Transcription Factor MYB26 Is Key to Spatial Specificity in Anther Secondary Thickening Formation

ICE1 (Inducer of CBF Expression 1) Is Essential for the Jasmonate-Regulated Development of Stamen in Arabidopsis thaliana

Floral organ development, pollen germination and pollen tube growth are crucial for plant sexual reproduction. Phytohormones maintain these processes by regulating the expression and activity of various transcription factors. ICE1, a MYC-like bHLH transcription factor, has been revealed to be involved in cold acclimatisation of Arabidopsis. This study shows that ICE1 regulates multiple aspects of sexual reproduction, including stamen development, pollen development and germination. Loss-of-function mutants of ICE1 exhibit floral organs with shorter filaments, defective anther dehiscence and lower pollen viability compared to the wild type. These abnormalities result in disrupted fertilisation, leading to short siliques, a high rate of seed abortion, and dark, shriveled mature seeds. JAZ proteins (JAZ1 and JAZ9) interact with ICE1, inhibiting its transcriptional activity on jasmonic acid (JA)-responsive genes, including MYB21, MYB24 and MYB108. This study highlights the essential role of ICE1 as a signalling agent in the JA-regulated maintenance of sexual reproduction in Arabidopsis thaliana.

Genome-wide identification of the Medicago sativa L. MYB family and its transcriptional dynamics during pollen development

BACKGROUND

The myeloblastosis (MYB) gene family plays crucial roles in the development of anthers and the establishment of pollen morphology during plant growth. However, little is known about the role of MYB transcription factors in pollen development in alfalfa (Medicago sativa L.).

RESULTS

In this study, we identified 161 MsMYBs in the alfalfa genome, including 34 1R-MYBs, 123 R2R3-MYBs, 3 3R-MYBs, and 1 4R-MYBs (categorized by the number of repeats). These were classified into six subfamilies based on the phylogenetic analysis, conserved structural domains, and gene structures. All MsMYBs were predicted to be hydrophilic and localized in the cell nucleus. The promoter regions contained three classes of cis-regulatory elements related to pollen development, as well as a variable set of functionally diverse elements, including hormone responsiveness, growth and development, and stress responsiveness elements. A transcriptome and qRT-PCR analysis revealed 12 MsMYBs with anther-specific expression and exhibited distinct expression patterns. Some MsMYBs showed a close phylogenetic relationship with Arabidopsis MYBs related to pollen development, such as MsMYB49 and MsMYB100, were found to be localized in the nucleus upon subcellular localization analysis. This genetic proximity suggests a potential role for these MsMYBs in the developmental processes of pollen.

CONCLUSIONS

This study provides a comprehensive understanding of MsMYBs in alfalfa and elucidates their potential roles and expression patterns in pollen development.

Genomic and genetic insights into Mendel's pea genes

Mendel1 studied in detail seven pairs of contrasting traits in pea (Pisum sativum), establishing the foundational principles of genetic inheritance. Here we investigate the genetic architecture that underlies these traits and uncover previously undescribed alleles for the four characterized Mendelian genes2-7, including a rare revertant of Mendel's white-flowered a allele. Primarily, we focus on the three remaining uncharacterized traits and find that (1) an approximately 100-kb genomic deletion upstream of the Chlorophyll synthase (ChlG) gene disrupts chlorophyll biosynthesis through the generation of intergenic transcriptional fusion products, conferring the yellow pod phenotype of gp mutants; (2) a MYB gene with an upstream Ogre element insertion and a CLE peptide-encoding gene with an in-frame premature stop codon explain the v and p alleles, which disrupt secondary cell wall thickening and lignification, resulting in the parchmentless, edible-pod phenotype; and (3) a 5-bp exonic deletion in a CIK-like co-receptor kinase gene, in combination with a genetic modifier locus, is associated with the fasciated stem (fa) phenotype. Furthermore, we characterize genes and alleles associated with diverse agronomic traits, such as axil ring anthocyanin pigmentation, seed size and the 'semi-leafless' form. This study establishes a foundation for fundamental research, education in biology and genetics, and pea breeding practices.

The LoMYB26/LoJAZ4-LoCOMT module regulates anther dehiscence via Jasmonic acid-mediated endothecium lignification in lily

INTRODUCTION

Timely anther dehiscence is a key step for successful sexual reproduction in plants. Secondary cell wall thickening of anther endothecium is a vital process during anther dehiscence that provides an indispensable mechanical force for successful dehiscence. Anther dehiscence depends on anther lignification, and it is a timely and sophisticated process regulated by phytohormones and transcription factors. However, whether endothecium lignification occurs during anther dehiscence in lily and underlying mechanisms are still largely unclear.

OBJECTIVES

Our work focuses on identifying the course of endothecium lignification during anther dehiscence and elucidating the molecular mechanisms underlying endothecium lignification-dependent anther dehiscence in lily.

METHODS

Lignin fluorescence analysis and ultraviolet spectrophotometry were employed to elucidate the endothecium lignification process. Target genes were isolated from the transcriptomic data of anther dehiscence and lignification process. Virus-induced gene silencing (VIGS) and transient overexpression in lily anthers were used to analyze the LoMYB26 function. Yeast one-hybrid (Y1H), electrophoretic mobility shift assay (EMSA), and dual-luciferase (LUC) assay analyzed the regulatory mechanisms. Yeast two-hybrid (Y2H), luciferase complementation imaging (LCI), and bimolecular fluorescence complementation (BiFC) assays illustrated the interaction between LoMYB26 and LoJAZ4.

RESULTS

Our results showed that endothecium lignification occurred in S6-S7 stages when anther dehiscence had not yet occurred. The R2R3-type MYB transcription factor, LoMYB26, was found to promote endothecium lignification. LoMYB26 directly bound to the Caffeic Acid O-methyltransferase (LoCOMT) promoter and activated its transcription. Meanwhile, LoMYB26 interacted with jasmonate-ZIM domain protein 4 (LoJAZ4), which repressed the LoMYB26-mediated activation of LoCOMT transcription. Additionally, the exogenous application of methyl-jasmonate (Me-JA) induced LoMYB26 transcription and promoted endothecium lignification.

CONCLUSION

Our findings demonstrate that LoMYB26 promotes endothecium lignification and anther dehiscence. LoMYB26 interacted with LoJAZ4, forming a heterodimer that participates in JA-mediated endothecium lignification and anther dehiscence. This study offers valuable insights and a theoretical foundation for the breeding of anther-indehiscent lily.

CRISPR-Cas9-mediated deletions of FvMYB46 in Fragaria vesca reveal its role in regulation of fruit set and phenylpropanoid biosynthesis

The phenylpropanoid pathway, regulated by transcription factors of the MYB family, produces secondary metabolites that play important roles in fertilization and early phase of fruit development. The MYB46 transcription factor is a key regulator of secondary cell wall structure, lignin and flavonoid biosynthesis in many plants, but little is known about its activity in flowers and berries in F. vesca. For functional analysis of FvMYB46, we designed a CRISPR-Cas9 construct with an endogenous F. vesca-specific U6 promoter for efficient and specific expression of two gRNAs targeting the first exon of FvMYB46. This generated mutants with an in-frame 81-bp deletion of the first conserved MYB domain or an out-of-frame 82-bp deletion potentially knocking out gene function. In both types of mutant plants, pollen germination and fruit set were significantly reduced compared to wild type. Transcriptomic analysis of flowers revealed that FvMYB46 positively regulates the expression of genes involved in processes like xylan biosynthesis and metabolism, homeostasis of reactive oxygen species (ROS) and the phenylpropanoid pathway, including secondary cell wall biosynthesis and flavonoid biosynthesis. Genes regulating carbohydrate metabolism and signalling were also deregulated, suggesting that FvMYB46 might regulate the crosstalk between carbohydrate metabolism and phenylpropanoid biosynthesis. In the FvMYB46-mutant flowers, the flavanol and flavan-3-ol contents, especially epicatechin, quercetin-glucoside and kaempferol-3-coumaroylhexoside, were reduced, and we observed a local reduction in the lignin content in the anthers. Together, these results suggest that FvMYB46 controls fertility and efficient fruit set by regulating the cell wall structure, flavonoid biosynthesis, carbohydrate metabolism, and sugar and ROS signalling in flowers and early fruit development in F. vesca.

