Suppressing a Putative Sterol Carrier Gene Reduces Plasmodesmal Permeability and Activates Sucrose Transporter Genes during Cotton Fiber Elongation

GhLPF1 Associated Network Is Involved with Cotton Lint Percentage Regulation Revealed by the Integrative Analysis of Spatial Transcriptome

Cotton fibers, derived from the epidermis of the ovule, provide a sustainable natural fiber source for the textile industry. Traits related to fiber yield are predominantly determined by molecular regulations in the epidermis of the outer integument (OI) region of the cotton ovule. Here, we identify an R2R3 MYB transcription factor coding gene GhLPF1 within the QTL-LP-ChrA06 locus for lint percentage (LP, percentage of lint to seed cotton) through constructing the 1-Day Post Anthesis Cotton Ovule Spatial Transcriptome Atlas. GhLPF1 is subjected as a downstream target of miR828 during fiber development. The direct downstream genes (DDGs) of GhLPF1 are biased to increased expression in GhLPF1-CR, and are preferentially expressed in OI, so that GhLPF1 is primarily a transcriptional repressor to its DDGs. Population-wide transcriptome analysis confirms that expression variation of GhLPF1-DDGs is significantly biased to negative correlation with LP, among which a type I homeobox protein-coding gene GhHB6 is further validated to be the directly downstream gene of GhLPF1. Given these data, it is demonstrated that GhLPF1 mediates a regulation network in LP as a transcriptional repressor, which makes it a valuable functional marker for fiber-trait improvement application from QTL-LP-ChrA06.

Spatial transcriptome and single-cell RNA sequencing reveal the molecular basis of cotton fiber initiation development

Recent advances in single-cell transcriptomics have greatly expanded our knowledge of plant development and cellular responses. However, analyzing fiber cell differentiation in plants, particularly in cotton, remains a complex challenge. A spatial transcriptomic map of ovule from -1 DPA, 0 DPA, and 1 DPA in cotton was successfully constructed, which helps to explain the important role of sucrose synthesis and lipid metabolism during early fiber development. Additionally, single-cell RNA sequencing (scRNA-seq) further highlighted the cellular heterogeneity and identified clusters of fiber developmental marker genes. Integration of spatial and scRNA-seq data unveiled key genes SVB and SVBL involved in fiber initiation, suggesting functional redundancy between them. These findings provide a detailed molecular landscape of cotton fiber development, offering valuable insights for enhancing lint yield.

The Disruptions of Sphingolipid and Sterol Metabolism in the Short Fiber of Ligon-Lintless-1 Mutant Revealed Obesity Impeded Cotton Fiber Elongation and Secondary Cell Wall Deposition

Boosting evidence indicated lipids play important roles in plants. To explore lipid function in cotton fiber development, the lipid composition and content were detected by untargeted and targeted lipidomics. Compared with rapid elongation fibers, the lipid intensity of 16 sub-classes and 56 molecular species decreased, while only 7 sub-classes and 26 molecular species increased in the fibers at the stage of secondary cell wall deposition. Unexpectedly, at the rapid elongation stage, 20 sub-classes and 60 molecular species increased significantly, while only 5 sub-classes and 8 molecular species decreased in the ligon lintless-1 (li-1) mutant compared with its wild-type Texas Maker-1 (TM-1). Particularly, campesteryl, sitosteryl, and total steryl ester increased by 21.8-, 48.7-, and 45.5-fold in the li-1 fibers, respectively. All the molecular species of sphingosine-1-P, phytoceramide-OHFA, and glucosylceramide increased while all sphingosine, phytosphingosine, and glycosyl inositol phospho ceramides decreased in the li-1 fibers. Similarly, the different expression genes between the mutant and wild type were enriched in many pathways involved in the lipid metabolism. Furthermore, the number of lipid droplets also increased in the li-1 leaf and fiber cells when compared with the wild type. These results illuminated that fiber cell elongation being blocked in the li-1 mutant was not due to a lack of lipids, but rather lipid over-accumulation (obesity), which may result from the disruption of sphingolipid and sterol metabolism. This study provides a new perspective for further studying the regulatory mechanisms of fiber development.

Unveiling the power of MYB transcription factors: Master regulators of multi-stress responses and development in cotton

Plants, being immobile, are subject to environmental stresses more than other creatures, necessitating highly effective stress tolerance systems. Transcription factors (TFs) play a crucial role in the adaptation mechanism as they can be activated by diverse signals and ultimately control the expression of stress-responsive genes. One of the most prominent plant TFs family is MYB (myeloblastosis), which is involved in secondary metabolites, developmental mechanisms, biological processes, cellular architecture, metabolic pathways, and stress responses. Extensive research has been conducted on the involvement of MYB TFs in crops, while their role in cotton remains largely unexplored. We also utilized genome-wide data to discover potential 440 MYB genes and investigated their plausible roles in abiotic and biotic stress conditions, as well as in different tissues across diverse transcriptome databases. This review primarily summarized the structure and classification of MYB TFs biotic and abiotic stress tolerance and their role in secondary metabolism in different crops, especially in cotton. However, it intends to identify gaps in current knowledge and emphasize the need for further research to enhance our understanding of MYB roles in plants.

Expression profile analysis of cotton fiber secondary cell wall thickening stage

To determine the genes associated with the fiber strength trait in cotton, three different cotton cultivars were selected: Sea Island cotton (Xinhai 32, with hyper-long fibers labeled as HL), and upland cotton (17-24, with long fibers labeled as L, and 62-33, with short fibers labeled as S). These cultivars were chosen to assess fiber samples with varying qualities. RNA-seq technology was used to analyze the expression profiles of cotton fibers at the secondary cell wall (SCW) thickening stage (20, 25, and 30 days post-anthesis (DPA)). The results showed that a large number of differentially expressed genes (DEGs) were obtained from the three assessed cotton cultivars at different stages of SCW development. For instance, at 20 DPA, Sea Island cotton (HL) had 6,215 and 5,364 DEGs compared to upland cotton 17-24 (L) and 62-33 (S), respectively. Meanwhile, there were 1,236 DEGs between two upland cotton cultivars, 17-24 (L) and 62-33 (S). Gene Ontology (GO) term enrichment identified 42 functions, including 20 biological processes, 11 cellular components, and 11 molecular functions. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis identified several pathways involved in SCW synthesis and thickening, such as glycolysis/gluconeogenesis, galactose metabolism, propanoate metabolism, biosynthesis of unsaturated fatty acids pathway, valine, leucine and isoleucine degradation, fatty acid elongation pathways, and plant hormone signal transduction. Through the identification of shared DEGs, 46 DEGs were found to exhibit considerable expressional differences at different fiber stages from the three cotton cultivars. These shared DEGs have functions including REDOX enzymes, binding proteins, hydrolases (such as GDSL thioesterase), transferases, metalloproteins (cytochromatin-like genes), kinases, carbohydrates, and transcription factors (MYB and WRKY). Therefore, RT-qPCR was performed to verify the expression levels of nine of the 46 identified DEGs, an approach which demonstrated the reliability of RNA-seq data. Our results provided valuable molecular resources for clarifying the cell biology of SCW biosynthesis during fiber development in cotton.

