Identification and profiling of upland cotton microRNAs at fiber initiation stage under exogenous IAA application

Genome-Wide Identification of the TGA Gene Family and Expression Analysis under Drought Stress in Brassica napus L

TGA transcription factors belong to Group D of the bZIP transcription factors family and play vital roles in the stress response of plants. Brassica napus is an oil crop with rich economic value. However, a systematic analysis of TGA gene family members in B. napus has not yet been reported. In this study, we identified 39 full-length TGA genes in B. napus, renamed TGA1~TGA39. Thirty-nine BnTGA genes were distributed on 18 chromosomes, mainly located in the nucleus, and differences were observed in their 3D structures. Phylogenetic analysis showed that 39 BnTGA genes could be divided into five groups. The BnTGA genes in the same group had similar structure and motif compositions, and all the BnTGA genes had the same conserved bZIP and DOG1 domains. Phylogenetic and synteny analysis showed that the BnTGA genes had a close genetic relationship with the TGA genes of the Brassica juncea, and BnTGA11 and BnTGA29 may play an important role in evolution. In addition, qRT-PCR revealed that three genes (BnTGA14/17/23) showed significant changes in eight experimental materials after drought treatment. Meanwhile, it can be inferred from the results of drought treatment on different varieties of rapeseed that the stress tolerance of parental rapeseed can be transmitted to the offspring through hybridization. In short, these findings have promoted the understanding of the B. napus TGA gene family and will contribute to future research aimed at B. napus resistant breeding.

Decoding drought resilience: a comprehensive exploration of the cotton Eceriferum (CER) gene family and its role in stress adaptation

BACKGROUND

The cuticular wax serves as a primary barrier that protects plants from environmental stresses. The Eceriferum (CER) gene family is associated with wax production and stress resistance.

RESULTS

In a genome-wide identification study, a total of 52 members of the CER family were discovered in four Gossypium species: G. arboreum, G. barbadense, G. raimondii, and G. hirsutum. There were variations in the physicochemical characteristics of the Gossypium CER (GCER) proteins. Evolutionary analysis classified the identified GCERs into five groups, with purifying selection emerging as the primary evolutionary force. Gene structure analysis revealed that the number of conserved motifs ranged from 1 to 15, and the number of exons varied from 3 to 13. Closely related GCERs exhibited similar conserved motifs and gene structures. Analyses of chromosomal positions, selection pressure, and collinearity revealed numerous fragment duplications in the GCER genes. Additionally, nine putative ghr-miRNAs targeting seven G. hirsutum CER (GhCER) genes were identified. Among them, three miRNAs, including ghr-miR394, ghr-miR414d, and ghr-miR414f, targeted GhCER09A, representing the most targeted gene. The prediction of transcription factors (TFs) and the visualization of the regulatory TF network revealed interactions with GhCER genes involving ERF, MYB, Dof, bHLH, and bZIP. Analysis of cis-regulatory elements suggests potential associations between the CER gene family of cotton and responses to abiotic stress, light, and other biological processes. Enrichment analysis demonstrated a robust correlation between GhCER genes and pathways associated with cutin biosynthesis, fatty acid biosynthesis, wax production, and stress response. Localization analysis showed that most GCER proteins are localized in the plasma membrane. Transcriptome and quantitative reverse transcription-polymerase chain reaction (qRT-PCR) expression assessments demonstrated that several GhCER genes, including GhCER15D, GhCER04A, GhCER06A, and GhCER12D, exhibited elevated expression levels in response to water deficiency stress compared to control conditions. The functional identification through virus-induced gene silencing (VIGS) highlighted the pivotal role of the GhCER04A gene in enhancing drought resistance by promoting increased tissue water retention.

CONCLUSIONS

This investigation not only provides valuable evidence but also offers novel insights that contribute to a deeper understanding of the roles of GhCER genes in cotton, their role in adaptation to drought and other abiotic stress and their potential applications for cotton improvement.

