups, which was supported by loop length, intron patterns, and key amino acid residues. The substantial increase after harvest and continuously elevated expression of AbbHLH1 during the development until the disruption of mushroom velum, and the preferential expression in cap and gill tissues suggest the important function of AbbHLH1 in postharvest development of A. bisporus. The relationship of arginine catabolism-related genes with the early stage of postharvest continuing development also was revealed by expression determination. Subcellular localization showed that AbbHLH1 could be localized in nucleus. Importantly, the electrophoretic mobility shift and dual-luciferase reporter assays showed that AbbHLH1 activated the promoters of AbOAT, AbSPDS, and AbSAMDC and suppressed the expression of AbARG, AbUREA, and AbODC, probably for the modulation of arginine catabolism and thus control of postharvest mushroom development. Taken together, the available data provide valuable functional insight into the role of AbbHLH proteins in postharvest mushrooms.

GhBES1 mediates brassinosteroid regulation of leaf size by activating expression of GhEXO2 in cotton (Gossypium hirsutum)

We proposed a working model of BR to promote leaf size through cell expansion. In the BR signaling pathway, GhBES1 affects cotton leaf size by binding to and activating the expression of the E-box element in the GhEXO2 promoter region. Brassinosteroid (BR) is an essential phytohormone that controls plant growth. However, the mechanisms of BR regulation of leaf size remain to be determined. Here, we found that the BR deficient cotton mutant pagoda1 (pag1) had a smaller leaf size than wild-type CRI24. The expression of EXORDIUM (GhEXO2) gene, was significantly downregulated in pag1. Silencing of BRI1-EMS-SUPPRESSOR 1 (GhBES1), inhibited leaf cell expansion and reduced leaf size. Overexpression of GhBES1.4 promoted leaf cell expansion and enlarged leaf size. Expression analysis showed GhEXO2 expression positively correlated with GhBES1 expression. In plants, altered expression of GhEXO2 promoted leaf cell expansion affecting leaf size. Furthermore, GhBES1.4 specifically binds to the E-box elements in the GhEXO2 promoter, inducing its expression. RNA-seq data revealed many down-regulated genes related to cell expansion in GhEXO2 silenced plants. In summary, we discovered a novel mechanism of BR regulation of leaf size through GhBES1 directly activating the expression of GhEXO2.

Expressed genes and their new alleles identification during fibre elongation reveal the genetic factors underlying improvements of fibre length in cotton

Interspecific breeding in cotton takes advantage of genetic recombination among desirable genes from different parental lines. However, the expression new alleles (ENAs) from crossovers within genic regions and their significance in fibre length (FL) improvement are currently not understood. Here, we generated resequencing genomes of 191 interspecific backcross inbred lines derived from CRI36 (Gossypium hirsutum) × Hai7124 (Gossypium barbadense) and 277 dynamic fibre transcriptomes to identify the ENAs and extremely expressed genes (eGenes) potentially influencing FL, and uncovered the dynamic regulatory network of fibre elongation. Of 35 420 eGenes in developing fibres, 10 366 ENAs were identified and preferentially distributed in chromosomes subtelomeric regions. In total, 1056-1255 ENAs showed transgressive expression in fibres at 5-15 dpa (days post-anthesis) of some BILs, 520 of which were located in FL-quantitative trait locus (QTLs) and GhFLA9 (recombination allele) was identified with a larger effect for FL than GhFLA9 of CRI36 allele. Using ENAs as a type of markers, we identified three novel FL-QTLs. Additionally, 456 extremely eGenes were identified that were preferentially distributed in recombination hotspots. Importantly, 34 of them were significantly associated with FL. Gene expression quantitative trait locus analysis identified 1286, 1089 and 1059 eGenes that were colocalized with the FL trait at 5, 10 and 15 dpa, respectively. Finally, we verified the Ghir_D10G011050 gene linked to fibre elongation by the CRISPR-cas9 system. This study provides the first glimpse into the occurrence, distribution and expression of the developing fibres genes (especially ENAs) in an introgression population, and their possible biological significance in FL.