A mechanohydraulic model supports a role for plasmodesmata in cotton fiber elongation

Plant cell growth depends on turgor pressure, the cell hydrodynamic pressure, which drives expansion of the extracellular matrix (the cell wall). Turgor pressure regulation depends on several physical, chemical, and biological factors, including vacuolar invertases, which modulate osmotic pressure of the cell, aquaporins, which determine the permeability of the plasma membrane to water, cell wall remodeling factors, which determine cell wall extensibility (inverse of effective viscosity), and plasmodesmata, which are membrane-lined channels that allow free movement of water and solutes between cytoplasms of neighboring cells, like gap junctions in animals. Plasmodesmata permeability varies during plant development and experimental studies have correlated changes in the permeability of plasmodesmal channels to turgor pressure variations. Here, we study the role of plasmodesmal permeability in cotton fiber growth, a type of cell that increases in length by at least three orders of magnitude in a few weeks. We incorporated plasmodesma-dependent movement of water and solutes into a classical model of plant cell expansion. We performed a sensitivity analysis to changes in values of model parameters and found that plasmodesmal permeability is among the most important factors for building up turgor pressure and expanding cotton fibers. Moreover, we found that nonmonotonic behaviors of turgor pressure that have been reported previously in cotton fibers cannot be recovered without accounting for dynamic changes of the parameters used in the model. Altogether, our results suggest an important role for plasmodesmal permeability in the regulation of turgor pressure.

Significance of Raffinose Family Oligosaccharides (RFOs) metabolism in plants

Raffinose Family Oligosaccharides (RFOs) are a kind of polysaccharide containing D-galactose, and they widely exist in higher plants. Synthesis of RFOs begins with galactinol synthase (GolS; EC 2.4.1.123) to convert myo-inositol into galactinol. The subsequent formation of raffinose and stachyose are catalyzed by raffinose synthase (RS; EC 2.4.1.82) and stachyose synthase (STS; EC 2.4.1.67) using sucrose and galactinol as substrate, respectively. The hydrolysis of RFOs is finished by α-galactosidase (α-Gal; EC 3.2.1.22) to produce sucrose and galactose. Importance of RFOs metabolism have been summarized, e.g. In RFOs translocating plants, the phloem loading and unloading of RFOs are widely reported in mediating the plant development process. Interference function of RFOs synthesis or hydrolysis enzymes caused growth defect. In addition, the metabolism of RFOs involved in the biotic or abiotic stresses was discussed in this review. Overall, this literature summarizes our current understanding of RFOs metabolism and points out knowledge gaps that need to be filled in future.

A cell wall-localized β-1,3-glucanase promotes fiber cell elongation and secondary cell wall deposition

β-1,3-glucanase functions in plant physiological and developmental processes. However, how β-1,3-glucanase participates in cell wall development remains largely unknown. Here, we answered this question by examining the role of GhGLU18, a β-1,3-glucanase, in cotton (Gossypium hirsutum) fibers, in which the content of β-1,3-glucan changes dynamically from 10% of the cell wall mass at the onset of secondary wall deposition to <1% at maturation. GhGLU18 was specifically expressed in cotton fiber with higher expression in late fiber elongation and secondary cell wall (SCW) synthesis stages. GhGLU18 largely localized to the cell wall and was able to hydrolyze β-1,3-glucan in vitro. Overexpression of GhGLU18 promoted polysaccharide accumulation, cell wall reconstruction, and cellulose synthesis, which led to increased fiber length and strength with thicker cell walls and shorter pitch of the fiber helix. However, GhGLU18-suppressed cotton resulted in opposite phenotypes. Additionally, GhGLU18 was directly activated by GhFSN1 (fiber SCW-related NAC1), a NAC transcription factor reported previously as the master regulator in SCW formation during fiber development. Our results demonstrate that cell wall-localized GhGLU18 promotes fiber elongation and SCW thickening by degrading callose and enhancing polysaccharide metabolism and cell wall synthesis.

Activation of Gossypium hirsutum ACS6 Facilitates Fiber Development by Improving Sucrose Metabolism and Transport

Cotton fiber yield depends on the density of fiber cell initials that form on the ovule epidermis. Fiber initiation is triggered by MYB-MIXTA-like transcription factors (GhMMLs) and requires a sucrose supply. Ethylene or its precursor ACC (1-aminocyclopropane-1-carboxylic acid) is suggested to affect fiber yield. The Gossypium hirsutum (L.) genome contains 35 ACS genes (GhACS) encoding ACC synthases. Here, we explored the role of a GhACS family member in the regulation of fiber initiation. Expression analyses showed that the GhACS6.3 gene pair was specifically expressed in the ovules during fiber initiation (3 days before anthesis to 5 days post anthesis, -3 to 5 DPA), especially at -3 DPA, whereas other GhACS genes were expressed at very low or undetectable levels. The expression profile of GhACS6.3 during fiber initial development was confirmed by qRT-PCR analysis. Transgenic lines overexpressing GhACS6.3 (GhACS6.3-OE) showed increased ACC accumulation in ovules, which promoted the formation of fiber initials and fiber yield components. This was accompanied by increased transcript levels of GhMML3 and increased transcript levels of genes encoding sucrose transporters and sucrose synthase. These findings imply that GhACS6.3 activation is required for fiber initial development. Our results lay the foundation for further research on increasing cotton fiber production.

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.

Genome-wide analysis and characterization of Dendrocalamus farinosus SUT gene family reveal DfSUT4 involvement in sucrose transportation in plants

Sucrose is the main transported form of photosynthetic products. Sucrose transporter (SUT) participates in the translocation of sucrose from source to sink, which is important for the growth and development of plants. Dendrocalamus farinosus is an important economic crop in southwestern China because of its high growth rate, high fiber content, and dual usage for food and timber, but the mechanism of sucrose transportation in D. farinosus is unclear. In this study, a total of 12 SUT transporter genes were determined in D. farinosus by whole-genome identification. DfSUT2, DfSUT7, and DfSUT11 were homologs of rice OsSUT2, while DfSUT4 was a homolog of OsSUT4, and these four DfSUT genes were expressed in the leaf, internode, node, and bamboo shoots of D. farinosus. In addition, DfSUT family genes were involved in photosynthetic product distribution, ABA/MeJA responses, and drought resistance, especially DfSUT4. The function of DfSUT4 was then verified in Nicotiana tabacum. DfSUT4 was localized mainly in the leaf mesophyll and stem phloem of pDfSUT4::GUS transgenic plant. The overexpression of DfSUT4 gene in transgenic plant showed increases of photosynthetic rate, above-ground biomass, thousand grain weight, and cellulose content. Our findings altogether indicate that DfSUT4 can be a candidate gene that can be involved in phloem sucrose transportation from the source leaves to the sink organs, phytohormone responses, abiotic stress, and fiber formation in plants, which is very important in the genetic improvement of D. farinosus and other crops.

