Origins and Evolution of Stomatal Development

Investigation on the Potential Functions of ZmEPF/EPFL Family Members in Response to Abiotic Stress in Maize

Maize is an important crop used for food, feed, and fuel. Abiotic stress is an important factor affecting maize yield. The EPF/EPFL gene family encodes class-specific secretory proteins that play an important role in the response to abiotic stress in plants. In order to explore and utilize the EPF/EPFL family in maize, the family members were systematically identified, and their chromosomal localization, physicochemical properties, cis-acting element prediction in promoters, phylogenetic tree construction, and expression pattern analysis were carried out using bioinformatics techniques. A total of 18 ZmEPF/EPFL proteins were identified in maize, which are mostly alkaline and a small portion acidic. Subcellular localization results showed that ZmEPF6, ZmEPF12, and ZmEPFL2 are localized in the nucleus and cytoplasm. Analysis of cis-acting elements revealed that members of the ZmEPF/EPFL family contain regulatory elements such as light response, anoxic, low temperature, and hormone response regulatory elements. RT-qPCR results showed that these family members are indeed responding to cold stress and hormone treatments. These results of this study provide a theoretical basis for improving the abiotic stress resistance of maize in future research.

Metagenome-assembled genome of the glacier alga Ancylonema yields insights into the evolution of streptophyte life on ice and land

Contemporary glaciers are inhabited by streptophyte algae that balance photosynthesis and growth with tolerance of low temperature, desiccation and UV radiation. These same environmental challenges have been hypothesised as the driving force behind the evolution of land plants from streptophyte algal ancestors in the Cryogenian (720-635 million years ago). We sequenced, assembled and analysed the metagenome-assembled genome of the glacier alga Ancylonema nordenskiöldii to investigate its adaptations to life in ice, and whether this represents a vestige of Cryogenian exaptations. Phylogenetic analysis confirms the placement of glacier algae within the sister lineage to land plants, Zygnematophyceae. The metagenome-assembled genome is characterised by an expansion of genes involved in tolerance of high irradiance and UV light, while lineage-specific diversification is linked to the novel screening pigmentation of glacier algae. We found no support for the hypothesis of a common genomic basis for adaptations to ice and to land in streptophytes. Comparative genomics revealed that the reductive morphological evolution in the ancestor of Zygnematophyceae was accompanied by reductive genome evolution. This first genome-scale data for glacier algae suggests an Ancylonema-specific adaptation to the cryosphere, and sheds light on the genome evolution of land plants and Zygnematophyceae.

Multiple mechanisms explain loss of anthocyanins from betalain-pigmented Caryophyllales, including repeated wholesale loss of a key anthocyanidin synthesis enzyme

In this study, we investigate the genetic mechanisms responsible for the loss of anthocyanins in betalain-pigmented Caryophyllales, considering our hypothesis of multiple transitions to betalain pigmentation. Utilizing transcriptomic and genomic datasets across 357 species and 31 families, we scrutinize 18 flavonoid pathway genes and six regulatory genes spanning four transitions to betalain pigmentation. We examined evidence for hypotheses of wholesale gene loss, modified gene function, altered gene expression, and degeneration of the MBW (MYB-bHLH-WD40) trasnscription factor complex, within betalain-pigmented lineages. Our analyses reveal that most flavonoid synthesis genes remain conserved in betalain-pigmented lineages, with the notable exception of TT19 orthologs, essential for the final step in anthocyanidin synthesis, which appear to have been repeatedly and entirely lost. Additional late-stage flavonoid pathway genes upstream of TT19 also manifest strikingly reduced expression in betalain-pigmented species. Additionally, we find repeated loss and alteration in the MBW transcription complex essential for canonical anthocyanin synthesis. Consequently, the loss and exclusion of anthocyanins in betalain-pigmented species appear to be orchestrated through several mechanisms: loss of a key enzyme, downregulation of synthesis genes, and degeneration of regulatory complexes. These changes have occurred iteratively in Caryophyllales, often coinciding with evolutionary transitions to betalain pigmentation.

Integrating the multiple functions of CHLH into chloroplast-derived signaling fundamental to plant development and adaptation as well as fruit ripening

Chlorophyll (Chl)-mediated oxygenic photosynthesis sustains life on Earth. Greening leaves play fundamental roles in plant growth and crop yield, correlating with the idea that more Chls lead to better adaptation. However, they face significant challenges from various unfavorable environments. Chl biosynthesis hinges on the first committed step, which involves inserting Mg2+ into protoporphyrin. This step is facilitated by the H subunit of magnesium chelatase (CHLH) and features a conserved mechanism from cyanobacteria to plants. For better adaptation to fluctuating land environments, especially drought, CHLH evolves multiple biological functions, including Chl biosynthesis, retrograde signaling, and abscisic acid (ABA) responses. Additionally, it integrates into various chloroplast-derived signaling pathways, encompassing both retrograde signaling and hormonal signaling. The former comprises ROS (reactive oxygen species), heme, GUN (genomes uncoupled), MEcPP (methylerythritol cyclodiphosphate), β-CC (β-cyclocitral), and PAP (3'-phosphoadenosine-5'-phosphate). The latter involves phytohormones like ABA, ethylene, auxin, cytokinin, gibberellin, strigolactone, brassinolide, salicylic acid, and jasmonic acid. Together, these elements create a coordinated regulatory network tailored to plant development and adaptation. An intriguing example is how drought-mediated improvement of fruit quality provides insights into chloroplast-derived signaling, aiding the shift from vegetative to reproductive growth. In this context, we explore the integration of CHLH's multifaceted roles into chloroplast-derived signaling, which lays the foundation for plant development and adaptation, as well as fruit ripening and quality. In the future, manipulating chloroplast-derived signaling may offer a promising avenue to enhance crop yield and quality through the homeostasis, function, and regulation of Chls.

Natural polymorphisms in ZmIRX15A affect water-use efficiency by modulating stomatal density in maize

Stomatal density (SD) is closely related to crop drought resistance. Understanding the genetic basis for natural variation in SD may facilitate efforts to improve water-use efficiency. Here, we report a genome-wide association study for SD in maize seedlings, which identified 18 genetic variants that could be resolved to seven candidate genes. A 3-bp insertion variant (InDel1089) in the last exon of Zea mays (Zm) IRX15A (Irregular xylem 15A) had the most significant association with SD and modulated the translation of ZmIRX15A mRNA by affecting its secondary structure. Dysfunction of ZmIRX15A increased SD, leading to an increase in the transpiration rate and CO2 assimilation efficiency. ZmIRX15A encodes a xylan deposition enzyme and its disruption significantly decreased xylan abundance in secondary cell wall composition. Transcriptome analysis revealed a substantial alteration of the expression of genes involved in stomatal complex morphogenesis and drought response in the loss-of-function of ZmIRX15A mutant. Overall, our study provides important genetic insights into the natural variation of leaf SD in maize, and the identified loci or genes can serve as direct targets for enhancing drought resistance in molecular-assisted maize breeding.

Stomata variation in the process of polyploidization in Chinese chive (Allium tuberosum)

BACKGROUND

Stomatal variation, including guard cell (GC) density, size and chloroplast number, is often used to differentiate polyploids from diploids. However, few works have focused on stomatal variation with respect to polyploidization, especially for consecutively different ploidy levels within a plant species. For example, Allium tuberosum, which is mainly a tetraploid (2n = 4x = 32), is also found at other ploidy levels which have not been widely studied yet.

RESULTS

We recently found cultivars with different ploidy levels, including those that are diploid (2n = 2x = 16), triploid (2n = 3x = 24), pseudopentaploid (2n = 34-42, mostly 40) and pseudohexaploid (2n = 44-50, mostly 48). GCs were evaluated for their density, size (length and width) and chloroplast number. There was no correspondence between ploidy level and stomatal density, in which anisopolyploids (approximately 57 and 53 stomata/mm2 in triploid and pseudopentaploid, respectively) had a higher stomatal density than isopolyploids (approximately 36, 43, and 44 stomata/mm2 in diploid, tetraploid and pseudohexaploid, respectively). There was a positive relationship between ploidy level and GC chloroplast number (approximately 44, 45, 51, 72 and 90 in diploid to pseudohexaploid, respectively). GC length and width also increased with ploidy level. However, the length increased approximately 1.22 times faster than the width during polyploidization.