The bHLH/HLH transcription factors GhFP2 and GhACE1 antagonistically regulate fiber elongation in cotton

Basic helix-loop-helix/helix-loop-helix (bHLH/HLH) transcription factors play important roles in cell elongation in plants. However, little is known about how bHLH/HLH transcription factors antagonistically regulate fiber elongation in cotton (Gossypium hirsutum). In this study, we report that two bHLH/HLH transcription factors, fiber-related protein 2 (GhFP2) and ACTIVATOR FOR CELL ELONGATION 1 (GhACE1), function in fiber development of cotton. GhFP2 is an atypical bHLH protein without the basic region, and its expression is regulated by brassinosteroid (BR)-related BRASSINAZOLE RESISTANT 1 (GhBZR1). Overexpression of GhFP2 in cotton hindered fiber elongation, resulting in shortened fiber length. In contrast, suppression of GhFP2 expression in cotton promoted fiber development, leading to longer fibers compared with the wild-type. GhFP2 neither contains a DNA-binding domain nor has transcriptional activation activity. Furthermore, we identified GhACE1, a bHLH protein that interacts with GhFP2 and positively regulates fiber elongation. GhACE1 could bind to promoters of plasma membrane intrinsic protein 2;7 (GhPIP2;7) and expansions 8 (GhEXP8) for directly activating their expression, but the interaction between GhFP2 and GhACE1 suppressed transcriptional activation of these target genes by GhACE1. Taken together, our results indicate that GhACE1 promotes fiber elongation by activating expressions of GhPIP2;7 and GhEXP8, but its transcription activation on downstream genes may be obstructed by BR-modulated GhFP2. Thus, our data reveal a key mechanism for fiber cell elongation through a pair of antagonizing HLH/bHLH transcription factors in cotton.

Molecular Mechanisms of Plant Trichome Development

Plant trichomes, protrusions formed from specialized aboveground epidermal cells, provide protection against various biotic and abiotic stresses. Trichomes can be unicellular, bicellular or multicellular, with multiple branches or no branches at all. Unicellular trichomes are generally not secretory, whereas multicellular trichomes include both secretory and non-secretory hairs. The secretory trichomes release secondary metabolites such as artemisinin, which is valuable as an antimalarial agent. Cotton trichomes, also known as cotton fibers, are an important natural product for the textile industry. In recent years, much progress has been made in unraveling the molecular mechanisms of trichome formation in Arabidopsis thaliana, Gossypium hirsutum, Oryza sativa, Cucumis sativus, Solanum lycopersicum, Nicotiana tabacum, and Artemisia annua. Here, we review current knowledge of the molecular mechanisms underlying fate determination and initiation, elongation, and maturation of unicellular, bicellular and multicellular trichomes in several representative plants. We emphasize the regulatory roles of plant hormones, transcription factors, the cell cycle and epigenetic modifications in different stages of trichome development. Finally, we identify the obstacles and key points for future research on plant trichome development, and speculated the development relationship between the salt glands of halophytes and the trichomes of non-halophytes, which provides a reference for future studying the development of plant epidermal cells.

Revealing Genetic Differences in Fiber Elongation between the Offspring of Sea Island Cotton and Upland Cotton Backcross Populations Based on Transcriptome and Weighted Gene Coexpression Networks