Overexpression of TCP5 or Its Dominant Repressor Form, TCP5-SRDX, Causes Male Infertility in Arabidopsis

TCP transcription factors have long been known to play a crucial role in leaf development, but their significance in reproduction has recently been revealed. TCP5 is a member of class II of the TCP family, which predominantly regulates cell differentiation. This study used overexpression and SRDX fusion to evaluate the role of TCP5 in anther development. TCP5 overexpression resulted in lower fertility, primarily due to anther non-dehiscence. We also observed reduced lignin accumulation in the anther endothecium. In addition, TCP5 overexpression resulted in smaller anthers with fewer pollen sacs and pollen due to early-anther defects before meiosis. TCP5 showed expression in early anthers, including the epidermis, endothecium, middle layer, tapetum, sporogenous cells (pollen mother cells), and vascular bundles. Conversely, during meiosis, the TCP5 signal was only detected in the tapetum, PMCs, and vascular bundles. The TCP5 signal disappeared after meiosis, and no signal was observed in mature anthers. Interestingly, the TCP5-SRDX transgenic plants were also sterile, at least for the early-arising flowers, if not all of them. TCP5-SRDX expression also resulted in undersized anthers with fewer pollen sacs and pollen. However, the lignin accumulation in most of these anthers was comparable to that of the wild type, allowing these anthers to open. The qRT-PCR results revealed that several genes associated with secondary cell wall thickening had altered expression profiles in TCP5 overexpression transgenics, which supported the non-dehiscent anther phenotype. Furthermore, the expression levels of numerous critical anther genes were down-regulated in both TCP5 overexpression and TCP5-SRDX plants, indicating a comparable anther phenotype in these transgenic plants. These findings not only suggest that an appropriate TCP5 expression level is essential for anther development and plant fertility, but also improve our understanding of TCP transcription factor functioning in plant male reproduction and contribute information that may allow us to manipulate fertility and breeding in crops.

Xylan structural diversity, biosynthesis, and functional regulation in plants

Xylan is a vital component of plant cell walls, contributing to their structural integrity and flexibility through interactions with other polymers. Its structure varies among plant species, influencing the mechanical properties of cell walls. Xylan also has significant industrial potential, including in biofuels, biomaterials, food, and pharmaceuticals, due to its ability to be converted into valuable bioproducts. However, key aspects of xylan biosynthesis, regulation, and structural impact on plant growth and structures remain unclear. This review highlights current researches on xylan biosynthesis, modification, and applications, identifying critical gaps in knowledge. Meanwhile the review proposes new approaches to regulate xylan synthesis and understand its role in cell wall assembly and interactions with other polymers. Addressing these gaps could unlock the full industrial potential of xylan, leading to more sustainable applications.

EMBRYONIC FLOWER 1 regulates male reproduction by repressing the jasmonate pathway downstream transcription factor MYB26

The evolutionarily conserved Polycomb repressive complexes (PRCs) mediate genome-wide transcriptional silencing and regulate a plethora of development, as well as environmental responses in multicellular organisms. The PRC2-catalyzed trimethylation of lysine 27 on histone H3 (H3K27me3) is recognized by reader-effector modules of Polycomb repressive complex 1 (PRC1) to implement gene repression. Here, we report that the Arabidopsis (Arabidopsis thaliana) H3K27me3 effector EMBRYONIC FLOWER 1 (EMF1) interacts with and constrains the R2R3 DNA binding transcription factor MYB26 by a eudicot-conserved motif in the stamen. MYB26 activates the transcription of two NAC domain genes, NAC SECONDARY WALL THICKENING PROMOTING FACTOR1 (NST1) and NST2, whose encoded proteins mediate anther secondary cell thickening in jasmonate (JA)-regulated stamen maturation. In this process, the transcriptional activity of MYB26 is negatively modulated by the JAZ-PRC repressive complex to precisely regulate the expression of NST1 and NST2. Disruption of EMF1 repression stimulates MYB26, leading to the excessive transcription of the two NAC genes and male sterility. Our results reveal a novel mechanism in Polycomb-mediated gene silencing and illustrate that the plant Polycomb complex regulates stamen development by preventing the hypersensitivity of JA responses in male reproduction.

Paralogous Gene Recruitment in Multiple Families Constitutes Genetic Architecture and Robustness of Pod Dehiscence in Legumes

Pod dehiscence facilitates seed dispersal in wild legumes while indehiscence is a key domestication trait in cultivated ones. However, the evolutionary genetic mechanisms underlying its diversity are largely unclear. In this study, we compared transcriptomes of two warm-season (Glycine spp. and Phaseolus spp.) and two cool-season (Pisum spp. and Medicago ruthenica) legumes in analysis of dehiscent and indehiscent pod genotypes. Differentially expressed genes in AP2/ERF-like transcription factors and seven structural gene families, including lactoperoxidase, laccase, and cellulose synthase-interactive proteins, which are involved in secondary cell wall component accumulation, were identified to exert key roles in pod dehiscence variation. In accordance with this, higher lignin and cellulose contents were observed in pod secondary cell wall of dehiscent accessions of soybean and pea; however, the variation patterns of lignin polymers in soybean (accumulation) and pea (proportion) differed between dehiscent and indehiscent pods. Moreover, genome-wide comparative analysis revealed that orthogroups represented <1% of all identified differentially expressed genes could be traced among the four genera of legumes, while recruiting paralogous members may constitute the genetic robustness of legume pod dehiscence. This study compared the genetic mechanism among several legumes in pod dehiscence formation and revealed a compensating role of paralogous redundancy of involved gene families in seed dispersal, which can guide crop breeding.

Liana attachment to supports leads to profound changes in xylem anatomy and transcriptional profile of cambium and differentiating xylem

Wood serves crucial functions in plants, yet our understanding of the mechanisms governing the composition, arrangement, and dimensions of its cells remains limited. The abrupt transition from nonlianescent to lianescent xylem in lianas represents an excellent model to address the underlying mechanisms, although consistent triggering factors for this process remain uncertain. In this study we examined how physical support attachment impacts the development of lianescent xylem in Bignonia magnifica (Bignoniaceae), employing a comprehensive approach integrating detailed anatomical analysis with gene expression profiling of cambium and differentiating xylem. Our findings demonstrate that attachment to physical supports triggers the formation of lianescent xylem, leading to increased vessel size, broader vessel distribution, reduced fibre content, and higher potential specific water conductivity than nonlianescent xylem. These shifts in wood anatomy coincide with the downregulation of genes associated with cell division and cell wall biosynthesis, and the upregulation of transcription factors, defense/cell death, and hormone-responsive genes in the lianescent xylem. Our findings provide insights into the regulation of xylem differentiation, driven by response to environmental stimuli. Additionally, they shed light on the mechanisms underlying the adaptation of lianas to climbing.

Transcriptome and genome-wide analysis of the potential role of SKP1 gene family in the development of floral organs of two related species of Allium fistulosum

Allium fistulosum is an important plant germplasm resource, rich in nutrients and possessing unique medicinal value. However, due to its small floral organs, low seed setting rate of a single flower, high cost of artificial emasculation, and artificial pollination, the use of male sterile lines to prepare Allium hybrids has become a common choice. In this study, A. fistulosum var. viviparum Makino and A. galanthum were used as materials to study the regulation mechanism of anther development, aiming to provide a reference for male sterility. Through transcriptome differential gene screening and genome-wide bioinformatics analysis, 34 SKP1 (S-phase kinase-associated protein 1) genes (AfSKP1-1 to AfSKP1-34) were identified in the whole genome of A. fistulosum. The AfSKP1 genes are unevenly distributed on eight chromosomes. Furthermore, two pairs of collinear relationships are evident among family members, and fragment replication events between AfSKP1 genes have been identified. The phylogenetic tree analysis demonstrated that the AfSKP1, AtSKP1, OsSKP1, and SlSKP1 genes were clustered into six groups, exhibiting a gene structure analogous to that observed in members of an evolutionary classification. A combination of gene structure and phylogenetic analysis revealed the presence of cis-acting elements associated with growth, hormone regulation, and stress response within the AfSKP1 genes. Furthermore, expression analysis demonstrated that the AfSKP1 genes exhibited differential expression patterns across various tissues of A. fistulosum. The tissue-specific expression of the AfSKP1 gene was verified by Real-Time PCR. A comparison of the two materials revealed significant differences in the expression of the AfSKP1-8 gene in floral buds, the AfSKP1-11 gene in inflorescence meristems, and the AfSKP1-14 gene in inflorescence meristems, scapes, and floral buds. The results indicated that the three genes may be involved in anther development, thereby providing a theoretical basis for further study of floral organ development and pollen development in AfSKP1 family members.

