The KNOXI Transcription Factor SHOOT MERISTEMLESS Regulates Floral Fate in Arabidopsis

Identification of the KNOX Gene Family in Salvia miltiorrhiza Revealing Its Response Characteristics to Salt Stress

Salvia miltiorrhiza is a herbaceous plant that possesses significant medicinal value. Land salinization affects the growth of S. miltiorrhiza, resulting in a decline in its quality and yield. Knotted1-like homeobox (KNOX) genes are transcription factors that play important roles in plant growth and abiotic stress. The characteristics and functions of KNOX genes in S. miltiorrhiza remain unclear. Here, we identified ten KNOX genes in S. miltiorrhiza, all of which possess the characteristic four domains: KNOX1, KNOX2, ELK, and HD. These SmKNOXs were divided into two groups together with homologous genes. Cis-acting element analysis indicated all SmKNOXs contained elements associated with phytohormone, light, and stress response. The SmKNOXs show tissue-specific expression among roots, stems, leaves, and flowers. We assessed the response of the SmKNOXs to salt stress using quantitative RT-PCR analysis. Notably, SmKNOX4 expression significantly decreased within 24 h of salt exposure, while SmKNOX1, SmKNOX2, SmKNOX3, SmKNOX8, and SmKNOX9 showed significant increases. The expression of SmKNOX1, SmKNOX2, and SmKNOX3 was significantly positively correlated with that of their target genes, GA20ox1 and S11 MYB. These findings suggest that SmKNOXs and their target genes respond to salt stress, providing a foundation for studies of SmKNOXs and the potential genetic improvement of S. miltiorrhiza.

Single-cell transcriptomic analysis of flowering regulation and vernalization in Chinese cabbage shoot apex

In Chinese cabbage development the interplay between shoot apex activity and vernalization is pivotal for flowering timing. The intricate relationship between various cell types in the shoot apex meristem and their roles in regulating flowering gene expression in Chinese cabbage is not yet fully understood. A thorough analysis of single-cell types in the Chinese cabbage shoot apex and their influence on flowering genes and vernalization is essential for deeper insight. Our study first established a single-cell transcriptomic atlas of Chinese cabbage after 25 days of non-vernalization. Analyzing 19 602 single cells, we differentiated them into 15 distinct cell clusters using established marker genes. We found that key genes in shoot apex development and flowering were primarily present in shoot meristematic cells (SMCs), companion cells (CCs), and mesophyll cells (MCs). MADS-box protein FLOWERING LOCUS C 2 (BrFLC2), a gene suppressing flowering, was observed in CCs, mirroring patterns found in Arabidopsis. By mapping developmental trajectories of SMCs, CCs, and MCs, we elucidated the evolutionary pathways of crucial genes in shoot apex development and flowering. The creation of a single-cell transcriptional atlas of the Chinese cabbage shoot apex under vernalization revealed distinct alterations in the expression of known flowering genes, such as VERNALIZATION INSENSITIVE 3 (VIN3), VERNALIZATION 1 (VRN1), VERNALIZATION 2 (VRN2), BrFLC, and FLOWERING LOCUS T (FT), which varied by cell type. Our study underscores the transformative impact of single-cell RNA sequencing (scRNA-seq) for unraveling the complex differentiation and vernalization processes in the Chinese cabbage shoot apex. These insights are pivotal for enhancing breeding strategies and cultivation management of this vital vegetable.

Gibberellins regulate masculinization through the SpGAI-SpSTM module in dioecious spinach