Fiber length is an important indicator of cotton fiber quality, and the time and rate of cotton fiber cell elongation are key factors in determining the fiber length of mature cotton. To gain insight into the differences in fiber elongation mechanisms in the offspring of backcross populations of Sea Island cotton Xinhai 16 and land cotton Line 9, we selected two groups with significant differences in fiber length (long-fiber group L and short-fiber group S) at different fiber development stages 0, 5, 10 and 15 days post-anthesis (DPA) for transcriptome comparison. A total of 171.74 Gb of clean data was obtained by RNA-seq, and eight genes were randomly selected for qPCR validation. Data analysis identified 6055 differentially expressed genes (DEGs) between two groups of fibers, L and S, in four developmental periods, and gene ontology (GO) term analysis revealed that these DEGs were associated mainly with microtubule driving, reactive oxygen species, plant cell wall biosynthesis, and glycosyl compound hydrolase activity. Kyoto encyclopedia of genes and genomes (KEGG) pathway analysis indicated that plant hormone signaling, mitogen-activated protein kinase (MAPK) signaling, and starch and sucrose metabolism pathways were associated with fiber elongation. Subsequently, a sustained upregulation expression pattern, profile 19, was identified and analyzed using short time-series expression miner (STEM). An analysis of the weighted gene coexpression network module uncovered 21 genes closely related to fiber development, mainly involved in functions such as cell wall relaxation, microtubule formation, and cytoskeletal structure of the cell wall. This study helps to enhance the understanding of the Sea Island–Upland backcross population and identifies key genes for cotton fiber development, and these findings will provide a basis for future research on the molecular mechanisms of fiber length formation in cotton populations.

Multi-Dimensional Molecular Regulation of Trichome Development in Arabidopsis and Cotton

Plant trichomes are specialized epidermal cells that are widely distributed on plant aerial tissues. The initiation and progression of trichomes are controlled in a coordinated sequence of multiple molecular events. During the past decade, major breakthroughs in the molecular understanding of trichome development were achieved through the characterization of various trichomes defective mutants and trichome-associated genes, which revealed a highly complex molecular regulatory network underlying plant trichome development. This review focuses on the recent millstone in plant trichomes research obtained using genetic and molecular studies, as well as 'omics' analyses in model plant Arabidopsis and fiber crop cotton. In particular, we discuss the latest understanding and insights into the underlying molecular mechanisms of trichomes formation at multiple dimensions, including at the chromatin, transcriptional, post-transcriptional, and post-translational levels. We summarize that the integration of multi-dimensional trichome-associated genes will enable us to systematically understand the molecular regulation network that landscapes the development of the plant trichomes. These advances will enable us to address the unresolved questions regarding the molecular crosstalk that coordinate concurrent and ordered the changes in cotton fiber initiation and progression, together with their possible implications for genetic improvement of cotton fiber.

Feedback Inhibition Might Dominate the Accumulation Pattern of BR in the New Shoots of Tea Plants (Camellia sinensis)

Brassinosteroid (BR), a kind of polyhydroxylated steroid hormone, plays an important role in physiological and biochemical processes in plants. Studies were mainly focused on BR signaling and its exogenous spraying to help enhance crop yields. Few research studies are centered on the accumulation pattern of BR and its mechanism. Yet, it is crucial to unlock the mystery of the function of BR and its cross action with other hormones. Tea (Camellia sinensis (L.) O. Kuntze) is one of the important economic crops in some countries, and new shoots are the raw materials for the preparation of various tea products. Different concentrations of exogenous BR were reported to have different effects on growth and development. New shoots of tea plants can thus be considered a valuable research object to study the accumulation pattern of BR. In this study, the quantity of five BR components (brassinolide, 28-norbrassinolide, 28-homobrassinolide, castasterone, and 28-norcastasterone) in different tissues of tea plants, including buds (Bud), different maturity of leaves (L1, L2), and stems (S1, S2) were determined by UPLC-MS/MS. A total of 15 cDNA libraries of the same tissue with three repetitions for each were constructed and sequenced. The BR-accumulation pattern and gene expression pattern were combined together for weighted gene co-expression network analysis (WGCNA). BR-accumulation-relative genes were then screened using two methods, based on the K.in value and BR biosynthetic pathway (ko00905), respectively. The result showed that photosynthesis-related genes and CYP450 family genes were actively involved and might play important roles in BR accumulation and/or its accumulation pattern. First and foremost, feedback inhibition was more likely to dominate the accumulation pattern of BR in the new shoots of tea plants. Moreover, three conserved miRNAs with their target transcriptional factors and target mRNAs had been figured out from negative correlation modules that might be strongly linked to the BR-accumulation pattern. Our study provided an experimental basis for the role of BR in tea plants. The excavation of genes related to the accumulation pattern of BR provided the possibility of cross-action studies on the regulation of BR biosynthesis and the study between BR and other hormones.