Research on Coix seed as a food and medicinal resource, it's chemical components and their pharmacological activities: A review

ETHNOPHARMACOLOGICAL RELEVANCE

Coix lacryma-jobi var. ma-yuen (Romanet du Caillaud) Stapf is a plant of the genus Coix in the Gramineae family. Coix seed is cultivated in various regions throughout China. In recent years, with the research on the medicinal value of Coix seed, it has received more and more widespread attention from people. Numerous pharmacological effects of Coix seed have been demonstrated through modern pharmacological studies, such as hypoglycemia, improving liver function, anti-tumor, regulating intestinal microbiota, improving spleen function, and anti-inflammatory effects.

AIMS OF THE STUDY

This article is a literature review. In recent years, despite the extensive research on Coix seed, there has yet to be a comprehensive review of its traditional usage, medicinal resources, chemical components, and pharmacological effects is still lacking. To fill this gap, the paper provides an overview of the latest research progress on Coix seed, aiming to offer guidance and references for its further development and comprehensive utilization.

MATERIAL AND METHODS

To gather information on the traditional usage, phytochemical ingredients, and pharmacological properties of Coix seed, we conducted a literature search using both Chinese and English languages in five databases: PubMed, Web of Science, China National Knowledge Infrastructure (CNKI), and Springer.

RESULTS

This article is a literature review. The chemical constituents of Coix seed include various fatty acids, esters, polysaccharides, sterols, alkaloids, triterpenes, tocopherols, lactams, lignans, phenols, flavonoids and other constituents. Modern pharmacological research has indeed shown that Coix seed has many pharmacological effects and is a natural anti-tumor drug. In addition to its anti-tumor effect, it also has pharmacological effects such as hypoglycemia, improving liver function, regulating intestinal microbiota, improving spleen function, and anti-inflammatory effects.

CONCLUSIONS

This article provides a brief overview of the traditional uses, biotechnological applications, chemical components, and pharmacological effects of Coix seed. It highlights the importance of establishing quality standards, discovering new active ingredients, and exploring pharmacological mechanisms in Coix seed research. The article also emphasizes the significance of clinical trials, toxicology studies, pharmacokinetics data, and multidisciplinary collaboration for further advancements in this field. Overall, it aims to enhance understanding of Coix seed and its potential in pharmaceutical development and wellness products.

Analysis of WAK Genes in Nine Cruciferous Species with a Focus on Brassica napus L

The wall-associated kinase family contributes to plant cell elongation and pathogen recognition. Nine Cruciferous species were studied for identification and molecular evolution of the WAK gene family. Firstly, 178 WAK genes were identified. A phylogenetic tree was constructed of the Cruciferous WAK proteins into four categories, of which the Brassica rapa, Brassica oleracea and Brassica napus genes in the U's triangle were more closely related. The WAK gene family was unevenly distributed in B. napus chromosomal imaging, with the largest number of BnWAK genes located on chromosome C08. In the expression analysis, the expression patterns of the WAK gene family varied under different stress treatments, and some members of BnWAKs were significantly different under stress treatments. This study lays a foundation for further revealing the functional mechanisms of the WAK gene family in Brassica napus.

Advances in understanding epigenetic regulation of plant trichome development: a comprehensive review

Plant growth and development are controlled by a complex gene regulatory network, which is currently a focal point of research. It has been established that epigenetic factors play a crucial role in plant growth. Trichomes, specialized appendages that arise from epidermal cells, are of great significance in plant growth and development. As a model system for studying plant development, trichomes possess both commercial and research value. Epigenetic regulation has only recently been implicated in the development of trichomes in a limited number of studies, and microRNA-mediated post-transcriptional regulation appears to dominate in this context. In light of this, we have conducted a review that explores the interplay between epigenetic regulations and the formation of plant trichomes, building upon existing knowledge of hormones and transcription factors in trichome development. Through this review, we aim to deepen our understanding of the regulatory mechanisms underlying trichome formation and shed light on future avenues of research in the field of epigenetics as it pertains to epidermal hair growth.