Eggplant NAC domain transcription factor SmNST1 as an activator promotes secondary cell wall thickening

NAC-domain transcription factors (TFs) are plant-specific transcriptional regulators playing crucial roles in plant secondary cell wall (SCW) biosynthesis. SCW is important for plant growth and development, maintaining plant morphology, providing rigid support, ensuring material transportation and participating in plant stress responses as a protective barrier. However, the molecular mechanisms underlying SCW in eggplant have not been thoroughly explored. In this study, the NAC domain TFs SmNST1 and SmNST2 were cloned from the eggplant line 'Sanyue qie'. SmNST1 and SmNST2 expression levels were the highest in the roots and stems. Subcellular localization analysis showed that they were localized in the cell membrane and nucleus. Their overexpression in transgenic tobacco showed that SmNST1 promotes SCW thickening. The expression of a set of SCW biosynthetic genes for cellulose, xylan and lignin, which regulate SCW formation, was increased in transgenic tobacco. Bimolecular fluorescence and luciferase complementation assays showed that SmNST1 interacted with SmNST2 in vivo. Yeast one-hybrid, electrophoretic mobility shift assay (EMSA) and Dual-luciferase reporter assays showed that SmMYB26 directly bound to the SmNST1 promoter and acted as an activator. SmNST1 and SmNST2 interact with the SmMYB108 promoter and repress SmMYB108 expression. Altogether, we showed that SmNST1 positively regulates SCW formation, improving our understanding of SCW biosynthesis transcriptional regulation.

Gene expression profiles and metabolic pathways responsible for male sterility in cybrid pummelo

KEY MESSAGE

Abnormal expression of genes regulating anther and pollen development and insufficient accumulation of male sterility (MS)- related metabolites lead to MS in cybrid pummelo Male sterility (MS) is a major cause of seedlessness in citrus, which is an important trait for fresh fruit. Understanding the mechanism of MS is important for breeding seedless citrus cultivars. In this study, we dissected the transcriptional, metabolic and physiological mechanisms of MS in somatic cybrid of pummelo (G1 + HBP). G1 + HBP exhibited severe male sterility, manifesting as retarded anther differentiation, abnormal anther wall development (especially tapetum and endothecium), and deficient pollen wall formation. In the anthers of G1 + HBP, the expression of genes regulating anther differentiation and tapetum development was abnormal, and the expression of genes regulating endothecium secondary lignification thickening and pollen wall formation was down-regulated. The transcription of genes involved in MS-related biological processes, such as jasmonic acid (JA) signaling pathway, primary metabolism, flavonoid metabolism, and programmed cell death, was altered in G1 + HBP anthers, and the accumulation of MS-associated metabolites, including fatty acids, amino acids, sugars, ATP, flavonols and reactive oxygen species (ROS), was down-regulated in G1 + HBP anthers. In summary, abnormal expression of key genes regulating anther and pollen development, altered transcription of key genes involved in MS-related metabolic pathways, and insufficient accumulation of MS-related metabolites together lead to MS in G1 + HBP. The critical genes and the metabolism pathways identified herein provide new insights into the formation mechanism of MS in citrus and candidate genes for breeding seedless citrus.

R2R3-MYB Gene Family in Coptis teeta Wall.: Genome-Wide Identification, Phylogeny, Evolutionary Expansion, and Expression Analyses during Floral Development

The R2R3-MYB gene family represents a widely distributed class of plant transcription factors. This gene family plays an important role in many aspects of plant growth and development. However, the characterization of R2R3-MYB genes present in the genome of Coptis teeta has not been reported. Here, we describe the bioinformatic identification and characterization of 88 R2R3-MYB genes in this species, and the identification of members of the R2R3-MYB gene family in species within the order Ranales most closely related to Coptis teeta. The CteR2R3-MYB genes were shown to exhibit a higher degree of conservation compared to those of A. thaliana, as evidenced by phylogeny, conserved motifs, gene structure, and replication event analyses. Cis-acting element analysis confirmed the involvement of CteR2R3-MYB genes in a variety of developmental processes, including growth, cell differentiation, and reproduction mediated by hormone synthesis. In addition, through homology comparisons with the equivalent gene family in A. thaliana, protein regulatory network prediction and transcriptome data analysis of floral organs across three time periods of flower development, 17 candidate genes were shown to exhibit biased expression in two floral phenotypes of C. teeta. This suggests their potential involvement in floral development (anther development) in this species.

The regulatory mechanism of rapid lignification for timely anther dehiscence

Anther dehiscence is a crucial event in plant reproduction, tightly regulated and dependent on the lignification of the anther endothecium. In this study, we investigated the rapid lignification process that ensures timely anther dehiscence in Arabidopsis. Our findings reveal that endothecium lignification can be divided into two distinct phases. During Phase I, lignin precursors are synthesized without polymerization, while Phase II involves simultaneous synthesis of lignin precursors and polymerization. The transcription factors MYB26, NST1/2, and ARF17 specifically regulate the pathway responsible for the synthesis and polymerization of lignin monomers in Phase II. MYB26-NST1/2 is the key regulatory pathway responsible for endothecium lignification, while ARF17 facilitates this process by interacting with MYB26. Interestingly, our results demonstrate that the lignification of the endothecium, which occurs within approximately 26 h, is much faster than that of the vascular tissue. These findings provide valuable insights into the regulation mechanism of rapid lignification in the endothecium, which enables timely anther dehiscence and successful pollen release during plant reproduction.

PbARF19-mediated auxin signaling regulates lignification in pear fruit stone cells

The stone cells in pear fruits cause rough flesh and low juice, seriously affecting the taste. Lignin has been demonstrated as the main component of stone cells. Auxin, one of the most important plant hormone, regulates most physiological processes in plants including lignification. However, the concentration effect and regulators of auxin on pear fruits stone cell formation remains unclear. Here, endogenous indole-3-acetic acid (IAA) and stone cells were found to be co-localized in lignified cells by immunofluorescence localization analysis. The exogenous treatment of different concentrations of IAA demonstrated that the application of 200 µM IAA significantly reduced stone cell content, while concentrations greater than 500 µM significantly increased stone cell content. Besides, 31 auxin response factors (ARFs) were identified in pear genome. Putative ARFs were predicted as critical regulators involved in the lignification of pear flesh cells by phylogenetic relationship and expression analysis. Furthermore, the negative regulation of PbARF19 on stone cell formation in pear fruit was demonstrated by overexpression in pear fruitlets and Arabidopsis. These results illustrated that the PbARF19-mediated auxin signal plays a critical role in the lignification of pear stone cell by regulating lignin biosynthetic genes. This study provides theoretical and practical guidance for improving fruit quality in pear production.

Gene Regulatory Network Controlling Flower Development in Spinach (Spinacia oleracea L.)

Spinach (Spinacia oleracea L.) is a dioecious, diploid, wind-pollinated crop cultivated worldwide. Sex determination plays an important role in spinach breeding. Hence, this study aimed to understand the differences in sexual differentiation and floral organ development of dioecious flowers, as well as the differences in the regulatory mechanisms of floral organ development of dioecious and monoecious flowers. We compared transcriptional-level differences between different genders and identified differentially expressed genes (DEGs) related to spinach floral development, as well as sex-biased genes to investigate the flower development mechanisms in spinach. In this study, 9189 DEGs were identified among the different genders. DEG analysis showed the participation of four main transcription factor families, MIKC_MADS, MYB, NAC, and bHLH, in spinach flower development. In our key findings, abscisic acid (ABA) and gibberellic acid (GA) signal transduction pathways play major roles in male flower development, while auxin regulates both male and female flower development. By constructing a gene regulatory network (GRN) for floral organ development, core transcription factors (TFs) controlling organ initiation and growth were discovered. This analysis of the development of female, male, and monoecious flowers in spinach provides new insights into the molecular mechanisms of floral organ development and sexual differentiation in dioecious and monoecious plants in spinach.

Morphological Innovation Drives Sperm Release in Bryophytes

Plant movements for survival are nontrivial. Antheridia in the moss Physcomitrium patens (P. patens) use motion to eject sperm in the presence of water. However, the biological and mechanical mechanisms that actuate the process are unknown. Here, the burst of the antheridium of P. patens, triggered by water, results from elastic instability and is determined by an asymmetric change in cell geometry. The tension generated in jacket cell walls of antheridium arises from turgor pressure, and is further promoted when the inner walls of apex burst in hydration, causing water and cellular contents of apex quickly influx into sperm chamber. The outer walls of the jacket cells are strengthened by NAC transcription factor VNS4 and serve as key morphomechanical innovations to store hydrostatic energy in a confined space in P. patens. However, the antheridium in liverwort Marchantia polymorpha (M. polymorpha) adopts a different strategy for sperm release; like jacket cell outer walls of P. patens, the cells surrounding the antheridium of M. polymorpha appear to play a similar role in the storage of energy. Collectively, the work shows that plants have evolved different ingenious devices for sperm discharge and that morphological innovations can differ.