CONCLUSIONS

This study shows that GC size increased with increasing DNA content, but the rate of increase differed between length and width. In the process of polyploidization, plants evolved longer and narrower stomata with more chloroplasts in the GCs.

Stomatal cell fate commitment via transcriptional and epigenetic control: Timing is crucial

The formation of stomata presents a compelling model system for comprehending the initiation, proliferation, commitment and differentiation of de novo lineage-specific stem cells. Precise, timely and robust cell fate and identity decisions are crucial for the proper progression and differentiation of functional stomata. Deviations from this precise specification result in developmental abnormalities and nonfunctional stomata. However, the molecular underpinnings of timely cell fate commitment have just begun to be unravelled. In this review, we explore the key regulatory strategies governing cell fate commitment, emphasizing the distinctions between embryonic and postembryonic stomatal development. Furthermore, the interplay of transcription factors and cell cycle machineries is pivotal in specifying the transition into differentiation. We aim to synthesize recent studies utilizing single-cell as well as cell-type-specific transcriptomics, epigenomics and chromatin accessibility profiling to shed light on how master-regulatory transcription factors and epigenetic machineries mutually influence each other to drive fate commitment and maintenance.

Targeting editing of tomato SPEECHLESS cis-regulatory regions generates plants with altered stomatal density in response to changing climate conditions

Flexible developmental programs enable plants to customize their organ size and cellular composition. In leaves of eudicots, the stomatal lineage produces two essential cell types, stomata and pavement cells, but the total numbers and ratio of these cell types can vary. Central to this flexibility is the stomatal lineage initiating transcription factor, SPEECHLESS (SPCH). Here we show, by multiplex CRISPR/Cas9 editing of SlSPCH cis-regulatory sequences in tomato, that we can identify variants with altered stomatal development responses to light and temperature cues. Analysis of tomato leaf development across different conditions, aided by newly-created tools for live-cell imaging and translational reporters of SlSPCH and its paralogues SlMUTE and SlFAMA, revealed the series of cellular events that lead to the environmental change-driven responses in leaf form. Plants bearing the novel SlSPCH variants generated in this study are powerful resources for fundamental and applied studies of tomato resilience in response to climate change.

Update on stomata development and action under abiotic stress

Stomata, key gatekeepers of plant hydration, have long been known to play a pivotal role in mitigating the impacts of abiotic stressors. However, the complex molecular mechanisms underscoring this role remain unresolved fully and continue to be the subject of research. In the context of water-use efficiency (WUE), a key indicator of a plant's ability to conserve water, this aspect links intrinsically with stomatal behavior. Given the pivotal role of stomata in modulating water loss, it can be argued that the complex mechanisms governing stomatal development and function will significantly influence a plant's WUE under different abiotic stress conditions. Addressing these calls for a concerted effort to strengthen plant adaptability through advanced, targeted research. In this vein, recent studies have illuminated how specific stressors trigger alterations in gene expression, orchestrating changes in stomatal pattern, structure, and opening. This reveals a complex interplay between stress stimuli and regulatory sequences of essential genes implicated in stomatal development, such as MUTE, SPCH, and FAMA. This review synthesizes current discoveries on the molecular foundations of stomatal development and behavior in various stress conditions and their implications for WUE. It highlights the imperative for continued exploration, as understanding and leveraging these mechanisms guarantee enhanced plant resilience amid an ever-changing climatic landscape.

Experimental validation of the mechanism of stomatal development diversification

Stomata are the structures responsible for gas exchange in plants. The established framework for stomatal development is based on the model plant Arabidopsis, but diverse patterns of stomatal development have been observed in other plant lineages and species. The molecular mechanisms behind these diversified patterns are still poorly understood. We recently proposed a model for the molecular mechanisms of the diversification of stomatal development based on the genus Callitriche (Plantaginaceae), according to which a temporal shift in the expression of key stomatal transcription factors SPEECHLESS and MUTE leads to changes in the behavior of meristemoids (stomatal precursor cells). In the present study, we genetically manipulated Arabidopsis to test this model. By altering the timing of MUTE expression, we successfully generated Arabidopsis plants with early differentiation or prolonged divisions of meristemoids, as predicted by the model. The epidermal morphology of the generated lines resembled that of species with prolonged or no meristemoid divisions. Thus, the evolutionary process can be reproduced by varying the SPEECHLESS to MUTE transition. We also observed unexpected phenotypes, which indicated the participation of additional factors in the evolution of the patterns observed in nature. This study provides novel experimental insights into the diversification of meristemoid behaviors.

A cell size threshold triggers commitment to stomatal fate in Arabidopsis

How flexible developmental programs integrate information from internal and external factors to modulate stem cell behavior is a fundamental question in developmental biology. Cells of the Arabidopsis stomatal lineage modify the balance of stem cell proliferation and differentiation to adjust the size and cell type composition of mature leaves. Here, we report that meristemoids, one type of stomatal lineage stem cell, trigger the transition from asymmetric self-renewing divisions to commitment and terminal differentiation by crossing a critical cell size threshold. Through computational simulation, we demonstrate that this cell size-mediated transition allows robust, yet flexible termination of stem cell proliferation, and we observe adjustments in the number of divisions before the differentiation threshold under several genetic manipulations. We experimentally evaluate several mechanisms for cell size sensing, and our data suggest that this stomatal lineage transition is dependent on a nuclear factor that is sensitive to DNA content.

Liverwort bHLH transcription factors and the origin of stomata in plants

Stomata are distributed in nearly all major groups of land plants, with the only exception being liverworts. Instead of having stomata on sporophytes, many complex thalloid liverworts possess air pores in their gametophytes. At present, whether stomata in land plants are derived from a common origin remains under debate.^1,2,3 In Arabidopsis thaliana, a core regulatory module for stomatal development comprises members of the bHLH transcription factor (TF) family, including AtSPCH, AtMUTE, and AtFAMA of subfamily Ia and AtSCRM1/2 of subfamily IIIb. Specifically, AtSPCH, AtMUTE, and AtFAMA each successively form heterodimers with AtSCRM1/2, which in turn regulate the entry, division, and differentiation of stomatal lineages.^4,5,6,7 In the moss Physcomitrium patens, two SMF (SPCH, MUTE and FAMA) orthologs have been characterized, one of which is functionally conserved in regulating stomatal development.^8,9 We here provide experimental evidence that orthologous bHLH TFs in the liverwort Marchantia polymorpha affect air pore spacing as well as the development of the epidermis and gametangiophores. We found that the bHLH Ia and IIIb heterodimeric module is highly conserved in plants. Genetic complementation experiments showed that liverwort SCRM and SMF genes weakly restored a stomata phenotype in atscrm1, atmute, and atfama mutant backgrounds in A. thaliana. In addition, homologs of stomatal development regulators FLP and MYB88 also exist in liverworts and weakly rescued the stomatal phenotype of atflp/myb88 double mutant. These results provide evidence not only for a common origin of all stomata in extant plants but also for relatively simple stomata in the ancestral plant.