Enhancing crop yields through improvements in the efficiency of photosynthesis and respiration

The rate with which crop yields per hectare increase each year is plateauing at the same time that human population growth and other factors increase food demand. Increasing yield potential (Y p ) of crops is vital to address these challenges. In this review, we explore a component ofY p that has yet to be optimised - that being improvements in the efficiency with which light energy is converted into biomass (ε c ) via modifications to CO2 fixed per unit quantum of light (α), efficiency of respiratory ATP production (ε prod ) and efficiency of ATP use (ε use ). For α, targets include changes in photoprotective machinery, ribulose bisphosphate carboxylase/oxygenase kinetics and photorespiratory pathways. There is also potential forε prod to be increased via targeted changes to the expression of the alternative oxidase and mitochondrial uncoupling pathways. Similarly, there are possibilities to improveε use via changes to the ATP costs of phloem loading, nutrient uptake, futile cycles and/or protein/membrane turnover. Recently developed high-throughput measurements of respiration can serve as a proxy for the cumulative energy cost of these processes. There are thus exciting opportunities to use our growing knowledge of factors influencing the efficiency of photosynthesis and respiration to create a step-change in yield potential of globally important crops.

Retrieving a disrupted gene encoding phospholipase A for fibre enhancement in allotetraploid cultivated cotton

After polyploidization originated from one interspecific hybridization event in Gossypium, Gossypium barbadense evolved to produce extra-long staple fibres than Gossypium hirsutum (Upland cotton), which produces a higher fibre yield. The genomic diversity between G. barbadense and G. hirsutum thus provides a genetic basis for fibre trait variation. Recently, rapid accumulation of gene disruption or deleterious mutation was reported in allotetraploid cotton genomes, with unknown impacts on fibre traits. Here, we identified gene disruptions in allotetraploid G. hirsutum (18.14%) and G. barbadense (17.38%) through comparison with their presumed diploid progenitors. Relative to conserved genes, these disrupted genes exhibited faster evolution rate, lower expression level and altered gene co-expression networks. Within a module regulating fibre elongation, a hub gene experienced gene disruption in G. hirsutum after polyploidization, with a 2-bp deletion in the coding region of GhNPLA1D introducing early termination of translation. This deletion was observed in all of the 34 G. hirsutum landraces and 36 G. hirsutum cultivars, but not in 96% of 57 G. barbadense accessions. Retrieving the disrupted gene GhNPLA1D using its homoeolog GhNPLA1A achieved longer fibre length in G. hirsutum. Further enzyme activity and lipids analysis confirmed that GhNPLA1A encodes a typical phospholipase A and promotes cotton fibre elongation via elevating intracellular levels of linolenic acid and 34:3 phosphatidylinositol. Our work opens a strategy for identifying disrupted genes and retrieving their functions in ways that can provide valuable resources for accelerating fibre trait enhancement in cotton breeding.

Control of root-to-shoot long-distance flow by a key ROS-regulating factor in Arabidopsis

Inter-tissue communication is instrumental to coordinating the whole-body level behaviour for complex multicellular organisms. However, little is known about the regulation of inter-tissue information exchange. Here we carried out genetic screens for root-to-shoot mobile silencing in Arabidopsis plants with a compromised small RNA-mediated gene silencing movement rate and identified radical-induced cell death 1 (RCD1) as a critical regulator of root-shoot communication. RCD1 belongs to a family of poly (ADP-ribose) polymerase proteins, which are highly conserved across land plants. We found that RCD1 coordinates symplastic and apoplastic movement by modulating the sterol level of lipid rafts. The higher superoxide production in rcd1-knockout plants resulted in lower plasmodesmata (PD) frequency and altered PD structure in the symplasm of the hypocotyl cortex. Furthermore, the mutants showed increased lateral area of tracheary pits, which reduced axial movement. Our study highlights a novel mechanism through which root-to-shoot long-distance signalling can be modulated both symplastically and apoplastically.

Data mining of transcriptional biomarkers at different cotton fiber developmental stages

Advancement of the gene expression study provides comprehensive information on pivotal genes at different cotton fiber development stages. For the betterment of cotton fiber yield and their quality, genetic improvement is a major target point for the cotton community. Therefore, various studies were carried out to understand the transcriptional machinery of fiber leading to the detailed integrative as well as innovative study. Through data mining and statistical approaches, we identified and validated the transcriptional biomarkers for staged specific differentiation of fiber. With the unique mapping read matrix of ~ 200 cotton transcriptome data and sequential statistical analysis, we identified several important genes that have a deciding and specific role in fiber cell commitment, initiation and elongation, or secondary cell wall synthesis stage. Based on the importance score and validation analysis, IQ domain 26, Aquaporin, Gibberellin regulated protein, methionine gamma lyase, alpha/beta hydrolases, and HAD-like superfamily have shown the specific and determining role for fiber developmental stages. These genes are represented as transcriptional biomarkers that provide a base for molecular characterization for cotton fiber development which will ultimately determine the high yield.

Sphingolipids at Plasmodesmata: Structural Components and Functional Modulators

Plasmodesmata (PD) are plant-specific channels connecting adjacent cells to mediate intercellular communication of molecules essential for plant development and defense. The typical PD are organized by the close apposition of the plasma membrane (PM), the desmotubule derived from the endoplasmic reticulum (ER), and spoke-like elements linking the two membranes. The plasmodesmal PM (PD-PM) is characterized by the formation of unique microdomains enriched with sphingolipids, sterols, and specific proteins, identified by lipidomics and proteomics. These components modulate PD to adapt to the dynamic changes of developmental processes and environmental stimuli. In this review, we focus on highlighting the functions of sphingolipid species in plasmodesmata, including membrane microdomain organization, architecture transformation, callose deposition and permeability control, and signaling regulation. We also briefly discuss the difference between sphingolipids and sterols, and we propose potential unresolved questions that are of help for further understanding the correspondence between plasmodesmal structure and function.

Sugar conundrum in plant-pathogen interactions: roles of invertase and sugar transporters depend on pathosystems

It has been increasingly recognized that CWIN (cell wall invertase) and sugar transporters including STP (sugar transport protein) and SWEET (sugar will eventually be exported transporters) play important roles in plant-pathogen interactions. However, the information available in the literature comes from diverse systems and often yields contradictory findings and conclusions. To solve this puzzle, we provide here a comprehensive assessment of the topic. Our analyses revealed that the regulation of plant-microbe interactions by CWIN, SWEET, and STP is conditioned by the specific pathosystems involved. The roles of CWINs in plant resistance are largely determined by the lifestyle of pathogens (biotrophs versus necrotrophs or hemibiotrophs), possibly through CWIN-mediated salicylic acid or jasmonic acid signaling and programmed cell death pathways. The up-regulation of SWEETs and STPs may enhance or reduce plant resistance, depending on the cellular sites from which pathogens acquire sugars from the host cells. Finally, plants employ unique mechanisms to defend against viral infection, in part through a sugar-based regulation of plasmodesmatal development or aperture. Our appraisal further calls for attention to be paid to the involvement of microbial sugar metabolism and transport in plant-pathogen interactions, which is an integrated but overlooked component of such interactions.