The sex of dioecious plants is mainly determined by genetic factors, but it can also be converted by environmental cues such as exogenous phytohormones. Gibberellic acids (GAs) are well-known inducers of flowering and sexual development, yet the pathway of gibberellin-induced sex conversion in dioecious spinach (Spinacia oleracea L.) remains elusive. Based on sex detection before and after GA3 application using T11A and SSR19 molecular markers, we confirmed and elevated the masculinization effect of GA on a single female plant through exogenous applications of GA3, showing complete conversion and functional stamens. Silencing of GIBBERELLIC ACID INSENSITIVE (SpGAI), a single DELLA family protein that is a central GA signaling repressor, results in similar masculinization. We also show that SpGAI can physically interact with the spinach KNOX transcription factor SHOOT MERISTEMLESS (SpSTM), which is a homolog of the flower meristem identity regulator STM in Arabidopsis. The silencing of SpSTM also masculinized female flowers in spinach. Furthermore, SpSTM could directly bind the intron of SpPI to repress SpPI expression in developing female flowers. Overall, our results suggest that GA induces a female masculinization process through the SpGAI-SpSTM-SpPI regulatory module in spinach. These insights may help to clarify the molecular mechanism underlying the sex conversion system in dioecious plants while also elucidating the physiological basis for the generation of unisexual flowers so as to establish dioecy in plants.

Rewiring of a KNOXI regulatory network mediated by UFO underlies the compound leaf development in Medicago truncatula

Class I KNOTTED-like homeobox (KNOXI) genes are parts of the regulatory network that control the evolutionary diversification of leaf morphology. Their specific spatiotemporal expression patterns in developing leaves correlate with the degrees of leaf complexity between simple-leafed and compound-leafed species. However, KNOXI genes are not involved in compound leaf formation in several legume species. Here, we identify a pathway for dual repression of MtKNOXI function in Medicago truncatula. PINNATE-LIKE PENTAFOLIATA1 (PINNA1) represses the expression of MtKNOXI, while PINNA1 interacts with MtKNOXI and sequesters it to the cytoplasm. Further investigations reveal that UNUSUAL FLORAL ORGANS (MtUFO) is the direct target of MtKNOXI, and mediates the transition from trifoliate to pinnate-like pentafoliate leaves. These data suggest a new layer of regulation for morphological diversity in compound-leafed species, in which the conserved regulators of floral development, MtUFO, and leaf development, MtKNOXI, are involved in variation of pinnate-like compound leaves in M. truncatula.

KNOTTED1-like homeobox (KNOX) transcription factors - Hubs in a plethora of networks: A review

KNOX (KNOTTED1-like HOMEOBOX) belongs to a class of important homeobox genes, which encode the homeodomain proteins binding to the specific element of target genes, and widely participate in plant development. Advancements in genetics and molecular biology research generate a large amount of information about KNOX genes in model and non-model plants, and their functions in different developmental backgrounds are gradually becoming clear. In this review, we summarize the known and presumed functions of the KNOX gene in plants, focusing on horticultural plants and crops. The classification and structural characteristics, expression characteristics and regulation, interacting protein factors, functions, and mechanisms of KNOX genes are systematically described. Further, the current research gaps and perspectives were discussed. These comprehensive data can provide a reference for the directional improvement of agronomic traits through KNOX gene regulation.

What a tangled web it weaves: auxin coordination of stem cell maintenance and flower production

Robust agricultural yields require consistent flower production throughout fluctuating environmental conditions. Floral primordia are produced in the inflorescence meristem, which contains a pool of continuously dividing stem cells. Daughter cells of these divisions either retain stem cell identity or are pushed to the SAM periphery, where they become competent to develop into floral primordia after receiving the appropriate signal. Thus, flower production is inherently linked to regulation of the stem cell pool. The plant hormone auxin promotes flower development throughout its early phases and has been shown to interact with the molecular pathways regulating stem cell maintenance. Here, we will summarize how auxin signaling contributes to stem cell maintenance and promotes flower development through the early phases of initiation, outgrowth, and floral fate establishment. Recent advances in this area suggest that auxin may serve as a signal that integrates stem cell maintenance and new flower production.

Thinking outside the F-box: how UFO controls angiosperm development

The formation of inflorescences and flowers is essential for the successful reproduction of angiosperms. In the past few decades, genetic studies have identified the LEAFY transcription factor and the UNUSUAL FLORAL ORGANS (UFO) F-box protein as two major regulators of flower development in a broad range of angiosperm species. Recent research has revealed that UFO acts as a transcriptional cofactor, redirecting the LEAFY floral regulator to novel cis-elements. In this review, we summarize the various roles of UFO across species, analyze past results in light of new discoveries and highlight the key questions that remain to be solved.