The role of phytomelatonin receptor 1-mediated signaling in plant growth and stress response

Phytomelatonin is a pleiotropic signaling molecule that regulates plant growth, development, and stress response. In plant cells, phytomelatonin is synthesized from tryptophan via several consecutive steps that are catalyzed by tryptophan decarboxylase (TDC), tryptamine 5-hydroxylase (T5H), serotonin N-acyltransferase (SNAT), and N-acetylserotonin methyltransferase (ASMT) and/or caffeic acid-3-O-methyltransferase (COMT). Recently, the identification of the phytomelatonin receptor PMTR1 in Arabidopsis has been considered a turning point in plant research, with the function and signal of phytomelatonin emerging as a receptor-based regulatory strategy. In addition, PMTR1 homologs have been identified in several plant species and have been found to regulate seed germination and seedling growth, stomatal closure, leaf senescence, and several stress responses. In this article, we review the recent evidence in our understanding of the PMTR1-mediated regulatory pathways in phytomelatonin signaling under environmental stimuli. Based on structural comparison of the melatonin receptor 1 (MT1) in human and PMTR1 homologs, we propose that the similarity in the three-dimensional structure of the melatonin receptors probably represents a convergent evolution of melatonin recognition in different species.

What can hornworts teach us?

The hornworts are a small group of land plants, consisting of only 11 families and approximately 220 species. Despite their small size as a group, their phylogenetic position and unique biology are of great importance. Hornworts, together with mosses and liverworts, form the monophyletic group of bryophytes that is sister to all other land plants (Tracheophytes). It is only recently that hornworts became amenable to experimental investigation with the establishment of Anthoceros agrestis as a model system. In this perspective, we summarize the recent advances in the development of A. agrestis as an experimental system and compare it with other plant model systems. We also discuss how A. agrestis can help to further research in comparative developmental studies across land plants and to solve key questions of plant biology associated with the colonization of the terrestrial environment. Finally, we explore the significance of A. agrestis in crop improvement and synthetic biology applications in general.

Stomatal regulators are co-opted for seta development in the astomatous liverwort Marchantia polymorpha

The evolution of special types of cells requires the acquisition of new gene regulatory networks controlled by transcription factors (TFs). In stomatous plants, a TF module formed by subfamilies Ia and IIIb basic helix-loop-helix TFs (Ia-IIIb bHLH) regulates stomatal formation; however, how this module evolved during land plant diversification remains unclear. Here we show that, in the astomatous liverwort Marchantia polymorpha, a Ia-IIIb bHLH module regulates the development of a unique sporophyte tissue, the seta, which is found in mosses and liverworts. The sole Ia bHLH gene, MpSETA, and a IIIb bHLH gene, MpICE2, regulate the cell division and/or differentiation of seta lineage cells. MpSETA can partially replace the stomatal function of Ia bHLH TFs in Arabidopsis thaliana, suggesting that a common regulatory mechanism underlies setal and stomatal formation. Our findings reveal the co-option of a Ia-IIIb bHLH TF module for regulating cell fate determination and/or cell division of distinct types of cells during land plant evolution.

Intercellular Communication during Stomatal Development with a Focus on the Role of Symplastic Connection

Stomata are microscopic pores on the plant epidermis that serve as a major passage for the gas and water exchange between a plant and the atmosphere. The formation of stomata requires a series of cell division and cell-fate transitions and some key regulators including transcription factors and peptides. Monocots have different stomatal patterning and a specific subsidiary cell formation process compared with dicots. Cell-to-cell symplastic trafficking mediated by plasmodesmata (PD) allows molecules including proteins, RNAs and hormones to function in neighboring cells by moving through the channels. During stomatal developmental process, the intercellular communication between stomata complex and adjacent epidermal cells are finely controlled at different stages. Thus, the stomata cells are isolated or connected with others to facilitate their formation or movement. In the review, we summarize the main regulation mechanism underlying stomata development in both dicots and monocots and especially the specific regulation of subsidiary cell formation in monocots. We aim to highlight the important role of symplastic connection modulation during stomata development, including the status of PD presence at different cell-cell interfaces and the function of relevant mobile factors in both dicots and monocots.

Leaf physiology variations are modulated by natural variations that underlie stomatal morphology in Populus

Stomata are essential for photosynthesis and abiotic stress tolerance. Here, we used multiomics approaches to dissect the genetic architecture and adaptive mechanisms that underlie stomatal morphology in Populus tomentosa juvenile natural population (303 accessions). We detected 46 candidate genes and 15 epistatic gene-pairs, associated with 5 stomatal morphologies and 18 leaf development and photosynthesis traits, through genome-wide association studies. Expression quantitative trait locus mapping revealed that stomata-associated gene loci were significantly associated with the expression of leaf-related genes; selective sweep analysis uncovered significant differentiation in the allele frequencies of genes that underlie stomatal variations. An allelic regulatory network operating under drought stress and adequate precipitation conditions, with three key regulators (DUF538, TRA2 and AbFH2) and eight interacting genes, was identified that might regulate leaf physiology via modulation of stomatal shape and density. Validation of candidate gene variations in drought-tolerant and F₁ hybrid populations of P. tomentosa showed that the DUF538, TRA2 and AbFH2 loci cause functional stabilisation of spatiotemporal regulatory, whose favourable alleles can be faithfully transmitted to offspring. This study provides insights concerning leaf physiology and stress tolerance via the regulation of stomatal determination in perennial plants.

Stomata in Close Contact: The Case of Pancratium maritimum L. (Amaryllidaceae)

A special feature found in Amaryllidaceae is that some guard cells of the neighboring stomata form a "connection strand" between their dorsal cell walls. In the present work, this strand was studied in terms of both its composition and its effect on the morphology and function of the stomata in Pancratium maritimum L. leaves. The structure of stomata and their connection strand were studied by light and transmission electron microscopy. FM 4-64 and aniline blue staining and application of tannic acid were performed to detect cell membranes, callose, and pectins, respectively. A plasmolysis experiment was also performed. The composition of the connection strand was analyzed by fluorescence microscopy after immunostaining with several cell-wall-related antibodies, while pectinase treatment was applied to confirm the presence of pectins in the connection strand. To examine the effect of this connection on stomatal function, several morphological characteristics (width, length, size, pore aperture, stomatal distance, and cell size of the intermediate pavement cell) were studied. It is suggested that the connecting strand consists of cell wall material laid through the middle of the intermediate pavement cell adjoining the two stomata. These cell wall strands are mainly comprised of pectins, and crystalline cellulose and extensins were also present. Connected stomata do not open like the single stomata do, indicating that the connection strand could also affect stomatal function. This trait is common to other Amaryllidaceae representatives.

Signaling Transduction of ABA, ROS, and Ca2+ in Plant Stomatal Closure in Response to Drought

Drought is a global threat that affects agricultural production. Plants have evolved several adaptive strategies to cope with drought. Stomata are essential structures for plants to control water status and photosynthesis rate. Stomatal closure is an efficient way for plants to reduce water loss and improve survivability under drought conditions. The opening and closure of stomata depend on the turgor pressure in guard cells. Three key signaling molecules, including abscisic acid (ABA), reactive oxygen species (ROS), and calcium ion (Ca²⁺), play pivotal roles in controlling stomatal closure. Plants sense the water-deficit signal mainly via leaves and roots. On the one hand, ABA is actively synthesized in root and leaf vascular tissues and transported to guard cells. On the other hand, the roots sense the water-deficit signal and synthesize CLAVATA3/EMBRYO-SURROUNDING REGION RELATED 25 (CLE25) peptide, which is transported to the guard cells to promote ABA synthesis. ABA is perceived by pyrabactin resistance (PYR)/PYR1-like (PYL)/regulatory components of ABA receptor (RCAR) receptors, which inactivate PP2C, resulting in activating the protein kinases SnRK2s. Many proteins regulating stomatal closure are activated by SnRK2s via protein phosphorylation. ABA-activated SnRK2s promote apoplastic ROS production outside of guard cells and transportation into the guard cells. The apoplastic H₂O₂ can be directly sensed by a receptor kinase, HYDROGEN PEROXIDE-INDUCED CA²⁺ INCREASES1 (HPCA1), which induces activation of Ca²⁺ channels in the cytomembrane of guard cells, and triggers an increase in Ca²⁺ in the cytoplasm of guard cells, resulting in stomatal closure. In this review, we focused on discussing the signaling transduction of ABA, ROS, and Ca²⁺ in controlling stomatal closure in response to drought. Many critical genes are identified to have a function in stomatal closure under drought conditions. The identified genes in the process can serve as candidate genes for genetic engineering to improve drought resistance in crops. The review summarizes the recent advances and provides new insights into the signaling regulation of stomatal closure in response to water-deficit stress and new clues on the improvement of drought resistance in crops.