The MYB Transcription Factor GmMYB78 Negatively Regulates Phytophthora sojae Resistance in Soybean

Phytophthora root rot is a devastating disease of soybean caused by Phytophthora sojae. However, the resistance mechanism is not yet clear. Our previous studies have shown that GmAP2 enhances sensitivity to P. sojae in soybean, and GmMYB78 is downregulated in the transcriptome analysis of GmAP2-overexpressing transgenic hairy roots. Here, GmMYB78 was significantly induced by P. sojae in susceptible soybean, and the overexpressing of GmMYB78 enhanced sensitivity to the pathogen, while silencing GmMYB78 enhances resistance to P. sojae, indicating that GmMYB78 is a negative regulator of P. sojae. Moreover, the jasmonic acid (JA) content and JA synthesis gene GmAOS1 was highly upregulated in GmMYB78-silencing roots and highly downregulated in overexpressing ones, suggesting that GmMYB78 could respond to P. sojae through the JA signaling pathway. Furthermore, the expression of several pathogenesis-related genes was significantly lower in GmMYB78-overexpressing roots and higher in GmMYB78-silencing ones. Additionally, we screened and identified the upstream regulator GmbHLH122 and downstream target gene GmbZIP25 of GmMYB78. GmbHLH122 was highly induced by P. sojae and could inhibit GmMYB78 expression in resistant soybean, and GmMYB78 was highly expressed to activate downstream target gene GmbZIP25 transcription in susceptible soybean. In conclusion, our data reveal that GmMYB78 triggers soybean sensitivity to P. sojae by inhibiting the JA signaling pathway and the expression of pathogenesis-related genes or through the effects of the GmbHLH122-GmMYB78-GmbZIP25 cascade pathway.

Genome-Wide Identification and Characterization of MYB Gene Family and Analysis of Its Sex-Biased Expression Pattern in Spinacia oleracea L

The members of the myeloblastosis (MYB) family of transcription factors (TFs) participate in a variety of biological regulatory processes in plants, such as circadian rhythm, metabolism, and flower development. However, the characterization of MYB genes across the genomes of spinach Spinacia oleracea L. has not been reported. Here, we identified 140 MYB genes in spinach and described their characteristics using bioinformatics approaches. Among the MYB genes, 54 were 1R-MYB, 80 were 2R-MYB, 5 were 3R-MYB, and 1 was 4R-MYB. Almost all MYB genes were located in the 0-30 Mb region of autosomes; however, the 20 MYB genes were enriched at both ends of the sex chromosome (chromosome 4). Based on phylogeny, conserved motifs, and the structure of genes, 2R-MYB exhibited higher conservation relative to 1R-MYB genes. Tandem duplication and collinearity of spinach MYB genes drive their evolution, enabling the functional diversification of spinach genes. Subcellular localization prediction indicated that spinach MYB genes were mainly located in the nucleus. Cis-acting element analysis confirmed that MYB genes were involved in various processes of spinach growth and development, such as circadian rhythm, cell differentiation, and reproduction through hormone synthesis. Furthermore, through the transcriptome data analysis of male and female flower organs at five different periods, ten candidate genes showed biased expression in spinach males, suggesting that these genes might be related to the development of spinach anthers. Collectively, this study provides useful information for further investigating the function of MYB TFs and novel insights into the regulation of sex determination in spinach.

MYB transcription factors and their roles in the male reproductive development of flowering plants

As one of the largest transcription factor families with complex functional differentiation in plants, the MYB transcription factors (MYB TFs) play important roles in the physiological and biochemical processes of plant growth and development. Male reproductive development, an essential part of sexual reproduction in flowering plants, is undoubtedly regulated by MYB TFs. In this review, we summarize the roles of the MYB TFs involved in the three stages of male reproductive development: pollen grains formation and maturation, filament elongation and anther dehiscence, and fertilization. Also, the potential downstream target genes and upstream regulators of these MYB TFs are discussed. Furthermore, we propose the underlying regulatory mechanisms of these MYB TFs: (1) A complex network of MYB TFs regulates various aspects of male reproductive development; (2) MYB homologous genes in different species may be functionally conserved or differentiated; (3) MYB TFs often form regulatory complexes with bHLH TFs.

Identification of a novel viral factor inducing tumorous symptoms by disturbing vascular development in planta

Plant viruses induce various disease symptoms that substantially impact agriculture, but the underlying mechanisms of viral disease in plants are poorly understood. Kobu-sho is a disease in gentian that shows gall formation with ectopic development of lignified cells and vascular tissues such as xylem. Here, we show that a gene fragment of gentian Kobu-sho-associated virus, which is designated as Kobu-sho-inducing factor (KOBU), induces gall formation accompanied by ectopic development of lignified cells and xylem-like tissue in Nicotiana benthamiana. Transgenic gentian expressing KOBU exhibited tumorous symptoms, confirming the gall-forming activity of KOBU. Surprisingly, KOBU expression can also induce differentiation of an additional leaf-like tissue on the abaxial side of veins in normal N. benthamiana and gentian leaves. Transcriptome analysis with Arabidopsis thaliana expressing KOBU revealed that KOBU activates signaling pathways that regulate xylem development. KOBU protein forms granules and plate-like structures and co-localizes with mRNA splicing factors within the nucleus. Our findings suggest that KOBU is a novel pleiotropic virulence factor that stimulates vascular and leaf development. IMPORTANCE While various mechanisms determine disease symptoms in plants depending on virus-host combinations, the details of how plant viruses induce symptoms remain largely unknown in most plant species. Kobu-sho is a disease in gentian that shows gall formation with ectopic development of lignified cells and vascular tissues such as xylem. Our findings demonstrate that a gene fragment of gentian Kobu-sho-associated virus (GKaV), which is designated as Kobu-sho-inducing factor, induces the gall formation accompanied by the ectopic development of lignified cells and xylem-like tissue in Nicotiana benthamiana. The molecular mechanism by which gentian Kobu-sho-associated virus induces the Kobu-sho symptoms will provide new insight into not only plant-virus interactions but also the regulatory mechanisms underlying vascular and leaf development.

Comparative transcriptome analysis reveals the involvement of an MYB transcriptional activator, SmMYB108, in anther dehiscence in eggplant

Male sterility is a highly attractive agronomic trait as it effectively prevents self-fertilization and facilitates the production of high-quality hybrid seeds in plants. Timely release of mature pollen following anther dehiscence is essential for stamen development in flowering plants. Although several theories have been proposed regarding this, the specific mechanism of anther development in eggplant remains elusive. In this study, we selected an R2R3-MYB transcription factor gene, SmMYB108, that encodes a protein localized primarily in the nucleus by comparing the transcriptomics of different floral bud developmental stages of the eggplant fertile line, F142. Quantitative reverse transcription polymerase chain reaction revealed that SmMYB108 was preferentially expressed in flowers, and its expression increased significantly on the day of flowering. Overexpression of SmMYB108 in tobacco caused anther dehiscence. In addition, we found that SmMYB108 primarily functions as a transcriptional activator via C-terminal activation (amino acid 262-317). Yeast one-hybrid and dual-luciferase reporter assays revealed that genes (SmMYB21, SmARF6, and SmARF8) related to anther development targeted the SmMYB108 promoter. Overall, our results provide insights into the molecular mechanisms involved in the regulation of anther development by SmMYB108.

Transcriptomic analysis reveals candidate genes associated with anther development in Lilium Oriental Hybrid 'Siberia'

Lily (Lilium spp. and hybrids) is an important cut flower crop worldwide. Lily flowers have large anthers, which release a large amount of pollen that stains the tepals or clothing and thus can affect the commercial value of cut flowers. In this study, lily Oriental 'Siberia' was used to investigate the regulatory mechanism of lily anther development, which may provide information to prevent pollen pollution in the future. Based on the flower bud length, anther length and color, and anatomical observations, lily anther development was categorized into five stages: green (G), green-to-yellow 1 (GY1), green-to-yellow 2 (GY2), yellow (Y), and purple (P). Total RNA was extracted from the anthers at each stage for transcriptomic analysis. A total of 268.92-Gb clean reads were generated, and 81,287 unigenes were assembled and annotated. The number of differentially expressed genes (DEGs) and unique genes were largest for the pairwise comparison between the G and GY1 stages. The G and P samples were clustered separately, whereas the GY1, GY2, and Y samples were clustered together in scatter plots from a principal component analysis. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses of DEGs detected in the GY1, GY2, and Y stages revealed that the pectin catabolic process, hormone levels, and phenylpropanoid biosynthesis were enriched. The DEGs associated with jasmonic acid biosynthesis and signaling were highly expressed at the early stages (G and GY1), whereas the DEGs associated with phenylpropanoid biosynthesis were mainly expressed in the intermediate stages (GY1, GY2, and Y). The DEGs involved in the pectin catabolic process were expressed at advanced stages (Y and P). Cucumber mosaic virus-induced gene silencing of LoMYB21 and LoAMS caused a strongly inhibited anther dehiscence phenotype, but without affecting the development of other floral organs. These results provide novel insights for understanding the regulatory mechanism of anther development in lily and other plants.