Cotton phloem loads from the apoplast using a single member of its nine-member sucrose transporter gene family

Phloem loading and transport are fundamental processes for allocating carbon from source organs to sink tissues. Cotton (Gossypium spp.) has a high sink demand for the cellulosic fibers that grow on the seed coat and for the storage reserves in the developing embryo, along with the demands of new growth in the shoots and roots. Addressing how cotton mobilizes resources from source leaves to sink organs provides insight into processes contributing to fiber and seed yield. Plasmodesmata frequencies between companion cells and flanking parenchyma in minor veins are higher than expected for an apoplastic loader, and cotton's close relatedness to Tilia spp. hints at passive loading. Suc was the only canonical transport sugar in leaves and constituted 87% of 14C-labeled photoassimilate being actively transported. [14C]Suc uptake coupled with autoradiography indicated active [14C]Suc accumulation in minor veins, suggesting Suc loading from the apoplast; esculin, a fluorescent Suc analog, did not accumulate in minor veins. Of the nine sucrose transporter (SUT) genes identified per diploid genome, only GhSUT1-L2 showed appreciable expression in mature leaves, and silencing GhSUT1-L2 yielded phenotypes characteristic of blocked phloem transport. Furthermore, only GhSUT1-L2 cDNA stimulated esculin and [14C]Suc uptake into yeast, and only the GhSUT1-L2 promoter caused uidA (β-glucuronidase) reporter gene expression in minor vein phloem of Arabidopsis thaliana. Collectively, these results argue that apoplastic phloem loading mediated by GhSUT1-L2 is the dominant mode of phloem loading in cotton.

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

KEY MESSAGE

Genetic variation in a G. barbadense population was revealed using resquencing. GWAS on G.barbadense population identified several candidate genes associated with fiber strength and lint percentage. Gossypium barbadense is the second-largest cultivated cotton species planted in the world, which is characterized by high fiber quality. Here, we described the global pattern of genetic polymorphisms for 240 G. barbadense accessions based on the whole-genome resequencing. A total of 3,632,231 qualified single-nucleotide polymorphisms (SNPs) and 221,354 insertion-deletions (indels) were obtained. We conducted a genome-wide association study (GWAS) on 12 traits under four environments. Two traits with more stable associated variants, fiber strength and lint percentage, were chosen for further analysis. Three putative candidate genes, HD16 orthology (GB_D11G3437), WDL2 orthology (GB_D11G3460) and TUBA1 orthology (GB_D11G3471), on chromosome D11 were found to be associated with fiber strength, and one gene orthologous to Arabidopsis Receptor-like protein kinase HERK 1 (GB_A07G1034) was predicated to be the candidate gene for the lint percentage improvement. The identified genes may serve as promising targets for genetic engineering to accelerate the breeding process for G. barbadense and the high-density genome variation map constructed in this work may facilitate our understanding of the genetic architecture of cotton traits.

A Tale of Two Domains Pushing Lateral Roots

Successful plant organ development depends on well-coordinated intercellular communication between the cells of the organ itself, as well as with surrounding cells. Intercellular signals often move via the symplasmic pathway using plasmodesmata. Intriguingly, brief periods of symplasmic isolation may also be necessary to promote organ differentiation and functionality. Recent findings suggest that symplasmic isolation of a subset of parental root cells and newly forming lateral root primordia (LRPs) plays a vital role in modulating lateral root development and emergence. In this opinion article we discuss how two symplasmic domains may be simultaneously established within an LRP and its overlying cells, and the significance of plasmodesmata in this process.

Advances about the Roles of Membranes in Cotton Fiber Development

Cotton fiber is an extremely elongated single cell derived from the ovule epidermis and is an ideal model for studying cell development. The plasma membrane is tremendously expanded and accompanied by the coordination of various physiological and biochemical activities on the membrane, one of the three major systems of a eukaryotic cell. This review compiles the recent progress and advances for the roles of the membrane in cotton fiber development: the functions of membrane lipids, especially the fatty acids, sphingolipids, and phytosterols; membrane channels, including aquaporins, the ATP-binding cassette (ABC) transporters, vacuolar invertase, and plasmodesmata; and the regulation mechanism of membrane proteins, such as membrane binding enzymes, annexins, and receptor-like kinases.

Genome-wide association analysis reveals quantitative trait loci and candidate genes involved in yield components under multiple field environments in cotton (Gossypium hirsutum)

BACKGROUND

Numerous quantitative trait loci (QTLs) and candidate genes associated with yield-related traits have been identified in cotton by genome-wide association study (GWAS) analysis. However, most of the phenotypic data were from a single or few environments, and the stable loci remained to be validated under multiple field environments.

RESULTS

Here, 242 upland cotton accessions collected from different origins were continuously investigated for phenotypic data of four main yield components, including boll weight (BW) and lint percentage (LP) under 13 field environments, and boll number per plant (BN) and seed index (SI) under 11 environments. Correlation analysis revealed a positive correlation between BN and LP, BW and SI, while SI had a negative correlation with LP and BN. Genetic analysis indicated that LP had the highest heritability estimates of 94.97%, followed by 92.08% for SI, 86.09% for BW, and 72.92% for BN, indicating LP and SI were more suitable traits for genetic improvement. Based on 56,010 high-quality single nucleotide polymorphisms (SNPs) and GWAS analysis, a total of 95 non-redundant QTLs were identified, including 12 of BN, 23 of BW, 45 of LP, and 33 of SI, respectively. Of them, 10 pairs of homologous QTLs were detected between A and D sub-genomes. We also found that 15 co-located QTLs with more than two traits and 12 high-confidence QTLs were detected under more than six environments, respectively. Further, two NET genes (GH_A08G0716 and GH_A08G0783), located in a novel QTL hotspot (qtl24, qtl25 and qlt26) were predominately expressed in early fiber development stages, exhibited significant correlation with LP and SI. The GH_A07G1389 in the stable qtl19 region encoded a tetratricopeptide repeat (TPR)-like superfamily protein and was a homologous gene involved in short fiber mutant ligon lintless-y (Li_y), implying important roles in cotton yield.

CONCLUSIONS

The present study provides a foundation for understanding the regulatory mechanisms of yield components and may enhance yield improvement through molecular breeding in cotton.

Characterization of cotton ARF factors and the role of GhARF2b in fiber development

BACKGROUND

Cotton fiber is a model system for studying plant cell development. At present, the functions of many transcription factors in cotton fiber development have been elucidated, however, the roles of auxin response factor (ARF) genes in cotton fiber development need be further explored.