Stomatal morphological variation contributes to global ecological adaptation and diversification of Brassica napus

Stomatal density and guard cell length of 274 global core germplasms of rapeseed reveal that the stomatal morphological variation contributes to global ecological adaptation and diversification of Brassica napus. Stomata are microscopic structures of plants for the regulation of CO₂ assimilation and transpiration. Stomatal morphology has changed substantially in the adaptation to the external environment during land plant evolution. Brassica napus is a major crop to produce oil, livestock feed and biofuel in the world. However, there are few studies on the regulatory genes controlling stomatal development and their interaction with environmental factors as well as the genetic mechanism of adaptive variation in B. napus. Here, we characterized stomatal density (SD) and guard cell length (GL) of 274 global core germplasms at seedling stage. It was found that among the significant phenotypic variation, European germplasms are mostly winter rapeseed with high stomatal density and small guard cell length. However, the germplasms from Asia (especially China) are semi-winter rapeseed, which is characterized by low stomatal density and large guard cell length. Through selective sweep analysis and homology comparison, we identified several candidate genes related to stomatal density and guard cell length, including Epidermal Patterning Factor2 (EPF2; BnaA09g23140D), Epidermal Patterning Factor Like4 (EPFL4; BnaC01g22890D) and Suppressor of LLP1 (SOL1 BnaC01g22810D). Haplotype and phylogenetic analysis showed that natural variation in EPF2, EPFL4 and SOL1 is closely associated with the winter, spring, and semi-winter rapeseed ecotypes. In summary, this study demonstrated for the first time the relation between stomatal phenotypic variation and ecological adaptation in rapeseed, which is useful for future molecular breeding of rapeseed in the context of evolution and domestication of key stomatal traits and global climate change.

A Locus Controlling Leaf Rolling Degree in Wheat under Drought Stress Identified by Bulked Segregant Analysis

Drought stress frequently occurs, which seriously restricts the production of wheat (Triticum aestivum L.). Leaf rolling is a typical physiological phenomenon of plants during drought stress. To understand the genetic mechanism of wheat leaf rolling, we constructed an F₂ segregating population by crossing the slight-rolling wheat cultivar “Aikang 58” (AK58) with the serious-rolling wheat cultivar ″Zhongmai 36″ (ZM36). A combination of bulked segregant analysis (BSA) with Wheat 660K SNP Array was used to identify molecular markers linked to leaf rolling degree. A major locus for leaf rolling degree under drought stress was detected on chromosome 7A. We named this locus LEAF ROLLING DEGREE 1 (LERD1), which was ultimately mapped to a region between 717.82 and 720.18 Mb. Twenty-one genes were predicted in this region, among which the basic helix-loop-helix (bHLH) transcription factor TraesCS7A01G543300 was considered to be the most likely candidate gene for LERD1. The TraesCS7A01G543300 is highly homologous to the Arabidopsis ICE1 family proteins ICE/SCREAM, SCREAM2 and bHLH093, which control stomatal initiation and development. Two nucleotide variation sites were detected in the promoter region of TraesCS7A01G543300 between the two wheat cultivars. Gene expression assays indicated that TraesCS7A01G543300 was higher expressed in AK58 seedlings than that of ZM36. This research discovered a candidate gene related to wheat leaf rolling under drought stress, which may be helpful for understanding the leaf rolling mechanism and molecular breeding in wheat.

Genome-wide association study revealed TaHXK3-2A as a candidate gene controlling stomatal index in wheat seedlings

Stomata are important channels for the control of gas exchange between plants and the atmosphere. To examine the genetic architecture of wheat stomatal index, we performed a genome-wide association study (GWAS) using a panel of 539 wheat accessions and 450 678 polymorphic single nucleotide polymorphisms (SNPs) that were detected using wheat-specific 660K SNP array. A total of 130 SNPs were detected to be significantly associated with stomatal index in both leaf surfaces of wheat seedlings. These significant SNPs were distributed across 16 chromosomes and involved 2625 candidate genes which participate in stress response, metabolism and cell/organ development. Subsequent bulk segregant analysis (BSA), combined with GWAS identified one major haplotype on chromosome 2A, that is responsible for stomatal index on the abaxial leaf surface. Candidate gene association analysis revealed that genetic variation in the promoter region of the hexokinase gene TaHXK3-2A was significantly associated with the stomatal index. Moreover, transgenic analysis confirmed that TaHXK3-2A overexpression in wheat decreased the size of leaf pavement cells but increased stomatal density through the glucose metabolic pathway, resulting in drought sensitivity among TaHXK3-2A transgenic lines due to an increased transpiration rate. Taken together, these results provide valuable insights into the genetic control of the stomatal index in wheat seedlings.

Diversity, phylogeny, and adaptation of bryophytes: insights from genomic and transcriptomic data

Bryophytes including mosses, liverworts, and hornworts are among the earliest land plants, and occupy a crucial phylogenetic position to aid in the understanding of plant terrestrialization. Despite their small size and simple structure, bryophytes are the second largest group of extant land plants. They live ubiquitously in various habitats and are highly diversified, with adaptive strategies to modern ecosystems on Earth. More and more genomes and transcriptomes have been assembled to address fundamental questions in plant biology. Here, we review recent advances in bryophytes associated with diversity, phylogeny, and ecological adaptation. Phylogenomic studies have provided increasing supports for the monophyly of bryophytes, with hornworts sister to the Setaphyta clade including liverworts and mosses. Further comparative genomic analyses revealed that multiple whole-genome duplications might have contributed to the species richness and morphological diversity in mosses. We highlight that the biological changes through gene gain or neofunctionalization that primarily evolved in bryophytes have facilitated the adaptation to early land environments; among the strategies to adapt to modern ecosystems in bryophytes, desiccation tolerance is the most remarkable. More genomic information for bryophytes would shed light on key mechanisms for the ecological success of these 'dwarfs' in the plant kingdom.

RWP-RK domain-containing transcription factors in the Viridiplantae: biology and phylogenetic relationships

The RWP-RK protein family is a group of transcription factors containing the RWP-RK DNA-binding domain. This domain is an ancient motif that emerged before the establishment of the Viridiplantae-the green plants, consisting of green algae and land plants. The domain is mostly absent in other kingdoms but widely distributed in Viridiplantae. In green algae, a liverwort, and several angiosperms, RWP-RK proteins play essential roles in nitrogen responses and sexual reproduction-associated processes, which are seemingly unrelated phenomena but possibly interdependent in autotrophs. Consistent with related but diversified roles of the RWP-RK proteins in these organisms, the RWP-RK protein family appears to have expanded intensively, but independently, in the algal and land plant lineages. Thus, bryophyte RWP-RK proteins occupy a unique position in the evolutionary process of establishing the RWP-RK protein family. In this review, we summarize current knowledge of the RWP-RK protein family in the Viridiplantae, and discuss the significance of bryophyte RWP-RK proteins in clarifying the relationship between diversification in the RWP-RK protein family and procurement of sophisticated mechanisms for adaptation to the terrestrial environment.