ERF5 enhances protocorm-like body regeneration via enhancement of STM expression in Dendrobium orchid

Orchid plants develop protocorms upon germination and produce protocorm-like structures called protocorm-like bodies (PLBs) from protocorms and somatic cells via tissue culture. Protocorm-like bodies have broad technical application potential in the orchid industry and their regeneration is a distinct developmental process in the plant kingdom. However, little is known about this unparalleled developmental program. In this study, we identified a PLB-abundant gene, ethylene response factor (ERF), and a transcription factor named DoERF5, and determined its important role in PLB regeneration in Dendrobium orchid. Overexpression of DoERF5 in Dendrobium greatly enhanced the PLB regeneration from PLB and stem explants, and upregulated the expression of WOUND-INDUCED DEDIFFERENTIATION (DoWIND) homologs and SHOOT MERISTEMLESS (DoSTM), as well as the genes involved in cytokinin biosynthesis (DoIPT) and the cytokinin response factors (DoARRs). However, silencing DoERF5 reduced the regeneration rate of PLBs, and downregulated the expression of DoWIND homologs, DoSTM and DoARRs. We demonstrated that DoERF5 is directly bound to the DoSTM promoter and regulates its expression. In addition, overexpression of DoSTM in Dendrobium orchid resulted in favorable regeneration of PLBs. Our results clarify that DoERF5 regulates the regeneration of PLB by enhancing DoSTM expression. Our findings provide new insights into how DoERF5 mediates PLB regeneration and offers technical potential in improving clonal propagation, preservation, and the bioengineering of orchids.

Transcriptional Regulation of Female and Male Flower Bud Initiation and Development in Pecan (Carya illinoensis)

Pecan (Carya illinoensis) nuts are delicious and rich in unsaturated fatty acids, which are beneficial for human health. Their yield is closely related to several factors, such as the ratio of female and male flowers. We sampled and paraffin-sectioned female and male flower buds for one year and determined the stages of initial flower bud differentiation, floral primordium formation, and pistil and stamen primordium formation. We then performed transcriptome sequencing on these stages. Our data analysis suggested that FLOWERING LOCUS T (FT) and SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 play a role in flower bud differentiation. J3 was highly expressed in the early stage of female flower buds and may play a role in regulating flower bud differentiation and flowering time. Genes such as NF-YA1 and STM were expressed during male flower bud development. NF-YA1 belongs to the NF-Y transcription factor family and may initiate downstream events leading to floral transformation. STM promoted the transformation of leaf buds to flower buds. AP2 may have been involved in the establishment of floral meristem characteristics and the determination of floral organ characteristics. Our results lay a foundation for the control and subsequent regulation of female and male flower bud differentiation and yield improvement.

Targeted mutagenesis of BnaSTM leads to abnormal shoot apex development and cotyledon petiole fusion at the seedling stage in Brassica napus L

The Arabidopsis homeodomain transcription factor SHOOT MERISTEMLESS (STM) is crucial for shoot apical meristem (SAM) function, which cooperates with CLAVATA3 (CLV3)/WUSCHEL (WUS) feedback regulation loops to maintain the homeostasis of stem cells in SAM. STM also interacts with the boundary genes to regulate the tissue boundary formation. However, there are still few studies on the function of STM in Brassica napus, an important oil crop. There are two homologs of STM in B. napus (BnaA09g13310D and BnaC09g13580D). In the present study, CRISPR/Cas9 technology was employed to create the stable site-directed single and double mutants of the BnaSTM genes in B. napus. The absence of SAM could be observed only in the BnaSTM double mutants at the mature embryo of seed, indicating that the redundant roles of BnaA09.STM and BnaC09.STM are vital for regulating SAM development. However, different from Arabidopsis, the SAM gradually recovered on the third day after seed germination in Bnastm double mutants, resulting in delayed true leaves development but normal late vegetative and reproductive growth in B. napus. The Bnastm double mutant displayed a fused cotyledon petiole phenotype at the seedling stage, which was similar but not identical to the Atstm in Arabidopsis. Further, transcriptome analysis showed that targeted mutation of BnaSTM caused significant changes for genes involved in the SAM boundary formation (CUC2, CUC3, LBDs). In addition, Bnastm also caused significant changes of a sets of genes related to organogenesis. Our findings reveal that the BnaSTM plays an important yet distinct role during SAM maintenance as compared to Arabidopsis.