Analysis of Floral Organ Development and Sex Determination in Schisandra chinensis by Scanning Electron Microscopy and RNA-Sequencing

S. chinensis is a typical monoecious plant, and the number and development of female flowers determines the yield of S. chinensis. Due to a lack of genetic information, the molecular mechanism of sex differentiation in S. chinensis remains unclear. In this study, the combination of scanning electron microscopy (SEM) and RNA sequencing (RNA-seq) was used to understand the way of sex differentiation of S. chinensis and to mine the related genes of sex determination. The result shows the development of male and female S. chinensis flowers was completed at the same time, the unisexual S. chinensis flowers did not undergo a transition stage between sexes, and sex may have been determined at an early stage in flower development. The results of the gene function analysis of the plant hormone signaling pathway and sucrose metabolism pathway suggest that auxin and JA could be the key hormones for sex differentiation in S. chinensis, and sucrose may promote pollen maturation at the later stage of male flower development. Two AGAMOUS (GAG) genes, 10 AGAMOUS-like MADS-box (AGLs) genes, and the MYB, NAC, WRKY, bHLH, and Trihelix transcription factor families may play important roles in sex determination in S. chinensis. Taken together, the present findings provide valuable genetic information on flower development and sex determination in S. chinensis.

Spatio-temporal transcriptome profiling and subgenome analysis in Brassica napus

Brassica napus is an important oil crop and an allotetraploid species. However, the detailed analysis of gene function and homoeologous gene expression in all tissues at different developmental stages was not explored. In this study, we performed a global transcriptome analysis of 24 vegetative and reproductive tissues at six developmental stages (totally 111 tissues). These samples were clustered into eight groups. The gene functions of silique pericarp were similar to roots, stems and leaves. In particular, glucosinolate metabolic process was associated with root and silique pericarp. Genes involved in protein phosphorylation were often associated with stamen, anther and the early developmental stage of seeds. Transcription factor (TF) genes were more specific than structural genes. A total of 17 100 genes that were preferentially expressed in one tissue (tissue-preferred genes, TPGs), including 889 TFs (5.2%), were identified in the 24 tissues. Some TPGs were identified as hub genes in the co-expression network analysis, and some TPGs in different tissues were involved in different hormone pathways. About 67.0% of the homoeologs showed balanced expression, whereas biased expression of homoeologs was associated with structural divergence. In addition, the spatiotemporal expression of homoeologs was related to the presence of transposable elements (TEs) and regulatory elements (REs); more TEs and fewer REs in the promoters resulted in divergent expression in different tissues. This study provides a valuable transcriptional map for understanding the growth and development of B. napus, for identifying important genes for future crop improvement, and for exploring gene expression patterns in the B. napus.

Comparative Transcriptome Analysis Reveals Candidate Genes and Pathways for Potential Branch Growth in Elm (Ulmus pumila) Cultivars

Wood plays a vital role in human life. It is important to study the thickening mechanism of tree branches and explore the mechanism of wood formation. Elm (Ulmus pumila) is a strong essential wood, and it is widely used in cabinets, sculptures, and ship making. In the present study, phenotypic and comparative transcriptomic analyses were performed in U. pumila fast- (UGu17 and UZuantian) and slow-growing cultivars (U81-07 and U82-39). Phenotypic observation showed that the thickness of secondary xylem of 2-year-old fast-growing branches was greater compared with slow-growing cultivars. A total of 9367 (up = 4363, down = 5004), 7159 (3413/3746), 7436 (3566/3870), and 5707 (2719/2988) differentially expressed genes (DEGs) were identified between fast- and slow-growing cultivars. Moreover, GO and KEGG enrichment analyses predicted that many pathways were involved in vascular development and transcriptional regulation in elm, such as "plant-type secondary cell wall biogenesis", "cell wall thickening", and "phenylpropanoid biosynthesis". NAC domain transcriptional factors (TFs) and their master regulators (VND1/MYB26), cellulose synthase catalytic subunits (CESAs) (such as IRX5/IRX3/IRX1), xylan synthesis, and secondary wall thickness (such as IRX9/IRX10/IRX8) were supposed to function in the thickening mechanism of elm branches. Our results indicated that the general phenylpropanoid pathway (such as PAL/C4H/4CL) and lignin metabolism (such as HCL/CSE/CCoAOMT/CCR/F5H) had vital functions in the growth of elm branches. Our transcriptome data were consistent with molecular results for branch thickening in elm cultivars.

ZmCOI2a and ZmCOI2b redundantly regulate anther dehiscence and gametophytic male fertility in maize

In higher plants, the generation and release of viable pollen from anthers is vital for double fertilization and the initiation of seed development. Thus, the characterization of genes related to pollen development and anther dehiscence in plants is of great significance. The F-box protein COI1 plays a crucial role in the jasmonate (JA) signaling pathway and interacts with many JAZ family proteins in the presence of jasmonoyl-isoleucine (JA-Ile) or coronatine (COR). The mutation of AtCOI1 in Arabidopsis leads to defective anther dehiscence and male sterility (MS), although COI has not been shown to affect fertility in Zea mays (maize). Here we identified two genes, ZmCOI2a and ZmCOI2b, that redundantly regulate gametophytic male fertility. Both ZmCOI2a and ZmCOI2b are highly homologous and constitutively expressed in all tissues tested. Subcellular localization revealed that ZmCOI2a and ZmCOI2b were located in the nucleus. The coi2a coi2b double mutant, generated by CRISPR/Cas9, had non-dehiscent anthers, delayed anther development and MS. In addition, coi2a coi2b male gametes could not be transmitted to the next generation because of severe defects in pollen germination. The JA content of coi2a coi2b anthers was unaltered compared with those of the wild type, and the exogenous application of JA could not rescue the fertility defects of coi2a coi2b. Transcriptome analysis showed that the expression of genes involving the JA signaling transduction pathway, including ZmJAZ3, ZmJAZ4, ZmJAZ5 and ZmJAZ15, was affected in coi2a coi2b. However, yeast two-hybrid assays showed that ZmJAZs interacted with ZmCOI1s, but not with ZmCOI2s. In conclusion, ZmCOI2a and ZmCOI2b redundantly regulate anther dehiscence and gametophytic male fertility in maize.

MYB2 Is Important for Tapetal PCD and Pollen Development by Directly Activating Protease Expression in Arabidopsis

Tapetal programmed cell death (PCD) is a complex biological process that plays an important role in pollen formation and reproduction. Here, we identified the MYB2 transcription factor expressed in the tapetum from stage 5 to stage 11 that was essential for tapetal PCD and pollen development in Arabidopsis thaliana. Downregulation of MYB2 retarded tapetal degeneration, produced defective pollen, and decreased pollen vitality. EMSA and transcriptional activation analysis revealed that MYB2 acted as an upstream activator and directly regulated expression of the proteases CEP1 and βVPE. The expression of these proteases was lower in the buds of the myb2 mutant. Overexpression of either/both CEP1 or/and βVPE proteases partially recover pollen vitality in the myb2 background. Taken together, our results revealed that MYB2 regulates tapetal PCD and pollen development by directly activating expression of the proteases CEP1 and βVPE. Thus, a transcription factor/proteases regulatory and activated cascade was established for tapetal PCD during another development in Arabidopsis thaliana. Highlight: MYB2 is involved in tapetal PCD and pollen development by directly regulating expression of the protease CEP1 and βVPE and establishes a transcription factor/proteases regulatory and activated cascade.

Integrated transcriptome and small RNA sequencing in revealing miRNA-mediated regulatory network of floral bud break in Prunus mume

MicroRNAs is one class of small non-coding RNAs that play important roles in plant growth and development. Though miRNAs and their target genes have been widely studied in many plant species, their functional roles in floral bud break and dormancy release in woody perennials is still unclear. In this study, we applied transcriptome and small RNA sequencing together to systematically explore the transcriptional and post-transcriptional regulation of floral bud break in P. mume. Through expression profiling, we identified a few candidate genes and miRNAs during different developmental stage transitions. In total, we characterized 1,553 DEGs associated with endodormancy release and 2,084 DEGs associated with bud flush. Additionally, we identified 48 known miRNAs and 53 novel miRNAs targeting genes enriched in biological processes such as floral organ morphogenesis and hormone signaling transudation. We further validated the regulatory relationship between differentially expressed miRNAs and their target genes combining computational prediction, degradome sequencing, and expression pattern analysis. Finally, we integrated weighted gene co-expression analysis and constructed miRNA-mRNA regulatory networks mediating floral bud flushing competency. In general, our study revealed the miRNA-mediated networks in modulating floral bud break in P. mume. The findings will contribute to the comprehensive understanding of miRNA-mediated regulatory mechanism governing floral bud break and dormancy cycling in wood perennials.