Identification and Functional Analysis of SabHLHs in Santalum album L

Santalum album L., a semi-parasitic evergreen tree, contains economically important essential oil, rich in sesquiterpenoids, such as (Z) α- and (Z) β-santalol. However, their transcriptional regulations are not clear. Several studies of other plants have shown that basic-helix-loop-helix (bHLH) transcription factors (TFs) were involved in participating in the biosynthesis of sesquiterpene synthase genes. Herein, bHLH TF genes with similar expression patterns and high expression levels were screened by co-expression analysis, and their full-length ORFs were obtained. These bHLH TFs were named SaMYC1, SaMYC3, SaMYC4, SaMYC5, SabHLH1, SabHLH2, SabHLH3, and SabHLH4. All eight TFs had highly conserved bHLH domains and SaMYC1, SaMYC3, SaMYC4, and SaMYC5, also had highly conserved MYC domains. It was indicated that the eight genes belonged to six subfamilies of the bHLH TF family. Among them, SaMYC1 was found in both the nucleus and the cytoplasm, while SaMYC4 was only localized in the cytoplasm and the remaining six TFs were localized in nucleus. In a yeast one-hybrid experiment, we constructed decoy vectors pAbAi-SSy1G-box, pAbAi-CYP2G-box, pAbAi-CYP3G-box, and pAbAi-CYP4G-box, which had been transformed into yeast. We also constructed pGADT7-SaMYC1 and pGADT7-SabHLH1 capture vectors and transformed them into bait strains. Our results showed that SaMYC1 could bind to the G-box of SaSSy, and the SaCYP736A167 promoter, which SaSSy proved has acted as a key enzyme in the synthesis of santalol sesquiterpenes and SaCYP450 catalyzed the ligation of santalol sesquiterpenes into terpene. We have also constructed pGreenII 62-SK-SaMYC1, pGreenII 0800-LUC-SaSSy and pGreenII 0800-LUC-SaCYP736A167 via dual-luciferase fusion expression vectors and transformed them into Nicotiana benthamiana using an Agrobacterium-mediated method. The results showed that SaMYC1 was successfully combined with SaSSy or SaCYP736A167 promoter and the LUC/REN value was 1.85- or 1.55-fold higher, respectively, than that of the control group. Therefore, we inferred that SaMYC1 could activate both SaSSy and SaCYP736A167 promoters.

Water-related innovations in land plants evolved by different patterns of gene cooption and novelty

The origin of land plants and their descendants was marked by the evolution of key adaptations to life in terrestrial environments such as roots, vascular tissue and stomata. Though these innovations are well characterized, the evolution of the genetic toolkit underlying their development and function is poorly understood. We analysed molecular data from 532 species to investigate the evolutionary origin and diversification of genes involved in the development and regulation of these adaptations. We show that novel genes in the first land plants led to the single origin of stomata, but the stomatal closure of seed plants resulted from later gene expansions. By contrast, the major mechanism leading to the origin of vascular tissue was cooption of genes that emerged in the first land plants, enabling continuous water transport throughout the ancestral vascular plant. In turn, new key genes in the ancestors of plants with true leaves and seed plants led to the emergence of roots and lateral roots. The analysis highlights the different modes of evolution that enabled plants to conquer land, suggesting that gene expansion and cooption are the most common mechanisms of biological innovation in plant evolutionary history.

The origin and evolution of stomata

The acquisition of stomata is one of the key innovations that led to the colonisation of the terrestrial environment by the earliest land plants. However, our understanding of the origin, evolution and the ancestral function of stomata is incomplete. Phylogenomic analyses indicate that, firstly, stomata are ancient structures, present in the common ancestor of land plants, prior to the divergence of bryophytes and tracheophytes and, secondly, there has been reductive stomatal evolution, especially in the bryophytes (with complete loss in the liverworts). From a review of the evidence, we conclude that the capacity of stomata to open and close in response to signals such as ABA, CO₂ and light (hydroactive movement) is an ancestral state, is present in all lineages and likely predates the divergence of the bryophytes and tracheophytes. We reject the hypothesis that hydroactive movement was acquired with the emergence of the gymnosperms. We also conclude that the role of stomata in the earliest land plants was to optimise carbon gain per unit water loss. There remain many other unanswered questions concerning the evolution and especially the origin of stomata. To address these questions, it will be necessary to: find more fossils representing the earliest land plants, revisit the existing early land plant fossil record in the light of novel phylogenomic hypotheses and carry out more functional studies that include both tracheophytes and bryophytes.

The genome of the recretohalophyte Limonium bicolor provides insights into salt gland development and salinity adaptation during terrestrial evolution

Halophytes have evolved specialized strategies to cope with high salinity. The extreme halophyte sea lavender (Limonium bicolor) lacks trichomes but possesses salt glands on its epidermis that can excrete harmful ions, such as sodium, to avoid salt damage. Here, we report a high-quality, 2.92-Gb, chromosome-scale L. bicolor genome assembly based on a combination of Illumina short reads, single-molecule, real-time long reads, chromosome conformation capture (Hi-C) data, and Bionano genome maps, greatly enriching the genomic information on recretohalophytes with multicellular salt glands. Although the L. bicolor genome contains genes that show similarity to trichome fate genes from Arabidopsis thaliana, it lacks homologs of the decision fate genes GLABRA3, ENHANCER OF GLABRA3, GLABRA2, TRANSPARENT TESTA GLABRA2, and SIAMESE, providing a molecular explanation for the absence of trichomes in this species. We identified key genes (LbHLH and LbTTG1) controlling salt gland development among classical trichome homologous genes and confirmed their roles by showing that their mutations markedly disrupted salt gland initiation, salt secretion, and salt tolerance, thus offering genetic support for the long-standing hypothesis that salt glands and trichomes may share a common origin. In addition, a whole-genome duplication event occurred in the L. bicolor genome after its divergence from Tartary buckwheat and may have contributed to its adaptation to high salinity. The L. bicolor genome resource and genetic evidence reported in this study provide profound insights into plant salt tolerance mechanisms that may facilitate the engineering of salt-tolerant crops.

Stomata secretive ways: A commentary on Lamour et al. (2022)

The main responsibility of stomata is controlling the exchange of water and carbon dioxide between plants and the surrounding air. Stomata open or close accordingly to environmental conditions. For example, stomata are closed in the dark but gradually open as light levels increase. New aspects of stomata functioning are still surfacing enabling a better representation of the relationship between vegetation and the atmosphere, which is of great importance for global change research. photo credit: João M. Rosa/Nitro Imagens/AmazonFACE. This article is a Commentary on Lamour et al., https://doi.org/10.1111/gcb.16103.

Contrasting Phaseolus Crop Water Use Patterns and Stomatal Dynamics in Response to Terminal Drought

Terminal drought stress affects more than half of the areas planted with common bean (Phaseolus vulgaris), the main food legume globally, generating severe yield losses. Phenotyping water deficit responses and water use are central strategies to develop improved terminal drought resilience. The exploration and exploitation of genetic diversity in breeding programs are gaining importance, with a particular interest in related species with great adaptation to biotic and abiotic factors. This is the case with tepary beans (Phaseolus acutifolius), a bean that evolved and was domesticated in arid conditions and is considered well adapted to drought and heat stress. Under greenhouse conditions, using one genotype of tepary beans (resistant to drought) and two of common beans (one resistant and one susceptible to terminal drought), we evaluated phenotypic differences in traits such as water use efficiency (WUE), transpiration efficiency, rate of photosynthesis, photosynthetic efficiency, stomatal density, stomatal index, stomatal size, and the threshold for transpiration decline under well-watered and terminal drought conditions. Our results indicate two different water use strategies in drought-resistant genotypes: one observed in common bean aimed at conserving soil water by closing stomata early, inhibiting stomatal development, and limiting growth; and the other observed in tepary bean, where prolonged stomatal opening and higher carbon fixation, combined with no changes in stomata distribution, lead to higher biomass accumulation. Strategies that contribute to drought adaptation combined with other traits, such as greater mobilization of photoassimilates to the formation of reproductive structures, confer bean drought resistance and are useful targets in breeding programs.