Arabidopsis thaliana SHOOT MERISTEMLESS Substitutes for Medicago truncatula SINGLE LEAFLET1 to Form Complex Leaves and Petals

LEAFY plant-specific transcription factors, which are key regulators of flower meristem identity and floral patterning, also contribute to meristem activity. Notably, in some legumes, LFY orthologs such as Medicago truncatula SINGLE LEAFLET (SGL1) are essential in maintaining an undifferentiated and proliferating fate required for leaflet formation. This function contrasts with most other species, in which leaf dissection depends on the reactivation of KNOTTED-like class I homeobox genes (KNOXI). KNOXI and SGL1 genes appear to induce leaf complexity through conserved downstream genes such as the meristematic and boundary CUP-SHAPED COTYLEDON genes. Here, we compare in M. truncatula the function of SGL1 with that of the Arabidopsis thaliana KNOXI gene, SHOOT MERISTEMLESS (AtSTM). Our data show that AtSTM can substitute for SGL1 to form complex leaves when ectopically expressed in M. truncatula. The shared function between AtSTM and SGL1 extended to the major contribution of SGL1 during floral development as ectopic AtSTM expression could promote floral organ identity gene expression in sgl1 flowers and restore sepal shape and petal formation. Together, our work reveals a function for AtSTM in floral organ identity and a higher level of interchangeability between meristematic and floral identity functions for the AtSTM and SGL1 transcription factors than previously thought.

SKI-INTERACTING PROTEIN interacts with SHOOT MERISTEMLESS to regulate shoot apical meristem formation

The shoot apical meristem (SAM), which is formed during embryogenesis, generates leaves, stems, and floral organs during the plant life cycle. SAM development is controlled by SHOOT MERISTEMLESS (STM), a conserved Class I KNOX transcription factor that interacts with another subclass homeodomain protein, BELL, to form a heterodimer, which regulates gene expression at the transcriptional level in Arabidopsis (Arabidopsis thaliana). Meanwhile, SKI-INTERACTING PROTEIN (SKIP), a conserved protein in eukaryotes, works as both a splicing factor and as a transcriptional regulator in plants to control gene expression at the transcriptional and posttranscriptional levels by interacting with distinct partners. Here, we show that, similar to plants with a loss of function of STM, a loss of function of SKIP or the specific knockout of SKIP in the SAM region resulted in failed SAM development and the inability of the mutants to complete their life cycle. In comparison, Arabidopsis mutants that expressed SKIP specifically in the SAM region formed a normal SAM and were able to generate a shoot system, including leaves and floral organs. Further analysis confirmed that SKIP interacts with STM in planta and that SKIP and STM regulate the expression of a similar set of genes by binding to their promoters. In addition, STM also interacts with EARLY FLOWERING 7 (ELF7), a component of Polymerase-Associated Factor 1 complex, and mutation in ELF7 exhibits similar SAM defects to that of STM and SKIP. This work identifies a component of the STM transcriptional complex and reveals the mechanism underlying SKIP-mediated SAM formation in Arabidopsis.

Transcriptomic comparison sheds new light on regulatory networks for dimorphic flower development in response to photoperiod in Viola prionantha

BACKGROUND

Chasmogamous (CH)-cleistogamous (CL) dimorphic flowers are developed in Viola prionantha. However, the environmental and genetic factors necessary for the CH-CL transition are unknown.