RESULTS

Here, we identify auxin response factor (ARF) genes in three cotton species: the tetraploid upland cotton G. hirsutum, which has 73 ARF genes, and its putative extent parental diploids G. arboreum and G. raimondii, which have 36 and 35 ARFs, respectively. Ka and Ks analyses revealed that in G. hirsutum ARF genes have undergone asymmetric evolution in the two subgenomes. The cotton ARFs can be classified into four phylogenetic clades and are actively expressed in young tissues. We demonstrate that GhARF2b, a homolog of the Arabidopsis AtARF2, was preferentially expressed in developing ovules and fibers. Overexpression of GhARF2b by a fiber specific promoter inhibited fiber cell elongation but promoted initiation and, conversely, its downregulation by RNAi resulted in fewer but longer fiber. We show that GhARF2b directly interacts with GhHOX3 and represses the transcriptional activity of GhHOX3 on target genes.

CONCLUSION

Our results uncover an important role of the ARF factor in modulating cotton fiber development at the early stage.

Review: Membrane tethers control plasmodesmal function and formation

Cell-to-cell communication is crucial in coordinating diverse biological processes in multicellular organisms. In plants, communication between adjacent cells occurs via nanotubular passages called plasmodesmata (PD). The PD passage is composed of an appressed endoplasmic reticulum (ER) internally, and plasma membrane (PM) externally, that traverses the cell wall, and associates with the actin-cytoskeleton. The coordination of the ER, PM and cytoskeleton plays a potential role in maintaining the architecture and conductivity of PD. Many data suggest that PD-associated proteins can serve as tethers that connect these structures in a functional PD, to regulate cell-to-cell communication. In this review, we summarize the organization and regulation of PD activity via tethering proteins, and discuss the importance of PD-mediated cell-to-cell communication in plant development and defense against environmental stress.

Intercellular trafficking via plasmodesmata: molecular layers of complexity

Plasmodesmata are intercellular pores connecting together most plant cells. These structures consist of a central constricted form of the endoplasmic reticulum, encircled by some cytoplasmic space, in turn delimited by the plasma membrane, itself ultimately surrounded by the cell wall. The presence and structure of plasmodesmata create multiple routes for intercellular trafficking of a large spectrum of molecules (encompassing RNAs, proteins, hormones and metabolites) and also enable local signalling events. Movement across plasmodesmata is finely controlled in order to balance processes requiring communication with those necessitating symplastic isolation. Here, we describe the identities and roles of the molecular components (specific sets of lipids, proteins and wall polysaccharides) that shape and define plasmodesmata structural and functional domains. We highlight the extensive and dynamic interactions that exist between the plasma/endoplasmic reticulum membranes, cytoplasm and cell wall domains, binding them together to effectively define plasmodesmata shapes and purposes.

The miR319-Targeted GhTCP4 Promotes the Transition from Cell Elongation to Wall Thickening in Cotton Fiber

Plant cell growth involves a complex interplay among cell-wall expansion, biosynthesis, and, in specific tissues, secondary cell wall (SCW) deposition, yet the coordination of these processes remains elusive. Cotton fiber cells are developmentally synchronous, highly elongated, and contain nearly pure cellulose when mature. Here, we report that the transcription factor GhTCP4 plays an important role in balancing cotton fiber cell elongation and wall synthesis. During fiber development the expression of miR319 declines while GhTCP4 transcript levels increase, with high levels of the latter promoting SCW deposition. GhTCP4 interacts with a homeobox-containing factor, GhHOX3, and repressing its transcriptional activity. GhTCP4 and GhHOX3 function antagonistically to regulate cell elongation, thereby establishing temporal control of fiber cell transition to the SCW stage. We found that overexpression of GhTCP4A upregulated and accelerated activation of the SCW biosynthetic pathway in fiber cells, as revealed by transcriptome and promoter activity analyses, resulting in shorter fibers with varied lengths and thicker walls. In contrast, GhTCP4 downregulation led to slightly longer fibers and thinner cell walls. The GhHOX3-GhTCP4 complex may represent a general mechanism of cellular development in plants since both are conserved factors in many species, thus providing us a potential molecular tool for the design of fiber traits.

A cotton NAC transcription factor GhirNAC2 plays positive roles in drought tolerance via regulating ABA biosynthesis

NAC protein is a large plant specific transcription factor family, which plays important roles in the response to abiotic stresses. However, the regulation mechanism of most NAC proteins in drought stress remains to be further uncovered. In this study, we elucidated the molecular functions of a NAC protein, GhirNAC2, in response to drought stress in cotton. GhirNAC2 was greatly induced by drought and phytohormone abscisic acid (ABA). Subcellular localization demonstrated that GhirNAC2 was located in the nucleus. Co-suppression of GhirNAC2 in cotton led to larger stomata aperture, elevated water loss and finally reduced transgenic plants tolerance to drought stress. Furthermore, the endogenous ABA content was significantly lower in GhirNAC2-suppressed transgenic plant leaves compared to wild type. in vivo and in vitro studies showed that GhirNAC2 directly binds to the promoter of GhNCED3a/3c, key genes in ABA biosynthesis, which were both down-regulated in GhirNAC2-suppressed transgenic lines. Transient silencing of GhNCED3a/3c also significantly reduced the resistance to drought stress in cotton plants. However, ectopic expression of GhirNAC2 in tobacco significantly enhanced seed germination, root growth and plant survival under drought stress. Taken together, GhirNAC2 plays a positive role in cotton drought tolerance, which functions by modulating ABA biosynthesis and stomata closure via regulating GhNCED3a/3c expression.

Disequilibrium evolution of the Fructose-1,6-bisphosphatase gene family leads to their functional biodiversity in Gossypium species

Background

Fructose-1,6-bisphosphatase (FBP) is a key enzyme in the plant sucrose synthesis pathway, in the Calvin cycle, and plays an important role in photosynthesis regulation in green plants. However, no systemic analysis of FBPs has been reported in Gossypium species.

Results

A total of 41 FBP genes from four Gossypium species were identified and analyzed. These FBP genes were sorted into two groups and seven subgroups. Results revealed that FBP family genes were under purifying selection pressure that rendered FBP family members as being conserved evolutionarily, and there was no tandem or fragmental DNA duplication in FBP family genes. Collinearity analysis revealed that a FBP gene was located in a translocated DNA fragment and the whole FBP gene family was under disequilibrium evolution that led to a faster evolutionary progress of the members in G. barbadense and in A_t subgenome than those in other Gossypium species and in the D_t subgenome, respectively, in this study. Through RNA-seq analyses and qRT-PCR verification, different FBP genes had diversified biological functions in cotton fiber development (two genes in 0 DPA and 1DPA ovules and four genes in 20–25 DPA fibers), in plant responses to Verticillium wilt onset (two genes) and to salt stress (eight genes).

Conclusion

The FBP gene family displayed a disequilibrium evolution pattern in Gossypium species, which led to diversified functions affecting not only fiber development, but also responses to Verticillium wilt and salt stress. All of these findings provide the foundation for further study of the function of FBP genes in cotton fiber development and in environmental adaptability.