Structure of the Arabidopsis guard cell anion channel SLAC1 suggests activation mechanism by phosphorylation

Stomata play a critical role in the regulation of gas exchange and photosynthesis in plants. Stomatal closure participates in multiple stress responses, and is regulated by a complex network including abscisic acid (ABA) signaling and ion-flux-induced turgor changes. The slow-type anion channel SLAC1 has been identified to be a central controller of stomatal closure and phosphoactivated by several kinases. Here, we report the structure of SLAC1 in Arabidopsis thaliana (AtSLAC1) in an inactivated, closed state. The cytosolic amino (N)-terminus and carboxyl (C)-terminus of AtSLAC1 are partially resolved and form a plug-like structure which packs against the transmembrane domain (TMD). Breaking the interactions between the cytosolic plug and transmembrane domain triggers channel activation. An inhibition-release model is proposed for SLAC1 activation by phosphorylation that the cytosolic plug dissociates from the transmembrane domain upon phosphorylation, and induces conformational changes to open the pore. These findings facilitate our understanding of the regulation of SLAC1 activity and stomatal aperture in plants.

The anion channel SLAC1 controls stomatal closure upon phosphoactivation. Here via structural analysis and electrophysiology, the authors propose an inhibition-release model where phosphorylation causes dissociation of a cytosolic plug from the SLAC1 transmembrane domains to induce conformational change in the pore-forming helices.

In-silico evolutionary analysis of plant-OBERON proteins during compatible MYMV infection in respect of improving host resistance

Yellow mosaic disease (YMD) of pulses caused by mungbean yellow mosaic virus is a major threat to crop production. An infection that is compatible with regulating and interacting host proteins and the virus causes YMD. Oberon families of proteins OBE1-4 and VIN1-4 are imperative for plants, functions in meristem and vascular development, and were also regulated during compatible disease infection. Furthermore, in-silico expression results suggested the involvement of OBE1 and OBE2 proteins during virus infection of Vigna, Arabidopsis and soybean. Moreover, a common ancestor for the meristem and virus movement related Oberons was inferred through phylogenetic analysis. Protein interaction studies showed three amino acids (Aspartate, glutamate and lysine) in the plant homeodomain (PHD), involved in interaction with the N-terminal region of the virus movement protein and were also conserved in both monocot and dicots. Additionally, major differences in the nuclear localization signal (NLS) showing clade specific conservation and significant variation between dicots and monocots were ascertained in meristem and virus movement related Oberons. Consequently, a combination of PHD, CCD and their interactions with the VPg viral domain increases the susceptibility to YMD. Further, modification in the NLS regions of the viral movement clade Oberons, to knock out allele generation in the OBE1 and OBE2 homologs through genome-editing approaches could be established as alternate strategies for the improvement of host resistance and control yellow mosaic disease in plants, especially in pulse crops.

Leaf microscopy applications in photosynthesis research: identifying the gaps

Leaf imaging via microscopy has provided critical insights into research on photosynthesis at multiple junctures, from the early understanding of the role of stomata, through elucidating C4 photosynthesis via Kranz anatomy and chloroplast arrangement in single cells, to detailed explorations of diffusion pathways and light utilization gradients within leaves. In recent decades, the original two-dimensional (2D) explorations have begun to be visualized in three-dimensional (3D) space, revising our understanding of structure-function relationships between internal leaf anatomy and photosynthesis. In particular, advancing new technologies and analyses are providing fresh insight into the relationship between leaf cellular components and improving the ability to model net carbon fixation, water use efficiency, and metabolite turnover rate in leaves. While ground-breaking developments in imaging tools and techniques have expanded our knowledge of leaf 3D structure via high-resolution 3D and time-series images, there is a growing need for more in vivo imaging as well as metabolite imaging. However, these advances necessitate further improvement in microscopy sciences to overcome the unique challenges a green leaf poses. In this review, we discuss the available tools, techniques, challenges, and gaps for efficient in vivo leaf 3D imaging, as well as innovations to overcome these difficulties.

Phytomelatonin prevents bacterial invasion during nighttime

Phytomelatonin is an emerging new plant hormone. The identification of phytomelatonin receptor 1 (PMTR1) has been a turning point for understanding phytomelatonin functions, but many uncertainties remain. Here we highlight how PMTR1-mediated phytomelatonin signaling closes stomata, not just to avoid water loss but also to prevent bacterial invasion at night.

Genomic Survey and Cold-Induced Expression Patterns of bHLH Transcription Factors in Liriodendron chinense (Hemsl) Sarg

bHLH transcription factors play an animated role in the plant kingdom during growth and development, and responses to various abiotic stress. In this current study, we conducted, the genome-wide survey of bHLH transcription factors in Liriodendron chinense (Hemsl) Sarg., 91 LcbHLH family members were identified. Identified LcbHLH gene family members were grouped into 19 different subfamilies based on the conserved motifs and phylogenetic analysis. Our results showed that LcbHLH genes clustered in the same subfamily exhibited a similar conservative exon-intron pattern. Hydrophilicity value analysis showed that all LcbHLH proteins were hydrophilic. The Molecular weight (Mw) of LcbHLH proteins ranged from 10.19 kD (LcbHLH15) to 88.40 kD (LcbHLH50). A greater proportion, ~63%, of LcbHLH proteins had a theoretical isoelectric point (pI) less than seven. Additional analysis on the collinear relationships within species and among dissimilar species illustrated that tandem and fragment duplication are the foremost factors of amplification of this family in the evolution process, and they are all purified and selected. RNA-seq and real-time quantitative PCR analysis of LcbHLH members showed that the expression of LcbHLH35, 55, and 86 are up-regulated, and the expression of LcbHLH9, 20, 39, 54, 56, and 69 is down-regulated during cold stress treatments while the expression of LcbHLH24 was up-regulated in the short term and then later down-regulated. From our results, we concluded that LcbHLH genes might participate in cold-responsive processes of L. chinense. These findings provide the basic information of bHLH gene in L. chinense and their regulatory roles in plant development and cold stress response.

Evolution and conserved functionality of organ size and shape regulator PEAPOD

Transcriptional regulator PEAPOD (PPD) and its binding partners comprise a complex that is conserved throughout many core eudicot plants with regard to protein domain sequence and the function of controlling organ size and shape. Orthologues of PPD also exist in the basal angiosperm Amborella trichopoda, various gymnosperm species, the lycophyte Selaginella moellendorffii and several monocot genera, although until now it was not known if these are functional sequences. Here we report constitutive expression of orthologues from species representing diverse taxa of plant phylogeny in the Arabidopsis Δppd mutant. PPD orthologues from S. moellendorffii, gymnosperm Picea abies, A. trichopoda, monocot Musa acuminata, and dicot Trifolium repens were able to complement the mutant and return it to the wild-type phenotype, demonstrating the conserved functionality of PPD throughout vascular plants. In addition, analysis of bryophyte genomes revealed potential PPD orthologues in model liverwort and moss species, suggesting a more primitive lineage for this conserved regulator. The Poaceae (grasses) lack the genes for the PPD module and the reason for loss of the complex from this economically significant family is unclear, given that grasses were the last of the flowering plants to evolve. Bioinformatic analyses identified putative PPD orthologues in close relatives of the Poaceae, indicating that the explanation for absence of PPD in the grasses may be more complex than previously considered. Understanding the mechanisms which led to loss of PPD from the grasses will provide insight into evolution of the Poaceae.

Plant genome sequence assembly in the era of long reads: Progress, challenges and future directions

Third-generation long-read sequencing is transforming plant genomics. Oxford Nanopore Technologies and Pacific Biosciences are offering competing long-read sequencing technologies and enable plant scientists to investigate even large and complex plant genomes. Sequencing projects can be conducted by single research groups and sequences of smaller plant genomes can be completed within days. This also resulted in an increased investigation of genomes from multiple species in large scale to address fundamental questions associated with the origin and evolution of land plants. Increased accessibility of sequencing devices and user-friendly software allows more researchers to get involved in genomics. Current challenges are accurately resolving diploid or polyploid genome sequences and better accounting for the intra-specific diversity by switching from the use of single reference genome sequences to a pangenome graph.