Role of Actin Dynamics and GhACTIN1 Gene in Cotton Fiber Development: A Prototypical Cell for Study

Cotton crop is considered valuable for its fiber and seed oil. Cotton fiber is a single-celled outgrowth from the ovule epidermis, and it is a very dynamic cell for study. It has four distinct but overlapping developmental stages: initiation, elongation, secondary cell wall synthesis, and maturation. Among the various qualitative characteristics of cotton fiber, the important ones are the cotton fiber staple length, tensile strength, micronaire values, and fiber maturity. Actin dynamics are known to play an important role in fiber elongation and maturation. The current review gives an insight into the cotton fiber developmental stages, the qualitative traits associated with cotton fiber, and the set of genes involved in regulating these developmental stages and fiber traits. This review also highlights some prospects for how biotechnological approaches can improve cotton fiber quality.

Fine mapping and candidate gene analysis of qFL-A12-5: a fiber length-related QTL introgressed from Gossypium barbadense into Gossypium hirsutum

The fiber length-related qFL-A12-5 identified in CSSLs introgressed from Gossypium barbadense into Gossypium hirsutum was fine-mapped to an 18.8 kb region on chromosome A12, leading to the identification of the GhTPR gene as a potential regulator of cotton fiber length. Fiber length is a key determinant of fiber quality in cotton, and it is a key target of artificial selection for breeding and domestication. Although many fiber length-related quantitative trait loci have been identified, there are few reports on their fine mapping or candidate gene validation, thus hampering efforts to understand the mechanistic basis of cotton fiber development. Our previous study identified the qFL-A12-5 associated with superior fiber quality on chromosome A12 in the chromosome segment substitution line (CSSL) MBI7747 (BC₄F_3:5). A single segment substitution line (CSSL-106) screened from BC₆F₂ was backcrossed to construct a larger segregation population with its recurrent parent CCRI45, thus enabling the fine mapping of 2852 BC₇F₂ individuals using denser simple sequence repeat markers to narrow the qFL-A12-5 to an 18.8 kb region of the genome, in which six annotated genes were identified in Gossypium hirsutum. Quantitative real-time PCR and comparative analyses led to the identification of GH_A12G2192 (GhTPR) encoding a tetratricopeptide repeat-like superfamily protein as a promising candidate gene for qFL-A12-5. A comparative analysis of the protein-coding regions of GhTPR among Hai1, MBI7747, and CCRI45 revealed two non-synonymous mutations. The overexpression of GhTPR resulted in longer roots in Arabidopsis, suggesting that GhTPR may regulate cotton fiber development. These results provide a foundation for future efforts to improve cotton fiber length.

Potential Roles of 1-Aminocyclopropane-1-carboxylic Acid Synthase Genes in the Response of Gossypium Species to Abiotic Stress by Genome-Wide Identification and Expression Analysis

Ethylene plays a pivotal role in plant stress resistance and 1-aminocyclopropane-1-carboxylic acid synthase (ACS) is the rate-limiting enzyme in ethylene biosynthesis. Upland cotton (Gossypium hirsutum L.) is the most important natural fiber crop, but the function of ACS in response to abiotic stress has rarely been reported in this plant. We identified 18 GaACS, 18 GrACS, and 35 GhACS genes in Gossypiumarboreum, Gossypium raimondii and Gossypiumhirsutum, respectively, that were classified as types I, II, III, or IV. Collinearity analysis showed that the GhACS genes were expanded from diploid cotton by the whole-genome-duplication. Multiple alignments showed that the C-terminals of the GhACS proteins were conserved, whereas the N-terminals of GhACS10 and GhACS12 were different from the N-terminals of AtACS10 and AtACS12, probably diverging during evolution. Most type II ACS genes were hardly expressed, whereas GhACS10/GhACS12 were expressed in many tissues and in response to abiotic stress; for example, they were highly and hardly expressed at the early stages of cold and heat exposure, respectively. The GhACS genes showed different expression profiles in response to cold, heat, drought, and salt stress by quantitative PCR analysis, which indicate the potential roles of them when encountering the various adverse conditions, and provide insights into GhACS functions in cotton’s adaptation to abiotic stress.