RESULTS

In the present work, short-day (SD) conditions induced CH flowers, whereas long days (LDs) triggered CL flowers in V. prionantha. Compared to fully developed CH flowers, CL flowers had less mature stamens, no nectar glands, and immature petals. Comparative transcriptomics revealed differentially expressed genes (DEGs) during CL and CH development. Core genes in the photoperiod pathway, such as V. prionantha orthologs of GIGANTEA (GI), CONSTANS (CO), and SUPPRESSOR OF OVEREXPRESSION OF CONSTANS 1 (SOC1), which promote floral induction, were highly expressed in CL flowers, whereas UNUSUAL FLORAL ORGANS (UFO) and B-class MADS-box genes for floral organ identity and development showed an opposite alteration. Moreover, genes in the glycolytic process, sucrose metabolic process, and fatty acid biosynthetic process were all highly expressed in CH flowers. Interestingly, V. prionantha orthologs of the B-class MADS-box genes APETALA3 (AP3) and PISTILLATA (PI) might relate to these sugar-fatty acid processes and were co-expressed with GAIP-B-like and YABBY5 (YAB5), which regulate the development of the petal, stamen, and nectary. Compared to CH flowers, DEGs and hub genes in the most significantly correlated modules of the gene co-expression network, which are involved in abiotic and biotic responses, were upregulated in CL flowers.

CONCLUSIONS

We proposed an integrative model for transcription regulation of genes in the photoperiod pathway, floral organ development, stress response, and sugar-fatty acid processes to determine CH-CL flower development in V. prionantha. Particularly, under LDs, activated GI may induce genes involved in the stress-response pathways, and then downregulated AP3 and PI or UFO to inhibit the sugar-fatty acid metabolic processes, together forming CL flowers. In contrast, CH flowers were produced under SDs. This work provides novel insights into the developmental evolution of dimorphic flowers in Viola.

The F-box E3 ubiquitin ligase AtSDR is involved in salt and drought stress responses in Arabidopsis

F-box protein genes have been shown to play vital roles in plant development and stress respones. In Arabidopsis, there are more than 600 F-box proteins, and most of their functions are unclear. The present study shows that the F-box (SKP1-Cullin/CDC53-F-box) gene At5g15710 (Salt and Drought Responsiveness, SDR) is involved in abiotic stress responses in Arabidopsis. SDR is expressed in all tissues of Arabidopsis and is upregulated by salt and heat stresses and ABA treatment but downregulated by drought stress. Subcellular localization analysis shows that the SDR protein colocalizes with the nucleus. 35S:AntiSDR plants are hypersensitive to salt stress, but 35S:SDR plants display a salt-tolerant phenotype. Furthermore, 35S:SDR plants are hypersensitive to drought stress, while 35S:AntiSDR plants are significantly more drought tolerant. Overall, our results suggest that SDR is involved in salt and drought stress responses in Arabidopsis.

Genetic control and allele variation among soybean maturity groups 000 through IX

Soybean [Glycinemax (L.) Merr.] maturity determines the growing region of a given soybean variety and is a primary factor in yield and other agronomic traits. The objectives of this research were to identify the quantitative trait loci (QTL) associated with maturity groups (MGs) and determine the genetic control of soybean maturity in each MG. Using data from 16,879 soybean accessions, genome-wide association (GWA) analyses were conducted for each paired MG and across MGs 000 through IX. Genome-wide association analyses were also performed using 184 genotypes (MGs V-IX) with days to flowering (DTF) and maturity (DTM) collected in the field. A total of 58 QTL were identified to be significantly associated with MGs in individual GWAs, which included 12 reported maturity loci and two stem termination genes. Genome-wide associations across MGs 000-IX detected a total of 103 QTL and confirmed 54 QTL identified in the individual GWAs. Of significant loci identified, qMG-5.2 had effects on the highest number (9) of MGs, followed by E2, E3, Dt2, qMG-15.5, E1, qMG-13.1, qMG-7.1, and qMG-16.1, which affected five to seven MGs. A high number of genetic loci (8-25) that affected MGs 0-V were observed. Stem termination genes Dt1 and Dt2 mainly had significant allele variation in MGs II-V. Genome-wide associations for DTF, DTM, and reproductive period (RP) in the diversity panel confirmed 15 QTL, of which seven were observed in MGs V-IX. The results generated can help soybean breeders manipulate the maturity loci for genetic improvement of soybean yield.