Arabidopsis F-BOX STRESS INDUCED 4 is required to repress excessive divisions in stomatal development

During the terminal stage of stomatal development, the R2R3-MYB transcription factors FOUR LIPS (FLP/MYB124) and MYB88 limit guard mother cell division by repressing the transcript levels of multiple cell-cycle genes. In Arabidopsis thaliana possessing the weak allele flp-1, an extra guard mother cell division results in two stomata having direct contact. Here, we identified an ethylmethane sulfonate-mutagenized mutant, flp-1 xs01c, which exhibited more severe defects than flp-1 alone, producing giant tumor-like cell clusters. XS01C, encoding F-BOX STRESS-INDUCED 4 (FBS4), is preferentially expressed in epidermal stomatal precursor cells. Overexpressing FBS4 rescued the defective stomatal phenotypes of flp-1 xs01c and flp-1 mutants. The deletion or substitution of a conserved residue (Proline166) within the F-box domain of FBS4 abolished or reduced, respectively, its interaction with Arabidopsis Skp1-Like1 (ASK1), the core subunit of the Skp1/Cullin/F-box E3 ubiquitin ligase complex. Furthermore, the FBS4 protein physically interacted with CYCA2;3 and induced its degradation through the ubiquitin-26S proteasome pathway. Thus, in addition to the known transcriptional pathway, the terminal symmetric division in stomatal development is ensured at the post-translational level, such as through the ubiquitination of target proteins recognized by the stomatal lineage F-box protein FBS4.

Machine learning-enabled phenotyping for GWAS and TWAS of WUE traits in 869 field-grown sorghum accessions

Sorghum (Sorghum bicolor) is a model C4 crop made experimentally tractable by extensive genomic and genetic resources. Biomass sorghum is studied as a feedstock for biofuel and forage. Mechanistic modeling suggests that reducing stomatal conductance (gs) could improve sorghum intrinsic water use efficiency (iWUE) and biomass production. Phenotyping to discover genotype-to-phenotype associations remains a bottleneck in understanding the mechanistic basis for natural variation in gs and iWUE. This study addressed multiple methodological limitations. Optical tomography and a machine learning tool were combined to measure stomatal density (SD). This was combined with rapid measurements of leaf photosynthetic gas exchange and specific leaf area (SLA). These traits were the subject of genome-wide association study and transcriptome-wide association study across 869 field-grown biomass sorghum accessions. The ratio of intracellular to ambient CO2 was genetically correlated with SD, SLA, gs, and biomass production. Plasticity in SD and SLA was interrelated with each other and with productivity across wet and dry growing seasons. Moderate-to-high heritability of traits studied across the large mapping population validated associations between DNA sequence variation or RNA transcript abundance and trait variation. A total of 394 unique genes underpinning variation in WUE-related traits are described with higher confidence because they were identified in multiple independent tests. This list was enriched in genes whose Arabidopsis (Arabidopsis thaliana) putative orthologs have functions related to stomatal or leaf development and leaf gas exchange, as well as genes with nonsynonymous/missense variants. These advances in methodology and knowledge will facilitate improving C4 crop WUE.

Machine learning-enabled phenotyping for GWAS and TWAS of WUE traits in 869 field-grown sorghum accessions

Sorghum (Sorghum bicolor) is a model C4 crop made experimentally tractable by extensive genomic and genetic resources. Biomass sorghum is studied as a feedstock for biofuel and forage. Mechanistic modeling suggests that reducing stomatal conductance (gs) could improve sorghum intrinsic water use efficiency (iWUE) and biomass production. Phenotyping to discover genotype-to-phenotype associations remains a bottleneck in understanding the mechanistic basis for natural variation in gs and iWUE. This study addressed multiple methodological limitations. Optical tomography and a machine learning tool were combined to measure stomatal density (SD). This was combined with rapid measurements of leaf photosynthetic gas exchange and specific leaf area (SLA). These traits were the subject of genome-wide association study and transcriptome-wide association study across 869 field-grown biomass sorghum accessions. The ratio of intracellular to ambient CO2 was genetically correlated with SD, SLA, gs, and biomass production. Plasticity in SD and SLA was interrelated with each other and with productivity across wet and dry growing seasons. Moderate-to-high heritability of traits studied across the large mapping population validated associations between DNA sequence variation or RNA transcript abundance and trait variation. A total of 394 unique genes underpinning variation in WUE-related traits are described with higher confidence because they were identified in multiple independent tests. This list was enriched in genes whose Arabidopsis (Arabidopsis thaliana) putative orthologs have functions related to stomatal or leaf development and leaf gas exchange, as well as genes with nonsynonymous/missense variants. These advances in methodology and knowledge will facilitate improving C4 crop WUE.

Plant lectins and their many roles: Carbohydrate-binding and beyond

Lectins are ubiquitous proteins that reversibly bind to specific carbohydrates and, thus, serve as readers of the sugar code. In photosynthetic organisms, lectin family proteins play important roles in capturing and releasing photosynthates via an endogenous lectin cycle. Often, lectin proteins consist of one or more lectin domains in combination with other types of domains. This structural diversity of lectins is the basis for their current classification, which is consistent with their diverse functions in cell signaling associated with growth and development, as well as in the plant's response to biotic, symbiotic, and abiotic stimuli. Furthermore, the lectin family shows evolutionary expansion that has distinct clade-specific signatures. Although the function(s) of many plant lectin family genes are unknown, studies in the model plant Arabidopsis thaliana have provided insights into their diverse roles. Here, we have used a biocuration approach rooted in the critical review of scientific literature and information available in the public genomic databases to summarize the expression, localization, and known functions of lectins in Arabidopsis. A better understanding of the structure and function of lectins is expected to aid in improving agricultural productivity through the manipulation of candidate genes for breeding climate-resilient crops, or by regulating metabolic pathways by applications of plant growth regulators.

Evolutionary insight of plant cuticle biosynthesis in bryophytes

As an adaptive innovation in plant terrestrialization, cuticle covers the plant surface and greatly contributes to the development and stress tolerance in land plants. Although past decades have seen great progress in understanding the molecular mechanism of cuticle biosynthesis in flowering plants with the contribution of cuticle biosynthesis mutants and advanced cuticle composition profiling techniques, origins and evolution of cuticle biosynthesis are poorly understood. Recent chemical, phylogenomic, and molecular genetic studies on cuticle biosynthesis in early-diverging extant land plant lineages, the bryophytes, shed novel light on the origins and evolution of plant cuticle biosynthesis. In this mini-review, we highlighted these recent advances in the molecular biology of cuticle biosynthesis in bryophytes, and provided evolutionary insights into plant cuticle biosynthesis.

Morphology made for movement: formation of diverse stomatal guard cells

Stomata constantly open and close to optimize gas exchange. While the genetic programme guiding early development is well described, the formation of functional guard cells remains enigmatic. This review highlights recent findings on the developmental and morphogenetic processes shaping this essential and morphologically diverse cell type in Arabidopsis and grasses.

Stomatal development and genetic expression in Arabidopsis thaliana L

Stomata are turgor-driven microscopic epidermal valves of land plants. The controlled opening and closing of the valves are essential for regulating the gas exchange and minimizing the water loss and eventually regulating the internal temperatures. Stomata are also a major site of pathogen/microbe entry and plant defense system. Maintaining proper stomatal density, distribution, and development are pivotal for plant survival. Arabidopsis is a model plant to study molecular basis including signaling pathways, transcription factors, and key components for the growth and development of specific organs as well as the whole plant. It has intensively been studied and found out the driver for the development and patterning of stomata. In this review, we have explained how the MAPK signaling cascade is controlled by TOO MANY MOUTHS (TMM) receptor-like protein and the Erecta (ER) receptor-like kinase family. We have also summarized how this MAPK cascade affects primary transcriptional regulators to finally activate the main three basic Helix-Loop-Helix (bHLH) principal transcription factors, which are required for the development and patterning of stomata. Moreover, regulatory activity and cellular connections of polar proteins and environmentally mediated ligand-receptor interactions in the stomatal developmental pathways have extensively been discussed in this review.