Glucose regulates cotton fiber elongation by interacting with brassinosteroid

In plants, glucose (Glc) plays important roles, as a nutrient and signal molecule, in the regulation of growth and development. However, the function of Glc in fiber development of upland cotton (Gossypium hirsutum) is unclear. Here, using gas chromatography-mass spectrometry (GC-MS), we found that the Glc content in fibers was higher than that in ovules during the fiber elongation stage. In vitro ovule culture revealed that lower Glc concentrations promoted cotton fiber elongation, while higher concentrations had inhibitory effects. The hexokinase inhibitor N-acetylglucosamine (NAG) inhibited cotton fiber elongation in the cultured ovules, indicating that Glc-mediated fiber elongation depends on the Glc signal transduced by hexokinase. RNA sequencing (RNA-seq) analysis and hormone content detection showed that 150mM Glc significantly activated brassinosteroid (BR) biosynthesis, and the expression of signaling-related genes was also increased, which promoted fiber elongation. In vitro ovule culture clarified that BR induced cotton fiber elongation in a dose-dependent manner. In hormone recovery experiments, only BR compensated for the inhibitory effects of NAG on fiber elongation in a Glc-containing medium. However, the ovules cultured with the BR biosynthetic inhibitor brassinazole and from the BR-deficient cotton mutant pag1 had greatly reduced fiber elongation at all the Glc concentrations tested. This demonstrates that Glc does not compensate for the inhibition of fiber elongation caused by BR biosynthetic defects, suggesting that the BR signaling pathway works downstream of Glc during cotton fiber elongation. Altogether, our study showed that Glc plays an important role in cotton fibre elongation, and crosstalk occurs between Glc and BR signaling during modulation of fiber elongation.

Subgenome Bias and Temporal Postponement of Gene Expression Contributes to the Distinctions of Fiber Quality in Gossypium Species

As two cultivated widely allotetraploid cotton species, although Gossypium hirsutum and Gossypium barbadense evolved from the same ancestor, they differ in fiber quality; the molecular mechanism of that difference should be deeply studied. Here, we performed RNA-seq of fiber samples from four G. hirsutum and three G. barbadense cultivars to compare their gene expression patterns on multiple dimensions. We found that 15.90-37.96% of differentially expressed genes showed biased expression toward the A or D subgenome. In particular, interspecific biased expression was exhibited by a total of 330 and 486 gene pairs at 10 days post-anthesis (DPA) and 20 DPA, respectively. Moreover, 6791 genes demonstrated temporal differences in expression, including 346 genes predominantly expressed at 10 DPA in G. hirsutum (TM-1) but postponed to 20 DPA in G. barbadense (Hai7124), and 367 genes predominantly expressed at 20 DPA in TM-1 but postponed to 25 DPA in Hai7124. These postponed genes mainly participated in carbohydrate metabolism, lipid metabolism, plant hormone signal transduction, and starch and sucrose metabolism. In addition, most of the co-expression network and hub genes involved in fiber development showed asymmetric expression between TM-1 and Hai7124, like three hub genes detected at 10 DPA in TM-1 but not until 25 DPA in Hai7124. Our study provides new insights into interspecific expression bias and postponed expression of genes associated with fiber quality, which are mainly tied to asymmetric hub gene network. This work will facilitate further research aimed at understanding the mechanisms underlying cotton fiber improvement.