Evolutionary Relationships and Divergence of KNOTTED1-Like Family Genes Involved in Salt Tolerance and Development in Cotton (Gossypium hirsutum L.)

The KNOX (KNOTTED1-like homeobox) transcription factors play an important role in leaf, shoot apical meristem and seed development and respond to biotic and abiotic stresses. In this study, we analyzed the diversity and evolutionary history of the KNOX gene family in the genome of tetraploid cotton (Gossypium hirsutum). Forty-four putative KNOX genes were identified. All KNOX genes from seven higher plant species were classified into KNOXI, KNOXII, and KNATM clades based on a phylogenetic analysis. Chromosomal localization and collinearity analysis suggested that whole-genome duplication and a polyploidization event contributed to the expansion of the cotton KNOX gene family. Analyses of expression profiles revealed that the GhKNOX genes likely responded to diverse stresses and were involved in cotton growth developmental processes. Silencing of GhKNOX2 enhanced the salt tolerance of cotton seedlings, whereas silencing of GhKNOX10 and GhKNOX14 reduced seedling tolerance to salt stress. Silencing of GhSTM3 influenced the cotton flowering time and plant development. These findings clarify the evolution of the cotton KNOX gene family and provide a foundation for future functional studies of KNOX proteins in cotton growth and development and response to abiotic stresses.

Tomato SD1, encoding a kinase-interacting protein, is a major locus controlling stem development

Stems serve as key determinants of plant development by connecting and supporting parts of the plant body, transporting nutrients important for long-distance communication that affect crop yield, and producing new organs. Nonetheless, studies on the regulation of stem development in crops are rather limited. Here, we found a significant correlation (P<0.001) between stem diameter (SD) and fruit size in tomato (Solanum lycopersicum). We performed a genome-wide association study and identified a novel quantitative trait locus (QTL), SDR9 (stem diameter regulator on CHROMOSOME 9), that co-localized with a gene encoding a kinase-interacting family protein (KIP), which is the most likely candidate gene related to SD (hereafter referred to as SD1). Overexpression of SD1 in thin-stem accessions resulted in increased SD. In contrast, suppressed expression of SD1 in thick-stem accessions using RNA interference exhibited the opposite effect. Further microscopic analyses showed that SD1 affected the stem diameter by controlling the size and number of secondary phloem cells. An 11-bp indel in the promoter region of SD1 that disrupts a gibberellin-responsive cis-element was linked to SD. Expression analysis revealed that SD1 was mainly expressed at the cambium of the stem and positively regulates stem development. Evolutionary analysis revealed that the thick-stem allele of SD1 was selected during the recent process of tomato improvement. Our results provide novel genetic and molecular insight into natural variation of SD in tomato and may accelerate the breeding of high yield tomato.

Development of the VIGS System in the Dioecious Plant Silene latifolia

(1) Background: Silene latifolia is a dioecious plant, whose sex is determined by XY-type sex chromosomes. Microbotryum lychnidis-dioicae is a smut fungus that infects S. latifolia plants and causes masculinization in female flowers, as if Microbotryum were acting as a sex-determining gene. Recent large-scale sequencing efforts have promised to provide candidate genes that are involved in the sex determination machinery in plants. These candidate genes are to be analyzed for functional characterization. A virus vector can be a tool for functional gene analyses; (2) Methods: To develop a viral vector system in S. latifolia plants, we selected Apple latent spherical virus (ALSV) as an appropriate virus vector that has a wide host range; (3) Results: Following the optimization of the ALSV inoculation method, S. latifolia plants were infected with ALSV at high rates in the upper leaves. In situ hybridization analysis revealed that ALSV can migrate into the flower meristems in S. latifolia plants. Successful VIGS (virus-induced gene silencing) in S. latifolia plants was demonstrated with knockdown of the phytoene desaturase gene. Finally, the developed method was applied to floral organ genes to evaluate its usability in flowers; (4) Conclusion: The developed system enables functional gene analyses in S. latifolia plants, which can unveil gene functions and networks of S. latifolia plants, such as the mechanisms of sex determination and fungal-induced masculinization.