Multi-layered Regulation of Plant Cell Wall Thickening

Plants need to develop thickened cell walls with appropriate localization through precise regulation during the process of growth and development in order to support their body weight and to build long distance transportation systems. Wall thickening is achieved through a multitude of regulatory networks in various tissues under changeable environments. In this mini-review, we summarize current understanding of the regulatory pathways and mechanisms involved in cell wall thickening. Regulation of cell wall thickening is not only mechanistically essential to understand the plant structure accretion but also has applicable significance to plant cell wall biomass utilization.

Full-length transcriptomic identification of R2R3-MYB family genes related to secondary cell wall development in Cunninghamia lanceolata (Chinese fir)

BACKGROUND

R2R3-MYB is a class of transcription factor crucial in regulating secondary cell wall development during wood formation. The regulation of wood formation in gymnosperm has been understudied due to its large genome size. Using Single-Molecule Real-Time sequencing, we obtained full-length transcriptomic libraries from the developmental stem of Cunninghamia lanceolata, a perennial conifer known as Chinese fir. The R2R3-MYB of C. lanceolata (hereafter named as ClMYB) associated with secondary wall development were identified based on phylogenetic analysis, expression studies and functional study on transgenic line.

RESULTS

The evolutionary relationship of 52 ClMYBs with those from Arabidopsis thaliana, Eucalyptus grandis, Populus trichocarpa, Oryza sativa, two gymnosperm species, Pinus taeda, and Picea glauca were established by neighbour-joining phylogenetic analysis. A large number of ClMYBs resided in the woody-expanded subgroups that predominated with the members from woody dicots. In contrast, the woody-preferential subgroup strictly carrying the members of woody dicots contained only one candidate. The results suggest that the woody-expanded subgroup emerges before the gymnosperm/angiosperm split, while most of the woody-preferential subgroups are likely lineage-specific to woody dicots. Nine candidates shared the same subgroups with the A. thaliana orthologs, with known function in regulating secondary wall development. Gene expression analysis inferred that ClMYB1/2/3/4/5/26/27/49/51 might participate in secondary wall development, among which ClMYB1/2/5/26/27/49 were significantly upregulated in the highly lignified compression wood region, reinforcing their regulatory role associated with secondary wall development. ClMYB1 was experimentally proven a transcriptional activator that localised in the nucleus. The overexpression of ClMYB1 in Nicotiana benthamiana resulted in an increased lignin deposition in the stems. The members of subgroup S4, ClMYB3/4/5 shared the ERF-associated amphiphilic repression motif with AtMYB4, which is known to repress the metabolism of phenylpropanoid derived compounds. They also carried a core motif specific to gymnosperm lineage, suggesting divergence of the regulatory process compared to the angiosperms.

CONCLUSIONS

This work will enrich the collection of full-length gymnosperm-specific R2R3-MYBs related to stem development and contribute to understanding their evolutionary relationship with angiosperm species.

Identification and expression analysis of the glycosyltransferase GT43 family members in bamboo reveal their potential function in xylan biosynthesis during rapid growth

Background

Xylan is one of the most abundant hemicelluloses and can crosslink cellulose and lignin to increase the stability of cell walls. A number of genes encoding glycosyltransferases play vital roles in xylan biosynthesis in plants, such as those of the GT43 family. However, little is known about glycosyltransferases in bamboo, especially woody bamboo which is a good substitute for timber.

Results

A total of 17 GT43 genes (PeGT43–1 ~ PeGT43–17) were identified in the genome of moso bamboo (Phyllostachys edulis), which belong to three subfamilies with specific motifs. The phylogenetic and collinearity analyses showed that PeGT43s may have undergone gene duplication, as a result of collinearity found in 12 pairs of PeGT43s, and between 17 PeGT43s and 10 OsGT43s. A set of cis-acting elements such as hormones, abiotic stress response and MYB binding elements were found in the promoter of PeGT43s. PeGT43s were expressed differently in 26 tissues, among which the highest expression level was found in the shoots, especially in the rapid elongation zone and nodes. The genes coexpressed with PeGT43s were annotated as associated with polysaccharide metabolism and cell wall biosynthesis. qRT–PCR results showed that the coexpressed genes had similar expression patterns with a significant increase in 4.0 m shoots and a peak in 6.0 m shoots during fast growth. In addition, the xylan content and structural polysaccharide staining intensity in bamboo shoots showed a strong positive correlation with the expression of PeGT43s. Yeast one-hybrid assays demonstrated that PeMYB35 could recognize the 5′ UTR/promoter of PeGT43–5 by binding to the SMRE cis-elements.

Conclusions

PeGT43s were found to be adapted to the requirement of xylan biosynthesis during rapid cell elongation and cell wall accumulation, as evidenced by the expression profile of PeGT43s and the rate of xylan accumulation in bamboo shoots. Yeast one-hybrid analysis suggested that PeMYB35 might be involved in xylan biosynthesis by regulating the expression of PeGT43–5 by binding to its 5′ UTR/promoter. Our study provides a comprehensive understanding of PeGT43s in moso bamboo and lays a foundation for further functional analysis of PeGT43s for xylan biosynthesis during rapid growth.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-021-08192-y.

The role of ontogeny in wood diversity and evolution

Evolutionary developmental biology (evo-devo) explores the link between developmental patterning and phenotypic change through evolutionary time. In this review, we highlight the scientific advancements in understanding xylem evolution afforded by the evo-devo approach, opportunities for further engagement, and future research directions for the field. We review evidence that (1) heterochrony-the change in rate and timing of developmental events, (2) homeosis-the ontogenetic replacement of features, (3) heterometry-the change in quantity of a feature, (4) exaptation-the co-opting and repurposing of an ancestral feature, (5) the interplay between developmental and capacity constraints, and (6) novelty-the emergence of a novel feature, have all contributed to generating the diversity of woods. We present opportunities for future research engagement, which combine wood ontogeny within the context of robust phylogenetic hypotheses, and molecular biology.

Evolution and diversity of the angiosperm anther: trends in function and development

Anther development and dehiscence is considered from an evolutionary perspective to identify drivers for differentiation, functional conservation and to identify key questions for future male reproduction research. Development of viable pollen and its timely release from the anther are essential for fertilisation of angiosperm flowers. The formation and subsequent dehiscence of the anther are under tight regulatory control, and these processes are remarkably conserved throughout the diverse families of the angiosperm clade. Anther development is a complex process, which requires timely formation and communication between the multiple somatic anther cell layers (the epidermis, endothecium, middle layer and tapetum) and the developing pollen. These layers go through regulated development and selective degeneration to facilitate the formation and ultimate release of the pollen grains. Insight into the evolution and divergence of anther development and dehiscence, especially between monocots and dicots, is driving greater understanding of the male reproductive process and increased, resilient crop yields. This review focuses on anther structure from an evolutionary perspective by highlighting their diversity across plant species. We summarise new findings that illustrate the complexities of anther development and evaluate how they challenge established models of anther form and function, and how they may help to deliver future sustainable crop yields.

Vitis OneGenE: A Causality-Based Approach to Generate Gene Networks in Vitis vinifera Sheds Light on the Laccase and Dirigent Gene Families

The abundance of transcriptomic data and the development of causal inference methods have paved the way for gene network analyses in grapevine. Vitis OneGenE is a transcriptomic data mining tool that finds direct correlations between genes, thus producing association networks. As a proof of concept, the stilbene synthase gene regulatory network obtained with OneGenE has been compared with published co-expression analysis and experimental data, including cistrome data for MYB stilbenoid regulators. As a case study, the two secondary metabolism pathways of stilbenoids and lignin synthesis were explored. Several isoforms of laccase, peroxidase, and dirigent protein genes, putatively involved in the final oxidative oligomerization steps, were identified as specifically belonging to either one of these pathways. Manual curation of the predicted sequences exploiting the last available genome assembly, and the integration of phylogenetic and OneGenE analyses, identified a group of laccases exclusively present in grapevine and related to stilbenoids. Here we show how network analysis by OneGenE can accelerate knowledge discovery by suggesting new candidates for functional characterization and application in breeding programs.