Genome wide study of cysteine rich receptor like proteins in Gossypium sp

Cysteine-rich receptor-like-kinases (CRKs), a transmembrane subfamily of receptor-like kinase, play crucial roles in plant adaptation. As such cotton is the major source of fiber for the textile industry, but environmental stresses are limiting its growth and production. Here, we have performed a deep computational analysis of CRKs in five Gossypium species, including G. arboreum (60 genes), G. raimondii (74 genes), G. herbaceum (65 genes), G. hirsutum (118 genes), and G. barbadense (120 genes). All identified CRKs were classified into 11 major classes and 43 subclasses with the finding of several novel CRK-associated domains including ALMT, FUSC_2, Cript, FYVE, and Pkinase. Of these, DUF26_DUF26_Pkinase_Tyr was common and had elevated expression under different biotic and abiotic stresses. Moreover, the 35 land plants comparison identified several new CRKs domain-architectures. Likewise, several SNPs and InDels were observed in CLCuD resistant G. hirsutum. The miRNA target side prediction and their expression profiling in different tissues predicted miR172 as a major CRK regulating miR. The expression profiling of CRKs identified multiple clusters with co-expression under certain stress conditions. The expression analysis under CLCuD highlighted the role of GhCRK057, GhCRK059, GhCRK058, and GhCRK081 in resistant accession. Overall, these results provided primary data for future potential functional analysis as well as a reference study for other agronomically important crops.

RNA-Seq with a novel glabrous-ZM24fl reveals some key lncRNAs and the associated targets in fiber initiation of cotton

BACKGROUND

Cotton fiber is an important natural resource for textile industry and an excellent model for cell biology study. Application of glabrous mutant cotton and high-throughput sequencing facilitates the identification of key genes and pathways for fiber development and cell differentiation and elongation. LncRNA is a type of ncRNA with more than 200 nt in length and functions in the ways of chromatin modification, transcriptional and post-transcriptional modification, and so on. However, the detailed lncRNA and associated mechanisms for fiber initiation are still unclear in cotton.

RESULTS

In this study, we used a novel glabrous mutant ZM24fl, which is endowed with higher somatic embryogenesis, and functions as an ideal receptor for cotton genetic transformation. Combined with the high-throughput sequencing, fatty acid pathway and some transcription factors such as MYB, ERF and bHLH families were identified the important roles in fiber initiation; furthermore, 3,288 lncRNAs were identified, and some differentially expressed lncRNAs were also analyzed. From the comparisons of ZM24_0 DPA vs ZM24_-2 DPA and fl_0 DPA vs ZM24_0 DPA, one common lncRNA MSTRG 2723.1 was found that function upstream of fatty acid metabolism, MBY25-mediating pathway, and pectin metabolism to regulate fiber initiation. In addition, other lncRNAs MSTRG 3390.1, MSTRG 48719.1, and MSTRG 31176.1 were also showed potential important roles in fiber development; and the co-expression analysis between lncRNAs and targets showed the distinct models of different lncRNAs and complicated interaction between lncRNAs in fiber development of cotton.

CONCLUSIONS

From the above results, a key lncRNA MSTRG 2723.1 was identified that might mediate some key genes transcription of fatty acid metabolism, MYB25-mediating pathway, and pectin metabolism to regulate fiber initiation of ZM24 cultivar. Co-expression analysis implied that some other important lncRNAs (e.g., MSTRG 3390.1, MSTRG 48719.1, and MSTRG 31176.1) were also showed the different regulatory model and interaction between them, which proposes some valuable clues for the lncRNAs associated mechanisms in fiber development.