Stomatal development in the context of epidermal tissues

BACKGROUND

Stomata are adjustable pores on the surface of plant shoots for efficient gas exchange and water control. The presence of stomata is essential for plant growth and survival, and the evolution of stomata is considered as a key developmental innovation of the land plants, allowing colonization on land from aquatic environments some 450 million years ago. In the past two decades, molecular genetic studies using the model plant Arabidopsis thaliana identified key genes and signalling modules that regulate stomatal development: master regulatory transcription factors that orchestrate cell state transitions and peptide-receptor signal transduction pathways, which, together, enforce proper patterning of stomata within the epidermis. Studies in diverse plant species, ranging from bryophytes to angiosperm grasses, have begun to unravel the conservation and uniqueness of the core modules in stomatal development.

SCOPE

Here, I review the mechanisms of stomatal development in the context of epidermal tissue patterning. First, I introduce the core regulatory mechanisms of stomatal patterning and differentiation in the model species A. thaliana. Subsequently, experimental evidence is presented supporting the idea that different cell types within the leaf epidermis, namely stomata, hydathodes pores, pavement cells and trichomes, either share developmental origins or mutually influence each other's gene regulatory circuits during development. Emphasis is placed on extrinsic and intrinsic signals regulating the balance between stomata and pavement cells, specifically by controlling the fate of stomatal-lineage ground cells (SLGCs) to remain within the stomatal cell lineage or differentiate into pavement cells. Finally, I discuss the influence of intertissue layer communication between the epidermis and underlying mesophyll/vascular tissues on stomatal differentiation. Understanding the dynamic behaviours of stomatal precursor cells and their differentiation in the broader context of tissue and organ development may help design plants tailored for optimal growth and productivity in specific agricultural applications and a changing environment.

Variation in climatic tolerance, but not stomatal traits, partially explains Pooideae grass species distributions

BACKGROUND AND AIMS

Grasses in subfamily Pooideae live in some of the world's harshest terrestrial environments, from frigid boreal zones to the arid windswept steppe. It is hypothesized that the climate distribution of species within this group is driven by differences in climatic tolerance, and that tolerance can be partially explained by variation in stomatal traits.

METHODS

We determined the aridity index (AI) and minimum temperature of the coldest month (MTCM) for 22 diverse Pooideae accessions and one outgroup, and used comparative methods to assess predicted relationships for climate traits versus fitness traits, stomatal diffusive conductance to water (gw) and speed of stomatal closure following drought and/or cold.

KEY RESULTS

Results demonstrate that AI and MTCM predict variation in survival/regreening following drought/cold, and gw under drought/cold is positively correlated with δ 13C-measured water use efficiency (WUE). However, the relationship between climate traits and fitness under drought/cold was not explained by gw or speed of stomatal closure.

CONCLUSIONS

These findings suggest that Pooideae distributions are at least partly determined by tolerance to aridity and above-freezing cold, but that variation in tolerance is not uniformly explained by variation in stomatal traits.

Classical phenotyping and deep learning concur on genetic control of stomatal density and area in sorghum

Stomatal density (SD) and stomatal complex area (SCA) are important traits that regulate gas exchange and abiotic stress response in plants. Despite sorghum (Sorghum bicolor) adaptation to arid conditions, the genetic potential of stomata-related traits remains unexplored due to challenges in available phenotyping methods. Hence, identifying loci that control stomatal traits is fundamental to designing strategies to breed sorghum with optimized stomatal regulation. We implemented both classical and deep learning methods to characterize genetic diversity in 311 grain sorghum accessions for stomatal traits at two different field environments. Nearly 12,000 images collected from abaxial (Ab) and adaxial (Ad) leaf surfaces revealed substantial variation in stomatal traits. Our study demonstrated significant accuracy between manual and deep learning methods in predicting SD and SCA. In sorghum, SD was 32%-39% greater on the Ab versus the Ad surface, while SCA on the Ab surface was 2%-5% smaller than on the Ad surface. Genome-Wide Association Study identified 71 genetic loci (38 were environment-specific) with significant genotype to phenotype associations for stomatal traits. Putative causal genes underlying the phenotypic variation were identified. Accessions with similar SCA but carrying contrasting haplotypes for SD were tested for stomatal conductance and carbon assimilation under field conditions. Our findings provide a foundation for further studies on the genetic and molecular mechanisms controlling stomata patterning and regulation in sorghum. An integrated physiological, deep learning, and genomic approach allowed us to unravel the genetic control of natural variation in stomata traits in sorghum, which can be applied to other plants.

Moss stomata do not respond to light and CO2 concentration but facilitate carbon uptake by sporophytes: a gas exchange, stomatal aperture, and 13 C-labelling study

Stomata exert control on fluxes of CO₂ and water (H₂ O) in the majority of vascular plants and thus are pivotal for planetary fluxes of carbon and H₂ O. However, in mosses, the significance and possible function of the sporophytic stomata are not well understood, hindering understanding of the ancestral function and evolution of these key structures of land plants. Infrared gas analysis and ¹³ CO₂ labelling, with supporting data from gravimetry and optical and scanning electron microscopy, were used to measure CO₂ assimilation and water exchange on young, green, ± fully expanded capsules of 11 moss species with a range of stomatal numbers, distributions, and aperture sizes. Moss sporophytes are effectively homoiohydric. In line with their open fixed apertures, moss stomata, contrary to those in tracheophytes, do not respond to light and CO₂ concentration. Whereas the sporophyte cuticle is highly impermeable to gases, stomata are the predominant sites of ¹³ CO₂ entry and H₂ O loss in moss sporophytes, and CO₂ assimilation is closely linked to total stomatal surface areas. Higher photosynthetic autonomy of moss sporophytes, consequent on the presence of numerous stomata, may have been the key to our understanding of evolution of large, gametophyte-independent sporophytes at the onset of plant terrestrialization.

Mesophyll photosynthetic sensitivity to leaf water potential in Eucalyptus: a new dimension of plant adaptation to native moisture supply

Photosynthetic sensitivity to drought is a fundamental constraint on land-plant evolution and ecosystem function. However, little is known about how the sensitivity of photosynthesis to nonstomatal limitations varies among species in the context of phylogenetic relationships. Using saplings of 10 Eucalyptus species, we measured maximum CO₂ -saturated photosynthesis using A-c_i curves at several different leaf water potentials (ψ_leaf ) to quantify mesophyll photosynthetic sensitivity to ψ_leaf (MPS), a measure of how rapidly nonstomatal limitations to carbon uptake increase with declining ψ_leaf . MPS was compared to the macroclimatic moisture availability of the species' native habitats, while accounting for phylogenetic relationships. We found that species native to mesic habitats have greater MPS but higher maximum photosynthetic rates during non-water-stressed conditions, revealing a trade-off between maximum photosynthesis and drought sensitivity. Species with lower turgor loss points have lower MPS, indicating coordination among photosynthetic and water-relations traits. By accounting for phylogenetic relationships among closely related species, we provide the first compelling evidence that MPS in Eucalyptus evolved in an adaptive fashion with climatically determined moisture availability, opening the way for further study of this poorly explored dimension of plant adaptation to drought.

An Intrinsic Geometric Constraint on Morphological Stomatal Traits

A strong negative non-linear relationship exists between stomatal density (SD) and size (SS) or length (SL), which is of high importance in gas exchange and plant evolution. However, the cause of this relationship has not been clarified. In geometry, SD has an intrinsic relationship with SS-1 or SL-2, which is defined as a geometric constraint here. We compiled global data to clarify the influence of this geometric constraint on the SD-SS relationship. The log-log scaling slope of the relationship between SD and SS and between SD and SL was not significantly different from -1 and -2, respectively. Although the non-geometric effect drove the SD-SS curve away from the power function with -1, a larger influence of the geometric constraint on SD was found. Therefore, the higher geometric constraint possibly causes the SD-SS relationship to be inevitably non-linear and negative. Compared to pteridophyta and gymnosperms, the geometric constraint was lower for angiosperm species, possibly due to most of them having smaller stomata. The relaxation of the geometric constraint seems to extend the upper range of SD in angiosperm species and hence enable them to exploit a wide range of environments.