Combined GWAS and eQTL analysis uncovers a genetic regulatory network orchestrating the initiation of secondary cell wall development in cotton

The cotton fibre serves as a valuable experimental system to study cell wall synthesis in plants, but our understanding of the genetic regulation of this process during fibre development remains limited. We performed a genome-wide association study (GWAS) and identified 28 genetic loci associated with fibre quality in allotetraploid cotton. To investigate the regulatory roles of these loci, we sequenced fibre transcriptomes of 251 cotton accessions and identified 15 330 expression quantitative trait loci (eQTL). Analysis of local eQTL and GWAS data prioritised 13 likely causal genes for differential fibre quality in a transcriptome-wide association study (TWAS). Characterisation of distal eQTL revealed unequal genetic regulation patterns between two subgenomes, highlighted by an eQTL hotspot (Hot216) that established a genome-wide genetic network regulating the expression of 962 genes. The primary regulatory role of Hot216, and specifically the gene encoding a KIP-related protein, was found to be the transcriptional regulation of genes responsible for cell wall synthesis, which contributes to fibre length by modulating the developmental transition from rapid cell elongation to secondary cell wall synthesis. This study uncovered the genetic regulation of fibre-cell development and revealed the molecular basis of the temporal modulation of secondary cell wall synthesis during plant cell elongation.

Synchronization of developmental, molecular and metabolic aspects of source-sink interactions

Plants have evolved a multitude of strategies to adjust their growth according to external and internal signals. Interconnected metabolic and phytohormonal signalling networks allow adaption to changing environmental and developmental conditions and ensure the survival of species in fluctuating environments. In agricultural ecosystems, many of these adaptive responses are not required or may even limit crop yield, as they prevent plants from realizing their fullest potential. By lifting source and sink activities to their maximum, massive yield increases can be foreseen, potentially closing the future yield gap resulting from an increasing world population and the transition to a carbon-neutral economy. To do so, a better understanding of the interplay between metabolic and developmental processes is required. In the past, these processes have been tackled independently from each other, but coordinated efforts are required to understand the fine mechanics of source-sink relations and thus optimize crop yield. Here, we describe approaches to design high-yielding crop plants utilizing strategies derived from current metabolic concepts and our understanding of the molecular processes determining sink development.

Interplay between turgor pressure and plasmodesmata during plant development

Plasmodesmata traverse cell walls, generating connections between neighboring cells. They allow intercellular movement of molecules such as transcription factors, hormones, and sugars, and thus create a symplasmic continuity within a tissue. One important factor that determines plasmodesmal permeability is their aperture, which is regulated during developmental and physiological processes. Regulation of aperture has been shown to affect developmental events such as vascular differentiation in the root, initiation of lateral roots, or transition to flowering. Extensive research has unraveled molecular factors involved in the regulation of plasmodesmal permeability. Nevertheless, many plant developmental processes appear to involve feedbacks mediated by mechanical forces, raising the question of whether mechanical forces and plasmodesmal permeability affect each other. Here, we review experimental data on how one of these forces, turgor pressure, and plasmodesmal permeability may mutually influence each other during plant development, and we discuss the questions raised by these data. Addressing such questions will improve our knowledge of how cellular patterns emerge during development, shedding light on the evolution of complex multicellular plants.

Maize Carbohydrate Partitioning Defective33 Encodes an MCTP Protein and Functions in Sucrose Export from Leaves

To sustain plant growth, development, and crop yield, sucrose must be transported from leaves to distant parts of the plant, such as seeds and roots. To identify genes that regulate sucrose accumulation and transport in maize (Zea mays), we isolated carbohydrate partitioning defective33 (cpd33), a recessive mutant that accumulated excess starch and soluble sugars in mature leaves. The cpd33 mutants also exhibited chlorosis in the leaf blades, greatly diminished plant growth, and reduced fertility. Cpd33 encodes a protein containing multiple C2 domains and transmembrane regions. Subcellular localization experiments showed the CPD33 protein localized to plasmodesmata (PD), the plasma membrane, and the endoplasmic reticulum. We also found that a loss-of-function mutant of the CPD33 homolog in Arabidopsis, QUIRKY, had a similar carbohydrate hyperaccumulation phenotype. Radioactively labeled sucrose transport assays showed that sucrose export was significantly lower in cpd33 mutant leaves relative to wild-type leaves. However, PD transport in the adaxial-abaxial direction was unaffected in cpd33 mutant leaves. Intriguingly, transmission electron microscopy revealed fewer PD at the companion cell-sieve element interface in mutant phloem tissue, providing a possible explanation for the reduced sucrose export in mutant leaves. Collectively, our results suggest that CPD33 functions to promote symplastic transport into sieve elements.

Updates on molecular mechanisms in the development of branched trichome in Arabidopsis and nonbranched in cotton

Trichomes are specialized epidermal cells and a vital plant organ that protect plants from various harms and provide valuable resources for plant development and use. Some key genes related to trichomes have been identified in the model plant Arabidopsis thaliana through glabrous mutants and gene cloning, and the hub MYB-bHLH-WD40, consisting of several factors including GLABRA1 (GL1), GL3, TRANSPARENT TESTA GLABRA1 (TTG1), and ENHANCER OF GLABRA3 (EGL3), has been established. Subsequently, some upstream transcription factors, phytohormones and epigenetic modification factors have also been studied in depth. In cotton, a very important fibre and oil crop globally, in addition to the key MYB-like factors, more important regulators and potential molecular mechanisms (e.g. epigenetic modifiers, distinct metabolic pathways) are being exploited during different fibre developmental stages. This occurs due to increased cotton research, resulting in the discovery of more complex regulation mechanisms from the allotetraploid genome of cotton. In addition, some conservative as well as specific mediators are involved in trichome development in other species. This study summarizes molecular mechanisms in trichome development and provides a detailed comparison of the similarities and differences between Arabidopsis and cotton, analyses the possible reasons for the discrepancy in identification of regulators, and raises future questions and foci for understanding trichome development in more detail.

GhbHLH18 negatively regulates fiber strength and length by enhancing lignin biosynthesis in cotton fibers

Cotton fibers are developed epidermal cells of the seed coat and contain large amounts of cellulose and minor lignin-like components. Lignin in the cell walls of cotton fibers effectively provides mechanical strength and is also presumed to restrict fiber elongation and secondary cell wall synthesis. To analyze the effect of lignin and lignin-like phenolics on fiber quality and the transcriptional regulation of lignin synthesis in cotton fibers, we characterized the function of a bHLH transcription factor, GhbHLH18, during fiber elongation stage. GhbHLH18 knock-down plants have longer and stronger fibers, and accumulate less lignin-like phenolics in mature cotton fibers than control plants. By mining public transcriptomic data for developing fibers, we discovered that GhbHLH18 is coexpressed with most lignin synthesis pathway genes. Furthermore, we showed that GhbHLH18 strongly binds to the E-box in the promoter region of GhPER8 and activates its expression. Transient over expression of GhPER8 protein in tobacco leaves significantly decreased the content of coniferyl alcohol and sinapic alcohol-the substrate respectively for G-lignin and S-lignin biosynthesis. These results suggest that GhbHLH18 is negatively associated with fiber quality by activating peroxidase-mediated lignin metabolism, thus the paper represents an alternative strategy to improve fiber quality.