Genome-wide identification and analysis of Oleosin gene family in four cotton species and its involvement in oil accumulation and germination

BACKGROUND

Cotton is not only a major textile fiber crop but also a vital oilseed, industrial, and forage crop. Oleosins are the structural proteins of oil bodies, influencing their size and the oil content in seeds. In addition, the degradation of oleosins is involved in the mobilization of lipid and oil bodies during seed germination. However, comprehensive identification and the systematic analysis of the Oleosin gene (OLEOs) family have not been conducted in cotton.

RESULTS

An in-depth analysis has enabled us to identify 25 and 24 OLEOs in tetraploid cotton species G. hirsutum and G. barbadense, respectively, while 12 and 13 OLEOs were identified in diploid species G. arboreum and G. raimondii, respectively. The 74 OLEOs were further clustered into three lineages according to the phylogenetic tree. Synteny analysis revealed that most of the OLEOs were conserved and that WGD or segmental duplications might drive their expansion. The transmembrane helices in GhOLEO proteins were predicted, and three transmembrane models were summarized, in which two were newly proposed. A total of 24 candidate miRNAs targeting GhOLEOs were predicted. Three highly expressed oil-related OLEOs, GH_A07G0501 (SL), GH_D10G0941 (SH), and GH_D01G1686 (U), were cloned, and their subcellular localization and function were analyzed. Their overexpression in Arabidopsis increased seed oil content and decreased seed germination rates.

CONCLUSION

We identified OLEO gene family in four cotton species and performed comparative analyses of their relationships, conserved structure, synteny, and gene duplication. The subcellular localization and function of three highly expressed oil-related OLEOs were detected. These results lay the foundation for further functional characterization of OLEOs and improving seed oil content.

The emerging role of small RNAs in ovule development, a kind of magic

In plants, small RNAs have been recognized as key genetic and epigenetic regulators of development. Small RNAs are usually 20 to 30 nucleotides in length and they control, in a sequence specific manner, the transcriptional or post-transcriptional expression of genes. In this review, we present a comprehensive overview of the most recent findings about the function of small RNAs in ovule development, including megasporogenesis and megagametogenesis, both in sexual and apomictic plants. We discuss recent studies on the role of miRNAs, siRNAs and trans-acting RNAs (ta-siRNAs) in early female germline differentiation. The mechanistic complexity and unique regulatory features are reviewed, and possible directions for future research are provided.

GhGASA10-1 promotes the cell elongation in fiber development through the phytohormones IAA-induced

BACKGROUND

Cotton is an important cash crop. The fiber length has always been a hot spot, but multi-factor control of fiber quality makes it complex to understand its genetic basis. Previous reports suggested that OsGASR9 promotes germination, width, and thickness by GAs in rice, while the overexpression of AtGASA10 leads to reduced silique length, which is likely to reduce cell wall expansion. Therefore, this study aimed to explore the function of GhGASA10 in cotton fibers development.

RESULTS

To explore the molecular mechanisms underlying fiber elongation regulation concerning GhGASA10-1, we revealed an evolutionary basis, gene structure, and expression. Our results emphasized the conservative nature of GASA family with its origin in lower fern plants S. moellendorffii. GhGASA10-1 was localized in the cell membrane, which may synthesize and transport secreted proteins to the cell wall. Besides, GhGASA10-1 promoted seedling germination and root extension in transgenic Arabidopsis, indicating that GhGASA10-1 promotes cell elongation. Interestingly, GhGASA10-1 was upregulated by IAA at fiber elongation stages.

CONCLUSION

We propose that GhGASA10-1 may promote fiber elongation by regulating the synthesis of cellulose induced by IAA, to lay the foundation for future research on the regulation networks of GASA10-1 in cotton fiber development.