bHLH transcription factors LP1 and LP2 regulate longitudinal cell elongation

Basic helix-loop-helix/helix-loop-helix (bHLH/HLH) transcription factors play substantial roles in plant cell elongation. In this study, two bHLH/HLH homologous proteins leaf related protein 1 and leaf-related protein 2 (AtLP1 and AtLP2) were identified in Arabidopsis thaliana. LP1 and LP2 play similar positive roles in longitudinal cell elongation. Both LP1 and LP2 overexpression plants exhibited long hypocotyls, elongated cotyledons, and particularly long leaf blades. The elongated leaves resulted from increased longitudinal cell elongation. lp1 and lp2 loss-of-function single mutants did not display distinct phenotypes, but the lp1lp2 double mutant showed decreased leaf length associated with less longitudinal polar cell elongation. Furthermore, the phenotype of lp1lp2 could be rescued by the expression of LP1 or LP2. Expression of genes related to cell elongation was upregulated in LP1 and LP2 overexpression plants but downregulated in lp1lp2 double mutant plants compared with that of wild type. LP1 and LP2 proteins could directly bind to the promoters of Longifolia1 (LNG1) and LNG2 to activate the expression of these cell elongation related genes. Both LP1 and LP2 could interact with two other bHLH/HLH proteins, IBH1 (ILI1 binding BHLH Protein1) and IBL1 (IBH1-like1), thereby suppressing the transcriptional activation of LP1 and LP2 to the target genes LNG1 and LNG2. Thus, our data suggested that LP1 and LP2 act as positive regulators to promote longitudinal cell elongation by activating the expression of LNG1 and LNG2 genes in Arabidopsis. Moreover, homodimerization of LP1 and LP2 may be essential for their function, and interaction between LP1/LP2 and other bHLH/HLH proteins may obstruct transcriptional regulation of target genes by LP1 and LP2.

PtBRI1.2 promotes shoot growth and wood formation through a brassinosteroid-mediated PtBZR1-PtWNDs module in poplar

Brassinosteroid-insensitive-1 (BRI1) plays important roles in various signalling pathways controlling plant growth and development. However, the regulatory mechanism of BRI1 in brassinosteroid (BR)-mediated signalling for shoot growth and wood formation in woody plants is largely unknown. In this study, PtBRI1.2, a brassinosteroid-insensitive-1 gene, was overexpressed in poplar. Shoot growth and wood formation of transgenic plants were examined and the regulatory genes involved were verified. PtBRI1.2 was localized to the plasma membrane, with a predominant expression in leaves. Ectopic expression of PtBRI1.2 in Arabidopsis bri1-201 and bri1-5 mutants rescued their retarded-growth phenotype. Overexpression of PtBRI1.2 in poplar promoted shoot growth and wood formation in transgenic plants. Further studies revealed that overexpression of PtBRI1.2 promoted the accumulation of PtBZR1 (BRASSINAZOLE RESISTANT1) in the nucleus, which subsequently activated PtWNDs (WOOD-ASSOCIATED NAC DOMAIN transcription factors) to up-regulate expression of secondary cell wall biosynthesis genes involved in wood formation. Our results suggest that PtBRI1.2 plays a crucial role in regulating shoot growth and wood formation by activating BR signalling.

A Class II TCP Transcription Factor PaTCP4 from Platanus acerifolia Regulates Trichome Formation in Arabidopsis