Transcriptome profiling of Gossypium arboreum during fiber initiation and the genome-wide identification of trihelix transcription factors

Cotton fiber initiation is the first step in fiber development, and it determines the yield. Here, genome-wide transcriptome profiling of Gossypium arboreum was performed to determine the molecular basis of cotton fiber initiation. A comparison of the transcriptomes of fiber-bearing ovules at -0.5, 0, 0.5, 1, 1.5, 2, 2.5 and 3 d post-anthesis detected 12,049 differentially expressed genes that mainly participated in ribosome, carbon metabolism and amino acid biosynthesis pathways. Genes encoding alcohol dehydrogenase 1 and hydroxycinnamoyl-CoA shikimate/quinate hydroxycinnamoyl transferase, involving in fatty acid degradation and flavonoid biosynthesis, were enriched. Furthermore, 1049 differentially expressed transcription factors were identified. Among these, 17 were trihelix family transcription factors, which play important roles in plant development and responses to biotic and abiotic stresses. In total, 52 full-length trihelix genes, named as GaGTs, were identified in G. arboreum and located in 12 of the 13 cotton chromosomes. Transcriptomic data and a quantitative real-time PCR analysis indicated that several GaGTs were significantly induced during fiber initiation in G. arboreum. Thus, the genome-wide comprehensive analysis of gene expression in G. arboreum fiber initiation will serve as a useful resource for unraveling the functions of specific genes. The phylogenetic relationships and expression analyses of the G. arboreum trihelix genes established a solid foundation for future comprehensive functional analyses of the GaGTs.

Plasmodesmata-Related Structural and Functional Proteins: The Long Sought-After Secrets of a Cytoplasmic Channel in Plant Cell Walls

Plant cells are separated by cellulose cell walls that impede direct cell-to-cell contact. In order to facilitate intercellular communication, plant cells develop unique cell-wall-spanning structures termed plasmodesmata (PD). PD are membranous channels that link the cytoplasm, plasma membranes, and endoplasmic reticulum of adjacent cells to provide cytoplasmic and membrane continuity for molecular trafficking. PD play important roles for the development and physiology of all plants. The structure and function of PD in the plant cell walls are highly dynamic and tightly regulated. Despite their importance, plasmodesmata are among the few plant cell organelles that remain poorly understood. The molecular properties of PD seem largely elusive or speculative. In this review, we firstly describe the general PD structure and its protein composition. We then discuss the recent progress in identification and characterization of PD-associated plant cell-wall proteins that regulate PD function, with particular emphasis on callose metabolizing and binding proteins, and protein kinases targeted to and around PD.

Sphingolipid biosynthesis modulates plasmodesmal ultrastructure and phloem unloading

During phloem unloading, multiple cell-to-cell transport events move organic substances to the root meristem. Although the primary unloading event from the sieve elements to the phloem pole pericycle has been characterized to some extent, little is known about post-sieve element unloading. Here, we report a novel gene, PHLOEM UNLOADING MODULATOR (PLM), in the absence of which plasmodesmata-mediated symplastic transport through the phloem pole pericycle-endodermis interface is specifically enhanced. Increased unloading is attributable to a defect in the formation of the endoplasmic reticulum-plasma membrane tethers during plasmodesmal morphogenesis, resulting in the majority of pores lacking a visible cytoplasmic sleeve. PLM encodes a putative enzyme required for the biosynthesis of sphingolipids with very-long-chain fatty acid. Taken together, our results indicate that post-sieve element unloading involves sphingolipid metabolism, which affects plasmodesmal ultrastructure. They also raise the question of how and why plasmodesmata with no cytoplasmic sleeve facilitate molecular trafficking.

Modification of phytosterol composition influences cotton fiber cell elongation and secondary cell wall deposition

BACKGROUND

Cotton fiber is a single cell that arises from the epidermis of ovule. It is not only a main economic product of cotton, but an ideal material for studying on the growth and development of plant cell. Our previous study indicated that phytosterol content and the ratio of campesterol to sitosterol fluctuated regularly in cotton fiber development. However, what effects of modified phytosterol content and composition on the growth and development of cotton fiber cell is unknown. In this study, we overexpressed the GhSMT2-1, a cotton homologue of sterol C-24 methyltransferase 2 gene in transgenic upland cotton plants to modify phytosterol content and composition in fiber cells and investigated the changes on fiber elongation and secondary cell wall deposition.

RESULTS

GhSMT2-1 overexpression led to changes of phytosterol content and the ratio of campesterol to sitosterol in fiber cell. At the rapid elongation stage of fiber cell, total phytosterol and sitosterol contents were increased while campesterol content was decreased in transgenic fibers when compared to control fibers. Accordingly, the ratio of campesterol to sitosterol declined strikingly. Simultaneously, the transgenic fibers were shorter and thicker than control fibers. Exogenous application of sitosterol or campesterol separately inhibited control fiber cell elongation in cotton ovule culture system in vitro. In addition, campesterol treatment partially rescued transgenic fiber elongation.

CONCLUSION

These results elucidated that modification of phytosterol content and composition influenced fiber cell elongation and secondary cell wall formation. High sitosterol or low ratio of campesterol to sitosterol suppresses fiber elongation and/or promote secondary cell wall deposition. The roles of sitosterol and campesterol were discussed in fiber cell development. There might be a specific ratio of campesterol to sitosterol in different developmental stage of cotton fibers, in which GhSMT2-1 play an important role. Our study, at a certain degree, provides novel insights into the regulatory mechanisms of fiber cell development.

Cell Wall Invertase and Sugar Transporters Are Differentially Activated in Tomato Styles and Ovaries During Pollination and Fertilization

Flowering plants depend on pollination and fertilization to activate the transition from ovule to seed and ovary to fruit, namely seed and fruit set, which are key for completing the plant life cycle and realizing crop yield potential. These processes are highly energy consuming and rely on the efficient use of sucrose as the major nutrient and energy source. However, it remains elusive as how sucrose imported into and utilizated within the female reproductive organ is regulated in response to pollination and fertilization. Here, we explored this issue in tomato by focusing on genes encoding cell wall invertase (CWIN) and sugar transporters, which are major players in sucrose phloem unloading, and sink development. The transcript level of a major CWIN gene, LIN5, and CWIN activity were significantly increased in style at 4 h after pollination (HAP) in comparison with that in the non-pollination control, and this was sustained at 2 days after pollination (DAP). In the ovaries, however, CWIN activity and LIN5 expression did not increase until 2 DAP when fertilization occurred. Interestingly, a CWIN inhibitor gene INVINH1 was repressed in the pollinated style at 2 DAP. In response to pollination, the style exhibited increased expressions of genes encoding hexose transporters, SlHT1, 2, SlSWEET5b, and sucrose transporters SlSUT1, 2, and 4 from 4 HAP to 2 DAP. Upon fertilization, SlSUT1 and SlHT1 and 2, but not SlSWEETs, were also stimulated in fruitlets at 2 DAP. Together, the findings reveal that styles respond promptly and more broadly to pollination for activation of CWIN and sugar transporters to fuel pollen tube elongation, whereas the ovaries do not exhibit activation for some of these genes until fertilization occurs.