Profiling of MicroRNAs Involved in Mepiquat Chloride-Mediated Inhibition of Internode Elongation in Cotton (Gossypium hirsutum L.) Seedlings

Mepiquat chloride (MC) is the most important plant growth retardant that is widely used in cotton (Gossypium hirsutum L.) production to suppress excessive vegetative growth and improve plant architecture. MicroRNAs (miRNAs) are important gene expression regulators that control plant growth and development. However, miRNA-mediated post-transcriptional regulation in MC-induced growth inhibition remains unclear. In this study, the dynamic expression profiles of miRNAs responsive to MC in cotton internodes were investigated. A total of 508 known miRNAs belonging to 197 families and five novel miRNAs were identified. Among them, 104 miRNAs were differentially expressed at 48, 72, or 96 h post MC treatment compared with the control (0 h); majority of them were highly conserved miRNAs. The number of differentially expressed miRNAs increased with time after treatment. The expression of 14 known miRNAs was continuously suppressed, whereas 12 known miRNAs and one novel miRNA were continuously induced by MC. The expression patterns of the nine differentially expressed miRNAs were verified using qRT-PCR. The targets of the known and novel miRNAs were predicted. Four conserved and six novel targets were validated using the RLM-5' RACE assay. This study revealed that miRNAs play crucial regulatory roles in the MC-induced inhibition of internode elongation. It can improve our understanding of post-transcriptional gene regulation in MC-mediated growth inhibition and could potentially facilitate the breeding of dwarf cotton.

Emerging Connections between Small RNAs and Phytohormones

Small RNAs (sRNAs), mainly including miRNAs and siRNAs, are ubiquitous in eukaryotes. sRNAs mostly negatively regulate gene expression via (post-)transcriptional gene silencing through DNA methylation, mRNA cleavage, or translation inhibition. The mechanisms of sRNA biogenesis and function in diverse biological processes, as well as the interactions between sRNAs and environmental factors, like (a)biotic stress, have been deeply explored. Phytohormones are central in the plant's response to stress, and multiple recent studies highlight an emerging role for sRNAs in the direct response to, or the regulation of, plant hormonal pathways. In this review, we discuss recent progress on the unraveling of crossregulation between sRNAs and nine plant hormones.

Investigation of the EIL/EIN3 Transcription Factor Gene Family Members and Their Expression Levels in the Early Stage of Cotton Fiber Development

The ethylene-insensitive3-like/ethylene-insensitive3 (EIL/EIN3) protein family can serve as a crucial factor for plant growth and development under diverse environmental conditions. EIL/EIN3 protein is a form of a localized nuclear protein with DNA-binding activity that potentially contributes to the intricate network of primary and secondary metabolic pathways of plants. In light of recent research advances, next-generation sequencing (NGS) and novel bioinformatics tools have provided significant breakthroughs in the study of the EIL/EIN3 protein family in cotton. In turn, this paved the way to identifying and characterizing the EIL/EIN3 protein family. Hence, the high-throughput, rapid, and cost-effective meta sequence analyses have led to a remarkable understanding of protein families in addition to the discovery of novel genes, enzymes, metabolites, and other biomolecules of the higher plants. Therefore, this work highlights the recent advance in the genomic-sequencing analysis of higher plants, which has provided a plethora of function profiles of the EIL/EIN3 protein family. The regulatory role and crosstalk of different metabolic pathways, which are apparently affected by these transcription factor proteins in one way or another, are also discussed. The ethylene hormone plays an important role in the regulation of reactive oxygen species in plants under various environmental stress circumstances. EIL/EIN3 proteins are the key ethylene-signaling regulators and play important roles in promoting cotton fiber developmental stages. However, the function of EIL/EIN3 during initiation and early elongation stages of cotton fiber development has not yet been fully understood. The results provided valuable information on cotton EIL/EIN3 proteins, as well as a new vision into the evolutionary relationships of this gene family in cotton species.