London plane tree is widely grown as a landscaping and street tree, but the release of its trichomes creates a serious air-borne pollution problem. Identifying the key genes that regulate the development of trichomes is, therefore, an important tool for the molecular breeding of Platanus acerifolia. In this study, a sequence homologous with the Arabidopsis Class II TCP subfamily was identified from London plane, and named PaTCP4. The expression of PaTCP4 was detected in various organs of London plane trees, significantly in the trichomes. Overexpression of PaTCP4 in Arabidopsis reduced the trichome density on the first pair of true leaves, and atypical 5-branched trichomes were also detected on those leaves. The expression of endogenous AtCPC and AtTCL2 was significantly increased in PaTCP4 transgenic lines, and was associated with a decrease in the expression of endogenous AtGL2. Furthermore, the expression of endogenous AtGL3 was significantly increased. In addition, the protein product of PaTCP4 was shown to directly activate AtCPC, AtTCL2, AtGL3, AtGIS, PaGIS, and PaGL3 in yeast one-hybrid assays and in the dual-luciferase reporter system. Taken together, these results identify a role for PaTCP4 in trichome initiation and branching in Arabidopsis. Thus, PaTCP4 represents a strong candidate gene for regulating the development of trichomes in London plane trees.

Identification of BR biosynthesis genes in cotton reveals that GhCPD-3 restores BR biosynthesis and mediates plant growth and development

Brassinosteroid (BR) synthesis genes in different cotton species was comprehensively identified, and the participation of GhCPD-3 in the BR synthesis signaling pathway for regulating plant development was verified. Brassinosteroid is a natural steroidal phytohormone that plays fundamental roles in plant growth and development. In cotton, detailed characterization and functional validation of BR biosynthesis genes remain rare. Here, 16, 8 and 9 BR biosynthesis genes were identified in Gossypium hirsutum, Gossypium raimondii and Gossypium arboreum, respectively, and their phylogenetic relationships, gene structures, conserved motifs of the encoded proteins, chromosomal locations were determined and a synteny analysis was performed. Gossypium hirsutum and Arabidopsis BR biosynthesis genes closely clustered in the phylogenetic tree and fragment duplication was likely the primary cause promoting gene family expansion in G. hirsutum. Gene Ontology (GO) and KEGG (Kyoto Encyclopedia of Genes and Genomes) enrichment analysis showed their relevance as BR biosynthesis genes. GhCPD-3 was highly expressed in roots and stems and the loci of single nucleotide polymorphisms (SNPs) were significantly associated with these traits.Ectopic overexpression of GhCPD-3 in the cpd91 Arabidopsis mutant rescued the mutant phenotype by increasing plant height and leaf size in comparison to those of cpd91 and WT plants. Moreover, overexpressed GhCPD-3 in cpd91 mutants showed greater hypocotyl and root lengths than those of cpd91 and WT plants under light and dark conditions, respectively, indicating that BR actively promotes hypocotyl and root growth. Similar to CPD (CONSTITUTIVE PHOTOMORPHOGENIC DWARF), GhCPD-3 restores BR biosynthesis thereby mediating plant growth and development.

Phosphorylation of WRKY16 by MPK3-1 is essential for its transcriptional activity during fiber initiation and elongation in cotton (Gossypium hirsutum)

Cotton, one of the most important crops in the world, produces natural fiber materials for the textile industry. WRKY transcription factors play important roles in plant development and stress responses. However, little is known about whether and how WRKY transcription factors regulate fiber development of cotton so far. In this study, we show that a fiber-preferential WRKY transcription factor, GhWRKY16, positively regulates fiber initiation and elongation. GhWRKY16-silenced transgenic cotton displayed a remarkably reduced number of fiber protrusions on the ovule and shorter fibers compared to the wild-type. During early fiber development, GhWRKY16 directly binds to the promoters of GhHOX3, GhMYB109, GhCesA6D-D11, and GhMYB25 to induce their expression, thereby promoting fiber initiation and elongation. Moreover, GhWRKY16 is phosphorylated by the mitogen-activated protein kinase GhMPK3-1 at residues T-130 and S-260. Phosphorylated GhWRKY16 directly activates the transcription of GhMYB25, GhHOX3, GhMYB109, and GhCesA6D-D11 for early fiber development. Thus, our data demonstrate that GhWRKY16 plays a crucial role in fiber initiation and elongation, and that GhWRKY16 phosphorylation by GhMPK3-1 is essential for the transcriptional activation on downstream genes during the fiber development of cotton.