HIGHLIGHTS

Expression of genes encoding cell wall invertases and sugar transporters was stimulated in pollinated style and fertilized ovaries in tomato.

Cotton fiber elongation requires the transcription factor GhMYB212 to regulate sucrose transportation into expanding fibers

Cotton is white gold across the globe and composed of fiber cells derived from the outer integument of cotton ovules. Fiber elongation uses sucrose as a direct carbon source. The molecular mechanism transcriptionally controlling sucrose transport from ovules into the elongating fibers remains elusive. In this study the involvement of GhMYB212 in the regulation of sucrose transportion into expanding fibers was investigated. GhMYB212 RNAi plants (GhMYB212i) accumulated less sucrose and glucose in developing fibers, and had shorter fibers and a lower lint index. RNA-seq and protein-DNA binding assays revealed that GhMYB212 was closely linked to the pathways of sucrose and starch transportation and metabolism, directly controling the expression of a sucrose transporter gene GhSWEET12. GhSWEET12 RNAi plants (GhSWEET12i) possessed similar fiber phenotypes to those of GhMYB212i. Exogenous sucrose supplementation in ovule cultures did not rescue the shorter fiber phenotype of GhMYB212i and GhSWEET12i. This finding supported the idea that the attenuated rate of sucrose transport from the outer seed coat into the fibers is responsible for the retardation of fiber elongation. Current investigations support the idea that GhMYB212 functions as the main regulator of fiber elongation by controlling the expression of GhSWEET12, and therefore it is important to study cell expansion and sugar transportation during seed development.

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

Allotetraploid cotton is an economically important natural-fiber-producing crop worldwide. After polyploidization, Gossypium hirsutum L. evolved to produce a higher fiber yield and to better survive harsh environments than Gossypium barbadense, which produces superior-quality fibers. The global genetic and molecular bases for these interspecies divergences were unknown. Here we report high-quality de novo-assembled genomes for these two cultivated allotetraploid species with pronounced improvement in repetitive-DNA-enriched centromeric regions. Whole-genome comparative analyses revealed that species-specific alterations in gene expression, structural variations and expanded gene families were responsible for speciation and the evolutionary history of these species. These findings help to elucidate the evolution of cotton genomes and their domestication history. The information generated not only should enable breeders to improve fiber quality and resilience to ever-changing environmental conditions but also can be translated to other crops for better understanding of their domestication history and use in improvement.

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

Allotetraploid cotton is an economically important natural-fiber-producing crop worldwide. After polyploidization, Gossypium hirsutum L. evolved to produce a higher fiber yield and to better survive harsh environments than Gossypium barbadense, which produces superior-quality fibers. The global genetic and molecular bases for these interspecies divergences were unknown. Here we report high-quality de novo-assembled genomes for these two cultivated allotetraploid species with pronounced improvement in repetitive-DNA-enriched centromeric regions. Whole-genome comparative analyses revealed that species-specific alterations in gene expression, structural variations and expanded gene families were responsible for speciation and the evolutionary history of these species. These findings help to elucidate the evolution of cotton genomes and their domestication history. The information generated not only should enable breeders to improve fiber quality and resilience to ever-changing environmental conditions but also can be translated to other crops for better understanding of their domestication history and use in improvement.

Callose balancing at plasmodesmata

In plants, communication and molecular exchanges between different cells and tissues are dependent on the apoplastic and symplastic pathways. Symplastic molecular exchanges take place through the plasmodesmata, which connect the cytoplasm of neighboring cells in a highly controlled manner. Callose, a β-1,3-glucan polysaccharide, is a plasmodesmal marker molecule that is deposited in cell walls near the neck zone of plasmodesmata and controls their permeability. During cell differentiation and plant development, and in response to diverse stresses, the level of callose in plasmodesmata is highly regulated by two antagonistic enzymes, callose synthase or glucan synthase-like and β-1,3-glucanase. The diverse modes of regulation by callose synthase and β-1,3-glucanase have been uncovered in the past decades through biochemical, molecular, genetic, and omics methods. This review highlights recent findings regarding the function of plasmodesmal callose and the molecular players involved in callose metabolism, and provides new insight into the mechanisms maintaining plasmodesmal callose homeostasis.

Molecular Evolution and Stress and Phytohormone Responsiveness of SUT Genes in Gossypium hirsutum

Sucrose transporters (SUTs) play key roles in allocating the translocation of assimilates from source to sink tissues. Although the characteristics and biological roles of SUTs have been intensively investigated in higher plants, this gene family has not been functionally characterized in cotton. In this study, we performed a comprehensive analysis of SUT genes in the tetraploid cotton Gossypium hirsutum. A total of 18 G. hirsutum SUT genes were identified and classified into three groups based on their evolutionary relationships. Up to eight SUT genes in G. hirsutum were placed in the dicot-specific SUT1 group, while four and six SUT genes were, respectively, clustered into SUT4 and SUT2 groups together with members from both dicot and monocot species. The G. hirsutum SUT genes within the same group displayed similar exon/intron characteristics, and homologous genes in G. hirsutum At and Dt subgenomes, G. arboreum, and G. raimondii exhibited one-to-one relationships. Additionally, the duplicated genes in the diploid and polyploid cotton species have evolved through purifying selection, suggesting the strong conservation of SUT loci in these species. Expression analysis in different tissues indicated that SUT genes might play significant roles in cotton fiber elongation. Moreover, analyses of cis-acting regulatory elements in promoter regions and expression profiling under different abiotic stress and exogenous phytohormone treatments implied that SUT genes, especially GhSUT6A/D, might participate in plant responses to diverse abiotic stresses and phytohormones. Our findings provide valuable information for future studies on the evolution and function of SUT genes in cotton.

Evolution and Stress Responses of Gossypium hirsutum SWEET Genes

The SWEET (sugars will eventually be exported transporters) proteins are sugar efflux transporters containing the MtN3_saliva domain, which affects plant development as well as responses to biotic and abiotic stresses. These proteins have not been functionally characterized in the tetraploid cotton, Gossypium hirsutum, which is a widely cultivated cotton species. In this study, we comprehensively analyzed the cotton SWEET gene family. A total of 55 putative G. hirsutumSWEET genes were identified. The GhSWEET genes were classified into four clades based on a phylogenetic analysis and on the examination of gene structural features. Moreover, chromosomal localization and an analysis of homologous genes in Gossypium arboreum, Gossypium raimondii, and G. hirsutum suggested that a whole-genome duplication, several tandem duplications, and a polyploidy event contributed to the expansion of the cotton SWEET gene family, especially in Clade III and IV. Analyses of cis-acting regulatory elements in the promoter regions, expression profiles, and artificial selection revealed that the GhSWEET genes were likely involved in cotton developmental processes and responses to diverse stresses. These findings may clarify the evolution of G. hirsutum SWEET gene family and may provide a foundation for future functional studies of SWEET proteins regarding cotton development and responses to abiotic stresses.