Transcriptome and Metabolome Analyses Provide Insights into the Stomium Degeneration Mechanism in Lily

Lily (Lilium spp.) is a widely cultivated horticultural crop that has high ornamental and commercial value but also the serious problem of pollen pollution. However, mechanisms of anther dehiscence in lily remain largely unknown. In this study, the morphological characteristics of the stomium zone (SZ) from different developmental stages of ‘Siberia’ lily anthers were investigated. In addition, transcriptomic and metabolomic data were analyzed to identify the differentially expressed genes (DEGs) and secondary metabolites involved in stomium degeneration. According to morphological observations, SZ lysis occurred when flower buds were 6–8 cm in length and was completed in 9 cm. Transcriptomic analysis identified the genes involved in SZ degeneration, including those associated with hormone signal transduction, cell structure, reactive oxygen species (ROS), and transcription factors. A weighted co-expression network showed strong correlations between transcription factors. In addition, TUNEL (TdT-mediated dUTP nick-end labeling) assays showed that programmed cell death was important during anther SZ degeneration. Jasmonates might also have key roles in anther dehiscence by affecting the expression of the genes involved in pectin lysis, water transport, and cysteine protease. Collectively, the results of this study improve our understanding of anther dehiscence in lily and provide a data platform from which the molecular mechanisms of SZ degeneration can be revealed.

GhMYB7 promotes secondary wall cellulose deposition in cotton fibres by regulating GhCesA gene expression through three distinct cis-elements

Cotton fibre is the most important source for natural textiles. The secondary cell walls (SCWs) of mature cotton fibres contain the highest proportion of cellulose content (> 90%) in any plant. The onset and progression of SCW cellulose synthesis need to be tightly controlled to balance fibre elongation and cell wall deposition. However, regulatory mechanisms that control cellulose synthesis during cotton fibre growth remain elusive. Here, we conducted genetic and functional analyses demonstrating that the R2R3-MYB GhMYB7 controls cotton fibre cellulose synthesis. Overexpression of GhMYB7 in cotton sped up SCW cellulose biosynthesis in fibre cells, and led to shorter fibres with thicker walls. By contrast, RNA interference (RNAi) silencing of GhMYB7 delayed fibre SCW cellulose synthesis and resulted in elongated fibres with thinner walls. Furthermore, we demonstrated that GhMYB7 regulated cotton fibre SCW cellulose synthases by directly binding to three distinct cis-elements in the respective GhCesA4, GhCesA7 and GhCesA8 promoters. We found that this regulatory mechanism of cellulose synthesis was 'hi-jacked' also by other GhMYBs. Together, our findings uncover a hitherto-unknown mechanism that cotton fibre employs to regulate SCW cellulose synthesis. Our results also provide a strategy for genetic improvement of SCW thickness of cotton fibre.

A regulatory network driving shoot lignification in rapidly growing bamboo

Woody bamboo is environmentally friendly, abundant, and an alternative to conventional timber. Degree of lignification and lignin content and deposition affect timber properties. However, the lignification regulatory network in monocots is poorly understood. To elucidate the regulatory mechanism of lignification in moso bamboo (Phyllostachys edulis), we conducted integrated analyses using transcriptome, small RNA, and degradome sequencing followed by experimental verification. The lignification degree and lignin content increased with increased bamboo shoot height, whereas phenylalanine ammonia-lyase and Laccase activities first increased and then decreased with shoot growth. Moreover, we identified 11,504 differentially expressed genes (DEGs) in different portions of the 13th internodes of different height shoots; most DEGs associated with cell wall and lignin biosynthesis were upregulated, whereas some DEGs related to cell growth were downregulated. We identified a total of 1,502 miRNAs, of which 687 were differentially expressed. Additionally, in silico and degradome analyses indicated that 5,756 genes were targeted by 691 miRNAs. We constructed a regulatory network of lignification, including 11 miRNAs, 22 transcription factors, and 36 enzyme genes, in moso bamboo. Furthermore, PeLAC20 overexpression increased lignin content in transgenic Arabidopsis (Arabidopsis thaliana) plants. Finally, we proposed a reliable miRNA-mediated "MYB-PeLAC20" module for lignin monomer polymerization. Our findings provide definite insights into the genetic regulation of bamboo lignification. In addition to providing a platform for understanding related mechanisms in other monocots, these insights could be used to develop strategies to improve bamboo timber properties.

An insertion mutation located on putative enhancer regions of the MYB26-like gene induces inhibition of anther dehiscence resulting in novel genic male sterility in radish (Raphanus sativus L.)

A novel male-sterility trait was identified in a radish (Raphanus sativus L.) population. Although the size of male-sterile anthers was comparable to that of normal flowers, no pollen grain was observed during anther dehiscence. However, dissection of male-sterile anthers revealed an abundance of normal pollen grains. Analysis of segregating populations showed that a single recessive locus, designated RsMs1, conferred male sterility. Based on two radish draft genome sequences, molecular markers were developed to delimit the genomic region harboring the RsMs1. The region was narrowed down to approximately 24 kb after analyzing recombinants selected from 7511 individuals of a segregating population. Sequencing of the delimited region yielded six putative genes including four genes expressed in the floral tissue, and one gene with significant differential expression between male-fertile and male-sterile individuals of a segregating population. This differentially expressed gene was orthologous to the Arabidopsis MYB26 gene, which played a critical role in anther dehiscence. Excluding a synonymous single nucleotide polymorphism in exon3, no polymorphism involving coding and putative promoter regions was detected between alleles. A 955-bp insertion was identified 7.5 kb upstream of the recessive allele. Highly conserved motifs among four Brassicaceae species were identified around this insertion site, suggesting the presence of putative enhancer sequences. A functional marker was developed for genotyping of the RsMs1 based on the 955-bp insertion. A total of 120 PI accessions were analyzed using this marker, and 11 accessions were shown to carry the recessive rsms1 allele.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-021-01254-9.

Advances in the role of auxin for transcriptional regulation of lignin biosynthesis

Lignin is a natural polymer interlaced with cellulose and hemicellulose in secondary cell walls (SCWs). Auxin acts via its signalling transduction to regulate most of plant physiological processes. Lignification responds to auxin signals likewise and affects the development of anther and secondary xylem in plants. In this review, the research advances of AUXIN RESPONSE FACTOR (ARF)-dependent signalling pathways regulating lignin formation are discussed in detail. In an effort to facilitate the understanding of several key regulators in this process, we present a regulatory framework that comprises protein-protein interactions at the top and protein-gene regulation divided into five tiers. This characterises the regulatory roles of auxin in lignin biosynthesis and links auxin signalling transduction to transcriptional cascade of lignin biosynthesis. Our works further point to several of significant problems that need to be resolved in the future to gain a better understanding of the underlying mechanisms through which auxin regulates lignin biosynthesis.

Pod shattering in grain legumes: emerging genetic and environment-related patterns

A reduction in pod shattering is one of the main components of grain legume domestication. Despite this, many domesticated legumes suffer serious yield losses due to shattering, particularly under arid conditions. Mutations related to pod shattering modify the twisting force of pod walls or the structural strength of the dehiscence zone in pod sutures. At a molecular level, a growing body of evidence indicates that these changes are controlled by a relatively small number of key genes that have been selected in parallel across grain legume species, supporting partial molecular convergence. Legume homologs of Arabidopsis thaliana silique shattering genes play only minor roles in legume pod shattering. Most domesticated grain legume species contain multiple shattering-resistance genes, with mutants of each gene typically showing only partial shattering resistance. Hence, crosses between varieties with different genes lead to transgressive segregation of shattering alleles, producing plants with either enhanced shattering resistance or atavistic susceptibility to the trait. The frequency of these resistance pod-shattering alleles is often positively correlated with environmental aridity. The continued development of pod-shattering-related functional information will be vital for breeding crops that are suited to the increasingly arid conditions expected in the coming decades.

MYB Transcription Factors and Its Regulation in Secondary Cell Wall Formation and Lignin Biosynthesis during Xylem Development

The secondary wall is the main part of wood and is composed of cellulose, xylan, lignin, and small amounts of structural proteins and enzymes. Lignin molecules can interact directly or indirectly with cellulose, xylan and other polysaccharide molecules in the cell wall, increasing the mechanical strength and hydrophobicity of plant cells and tissues and facilitating the long-distance transportation of water in plants. MYBs (v-myb avian myeloblastosis viral oncogene homolog) belong to one of the largest superfamilies of transcription factors, the members of which regulate secondary cell-wall formation by promoting/inhibiting the biosynthesis of lignin, cellulose, and xylan. Among them, MYB46 and MYB83, which comprise the second layer of the main switch of secondary cell-wall biosynthesis, coordinate upstream and downstream secondary wall synthesis-related transcription factors. In addition, MYB transcription factors other than MYB46/83, as well as noncoding RNAs, hormones, and other factors, interact with one another to regulate the biosynthesis of the secondary wall. Here, we discuss the biosynthesis of secondary wall, classification and functions of MYB transcription factors and their regulation of lignin polymerization and secondary cell-wall formation during wood formation.