Recent Advances and Future Perspectives in Cotton Research

Cotton is not only the world's most important natural fiber crop, but it is also an ideal system in which to study genome evolution, polyploidization, and cell elongation. With the assembly of five different cotton genomes, a cotton-specific whole-genome duplication with an allopolyploidization process that combined the A- and D-genomes became evident. All existing A-genomes seemed to originate from the A₀-genome as a common ancestor, and several transposable element bursts contributed to A-genome size expansion and speciation. The ethylene production pathway is shown to regulate fiber elongation. A tip-biased diffuse growth mode and several regulatory mechanisms, including plant hormones, transcription factors, and epigenetic modifications, are involved in fiber development. Finally, we describe the involvement of the gossypol biosynthetic pathway in the manipulation of herbivorous insects, the role of GoPGF in gland formation, and host-induced gene silencing for pest and disease control. These new genes, modules, and pathways will accelerate the genetic improvement of cotton.

Phytohormone-Based Regulation of Trichome Development

Phytohormones affect plant growth and development. Many phytohormones are involved in the initiation of trichome development, which can help prevent damage from UV radiation and insect bites and produce fragrance, flavors, and compounds used as pharmaceuticals. Phytohormones promote the participation of transcription factors in the initiation of trichome development; for example, the transcription factors HDZIP, bHLH and MYB interact and form transcriptional complexes to regulate trichome development. Jasmonic acid (JA) mediates the progression of the endoreduplication cycle to increase the number of multicellular trichomes or trichome size. Moreover, there is crosstalk between phytohormones, and some phytohormones interact with each other to affect trichome development. Several new techniques, such as the CRISPR-Cas9 system and single-cell transcriptomics, are available for investigating gene function, determining the trajectory of individual trichome cells and elucidating the regulatory network underlying trichome cell lineages. This review discusses recent advances in the modulation of trichome development by phytohormones, emphasizes the differences and similarities between phytohormones initially present in trichomes and provides suggestions for future research.

A histone deacetylase, GhHDT4D, is positively involved in cotton response to drought stress

Acetylation and deacetylation of histones are important for regulating a series of biological processes in plants. Histone deacetylases (HDACs) control the histone deacetylation that plays an important role in plant response to abiotic stress. In our study, we show the evidence that GhHDT4D (a member of the HD2 subfamily of HDACs) is involved in cotton (Gossypium hirsutum) response to drought stress. Overexpression of GhHDT4D in Arabidopsis increased plant tolerance to drought, whereas silencing GhHDT4D in cotton resulted in plant sensitivity to drought. Simultaneously, the H3K9 acetylation level was altered in the GhHDT4D silenced cotton, compared with the controls. Further study revealed that GhHDT4D suppressed the transcription of GhWRKY33, which plays a negative role in cotton defense to drought, by reducing its H3K9 acetylation level. The expressions of the stress-related genes, such as GhDREB2A, GhDREB2C, GhSOS2, GhRD20-1, GhRD20-2 and GhRD29A, were significantly decreased in the GhHDT4D silenced cotton, but increased in the GhWRKY33 silenced cotton. Given these data together, our findings suggested that GhHDT4D may enhance drought tolerance by suppressing the expression of GhWRKY33, thereby activating the downstream drought response genes in cotton.

Regulation of Brassinosteroid Homeostasis in Higher Plants

Brassinosteroids (BRs) are known as one of the major classes of phytohormones essential for various processes during normal plant growth, development, and adaptations to biotic and abiotic stresses. Significant progress has been achieved on revealing mechanisms regulating BR biosynthesis, catabolism, and signaling in many crops and in model plant Arabidopsis. It is known that BRs control plant growth and development in a dosage-dependent manner. Maintenance of BR homeostasis is therefore critical for optimal functions of BRs. In this review, updated discoveries on mechanisms controlling BR homeostasis in higher plants in response to internal and external cues are discussed.