Pod indehiscence in common bean is associated with the fine regulation of PvMYB26

In legumes, pod shattering occurs when mature pods dehisce along the sutures, and detachment of the valves promotes seed dispersal. In Phaseolus vulgaris (L)., the major locus qPD5.1-Pv for pod indehiscence was identified recently. We developed a BC4/F4 introgression line population and narrowed the major locus down to a 22.5 kb region. Here, gene expression and a parallel histological analysis of dehiscent and indehiscent pods identified an AtMYB26 orthologue as the best candidate for loss of pod shattering, on a genomic region ~11 kb downstream of the highest associated peak. Based on mapping and expression data, we propose early and fine up-regulation of PvMYB26 in dehiscent pods. Detailed histological analysis establishes that pod indehiscence is associated with the lack of a functional abscission layer in the ventral sheath, and that the key anatomical modifications associated with pod shattering in common bean occur early during pod development. We finally propose that loss of pod shattering in legumes resulted from histological convergent evolution and that it is the result of selection at orthologous loci.

Development of the Middle Layer in the Anther of Arabidopsis

The middle layer is an essential cell layer of the anther wall located between the endothecium and tapetum in Arabidopsis. Based on sectioning, the middle layer was found to be degraded at stage 7, which led to the separation of the tapetum from the anther wall. Here, we established techniques for live imaging of the anther. We created a marker line with fluorescent proteins expressed in all anther layers to study anther development. Several staining methods were used in the intact anthers to study anther cell morphology. We clarified the initiation, development, and degradation of the middle layer in Arabidopsis. This layer is initiated from both the inner and outer secondary parietal cells at stage 4, stopped cell division at stage 6, and finally degraded at stage 11. The neighboring cell layers, the epidermis, and endothecium continued cell division until stage 10, which led to a thin middle layer. The degradation of the tapetum cell wall at stage 7 lead to its isolation from the anther wall. This work presents fundamental information on the development of the middle layer, which facilitates the further investigation of anther development and plant fertility. These live imaging methods could be useful in future studies.

Auxin and Flower Development: A Blossoming Field

The establishment of the species-specific floral organ body plan involves many coordinated spatiotemporal processes, which include the perception of positional information that specifies floral meristem and floral organ founder cells, coordinated organ outgrowth coupled with the generation and maintenance of inter-organ and inter-whorl boundaries, and the termination of meristem activity. Auxin is integrated within the gene regulatory networks that control these processes and plays instructive roles at the level of tissue-specific biosynthesis and polar transport to generate local maxima, perception, and signaling. Key features of auxin function in several floral contexts include cell nonautonomy, interaction with cytokinin gradients, and the central role of MONOPTEROS and ETTIN to regulate canonical and noncanonical auxin response pathways, respectively. Arabidopsis flowers are not representative of the enormous angiosperm floral diversity; therefore, comparative studies are required to understand how auxin underlies these developmental differences. It will be of great interest to compare the conservation of auxin pathways among flowering plants and to discuss the evolutionary role of auxin in floral development.

Histone methyltransferase ATX1 dynamically regulates fiber secondary cell wall biosynthesis in Arabidopsis inflorescence stem

Secondary wall thickening in the sclerenchyma cells is strictly controlled by a complex network of transcription factors in vascular plants. However, little is known about the epigenetic mechanism regulating secondary wall biosynthesis. In this study, we identified that ARABIDOPSIS HOMOLOG of TRITHORAX1 (ATX1), a H3K4-histone methyltransferase, mediates the regulation of fiber cell wall development in inflorescence stems of Arabidopsis thaliana. Genome-wide analysis revealed that the up-regulation of genes involved in secondary wall formation during stem development is largely coordinated by increasing level of H3K4 tri-methylation. Among all histone methyltransferases for H3K4me3 in Arabidopsis, ATX1 is markedly increased during the inflorescence stem development and loss-of-function mutant atx1 was impaired in secondary wall thickening in interfascicular fibers. Genetic analysis showed that ATX1 positively regulates secondary wall deposition through activating the expression of secondary wall NAC master switch genes, SECONDARY WALL-ASSOCIATED NAC DOMAIN PROTEIN1 (SND1) and NAC SECONDARY WALL THICKENING PROMOTING FACTOR1 (NST1). We further identified that ATX1 directly binds the loci of SND1 and NST1, and activates their expression by increasing H3K4me3 levels at these loci. Taken together, our results reveal that ATX1 plays a key role in the regulation of secondary wall biosynthesis in interfascicular fibers during inflorescence stem development of Arabidopsis.

Copper deficiency alters shoot architecture and reduces fertility of both gynoecium and androecium in Arabidopsis thaliana

Copper deficiency reduces plant growth, male fertility, and seed set. The contribution of copper to female fertility and the underlying molecular aspects of copper deficiency-caused phenotypes are not well known. We show that among copper deficiency-caused defects in Arabidopsis thaliana were also the increased shoot branching, delayed flowering and senescence, and entirely abolished gynoecium fertility. The increased shoot branching of copper-deficient plants was rescued by the exogenous application of auxin or copper. The delayed flowering was associated with the decreased expression of the floral activator, FT. Copper deficiency also decreased the expression of senescence-associated genes, WRKY53 and SAG13, but increased the expression of SAG12. The reduced fertility of copper-deficient plants stemmed from multiple factors including the abnormal stigma papillae development, the abolished gynoecium fertility, and the failure of anthers to dehisce. The latter defect was associated with reduced lignification, the upregulation of copper microRNAs and the downregulation of their targets, laccases, implicated in lignin synthesis. Copper-deficient plants accumulated ROS in pollen and had reduced cytochrome c oxidase activity in both leaves and floral buds. This study opens new avenues for the investigation into the relationship between copper homeostasis, hormone-mediated shoot architecture, gynoecium fertility, and copper deficiency-derived nutritional signals leading to the delay in flowering and senescence.

Integrative analysis of transcriptomic and proteomic changes related to male sterility in Tagetes erecta

Male sterile and male fertile two-type lines are important in heterosis utilization and breeding in Tagetes erecta, but the genes and pathways involved in male sterility are poorly understood. To explore these topics, transcriptome data (by RNA-seq) and proteome data (by iTRAQ) were gathered from flower buds of the male sterile line 'MS2-2' and male fertile line 'MF2-2' and integrated for a better understanding of the underlying molecular mechanisms of male sterility in T. erecta. The RNA-seq procedure generated 285,139,740 clean reads and 63359 unigenes and 6640 differentially expressed genes (DEGs) were identified, of which 4136 were downregulated and 2504 were upregulated in 'MS2-2'. DEGs related to flower development, pollen development, pollen wall assembly, endogenous hormones and transcription factors were identified. The iTRAQ analysis identified 3950 proteins in total; 789 were differentially expressed proteins (381 upregulated, 408 downregulated), which were mainly annotated to the Ribosome, Carbon metabolism and Biosynthesis of amino acids pathways. An association analysis revealed strong correlation (r Pearson = 0.6019) between the transcriptomic and proteomic data, and 256 and 34 proteins showed the same and opposite expression patterns with regard to their transcripts, respectively. Pathways such as photosynthesis, fatty acid biosynthesis and phenylpropanoid biosynthesis which influence tapetum and pollen development in male sterile plants, were significantly enriched at the transcript and protein levels. Most genes involved in these pathways were downregulated in 'MS2-2'. The low expression of these genes or functional loss of proteins could be associated with flower development, pollen development and related to changes in fertility in T. erecta. This study provided transcriptomic and proteomic information for T. erecta that could illuminate the mechanism of male sterility.

Integrated mRNA, MicroRNA Transcriptome and Degradome Analyses Provide Insights into Stamen Development in Moso Bamboo

A flower is an essential organ for sexual reproduction in flowering plants, which has been extensively studied in model plants. In this study, we used transcriptomic, small RNA and degradome analyses to characterize key microRNAs (miRNAs) and their targets in floral organs of moso bamboo. In total, we identified 13,051 differentially expressed genes and 109 known miRNAs from 26 miRNA families. We aligned the miRNAs to known miRNA databases and revealed some conserved as well as novel miRNAs. Sixteen conserved miRNAs were specifically and highly expressed in stamens, including miRNA159 and miRNA166. In situ hybridization shows that miRNA159 plays a key role in the regulation of stamen development, and the expression levels of its targets PheMYB98 and PheMYB42 were low. Furthermore, Phe-MIRNA159 partially recovers phenotypes of mir159ab double mutant. Overexpression of Phe-MIR159 could cause failure in anther dehisce, and the mature pollens could not be dispersed and further reduce fertility in Arabidopsis. Semi-thin section result shows that anther endothelial layer of Phe-MIRNA159 overexpressing lines is lack of secondary thickening, resulting in limited force for anther opening. Phe-miR159 may regulate the expression of genes related to secondary thickening through negative regulation of AtMYB33, affecting the anther dehiscence. Taken together, this study provides insights regarding molecular networks underlying floral organs development of moso bamboo.