Autoregulation of RCO by Low-Affinity Binding Modulates Cytokinin Action and Shapes Leaf Diversity

Leaf form diversity and evolution: a never-ending story in plant biology

Leaf form can vary at different levels, such as inter/intraspecies, and diverse leaf shapes reflect their remarkable ability to adapt to various environmental conditions. Over the past two decades, considerable progress has been made in unraveling the molecular mechanisms underlying leaf form diversity, particularly the regulatory mechanisms of leaf complexity. However, the mechanisms identified thus far are only part of the entire process, and numerous questions remain unanswered. This review aims to provide an overview of the current understanding of the molecular mechanisms driving leaf form diversity while highlighting the existing gaps in our knowledge. By focusing on the unanswered questions, this review aims to shed light on areas that require further research, ultimately fostering a more comprehensive understanding of leaf form diversity.

Interspersed expression of CUP-SHAPED COTYLEDON2 and REDUCED COMPLEXITY shapes Cardamine hirsuta complex leaf form

How genetically regulated growth shapes organ form is a key problem in developmental biology. Here, we investigate this problem using the leaflet-bearing complex leaves of Cardamine hirsuta as a model. Leaflet development requires the action of two growth-repressing transcription factors: REDUCED COMPLEXITY (RCO), a homeodomain protein, and CUP-SHAPED COTYLEDON2 (CUC2), a NAC-domain protein. However, how their respective growth-repressive actions are integrated in space and time to generate complex leaf forms remains unknown. By using live imaging, we show that CUC2 and RCO are expressed in an interspersed fashion along the leaf margin, creating a distinctive striped pattern. We find that this pattern is functionally important because forcing RCO expression in the CUC2 domain disrupts auxin-based marginal patterning and can abolish leaflet formation. By combining genetic perturbations with time-lapse imaging and cellular growth quantifications, we provide evidence that RCO-mediated growth repression occurs after auxin-based leaflet patterning and in association with the repression of cell proliferation. Additionally, through the use of genetic mosaics, we show that RCO is sufficient to repress both cellular growth and proliferation in a cell-autonomous manner. This mechanism of growth repression is different to that of CUC2, which occurs in proliferating cells. Our findings clarify how the two growth repressors RCO and CUC2 coordinate to subdivide developing leaf primordia into distinct leaflets and generate the complex leaf form. They also indicate different relationships between growth repression and cell proliferation in the patterning and post-patterning stages of organogenesis.

Is auxin enough? Cytokinins and margin patterning in simple leaves

The interplay between auxin and cytokinins affects facets of plant development as different as ovule formation and lateral root initiation. Moreover, cytokinins favor complexity in the development of Solanum lycopersicum and Cardamine hirsuta compound leaves. Nevertheless, no role has been proposed for cytokinins in patterning the margins of the simple leaves of Arabidopsis thaliana, a process that is assumed to be sufficiently explained by auxin localization. Here, we discuss evidence supporting the hypothesis that cytokinins play a role in simple leaf margin morphogenesis via crosstalk with auxin, as occurs in other plant developmental events. Indeed, mutant or transgenic arabidopsis plants defective in cytokinin biosynthesis or signaling, or with increased cytokinin degradation have leaf margins less serrated than the wild type.

Integrated Analysis of Transcriptome and Metabolome Reveals New Insights into the Formation of Purple Leaf Veins and Leaf Edge Cracks in Brassica juncea

Purple leaf veins and leaf edge cracks comprise the typical leaf phenotype of Brassica juncea; however, the molecular mechanisms and metabolic pathways of the formation of purple leaf veins and leaf edge cracks remain unclear. In this study, transcriptome and metabolome analyses were conducted to explore the regulation pathway of purple leaf vein and leaf edge crack formation based on four mustard samples that showed different leaf colors and degrees of cracking. The results showed genes with higher expression in purple leaf veins were mainly enriched in the flavonoid biosynthesis pathway. Integrating related genes and metabolites showed that the highly expressed genes of ANS (BjuA004031, BjuB014115, BjuB044852, and BjuO009605) and the excessive accumulation of dihydrokaempferol and dihydroquercetin contributed to the purple leaf veins by activating the synthetic pathways of pelargonidin-based anthocyanins and delphinidin-based anthocyanins. Meanwhile, “alpha-farnesene synthase activity” and “glucan endo-1, 3-beta-D-glucosidase activity” related to the adversity were mainly enriched in the serrated and lobed leaves, indicating that the environmental pressure was the dominant factor controlling the change in leaf shape. Overall, these results provided new insights into the regulation pathways for formation of purple leaf veins and leaf edge cracks, which could better accelerate the theoretical research on purple leaf vein color and leaf edge cracks in mustard.

The cellular basis for synergy between RCO and KNOX1 homeobox genes in leaf shape diversity

Leaves of seed plants provide an attractive system to study the development and evolution of form. Leaves show varying degrees of margin complexity ranging from simple, as in Arabidopsis thaliana, to fully dissected into leaflets in the closely related species Cardamine hirsuta. Leaflet formation requires actions of Class I KNOTTED1-LIKE HOMEOBOX (KNOX1) and REDUCED COMPLEXITY (RCO) homeobox genes, which are expressed in the leaves of C. hirsuta but not A. thaliana. Evolutionary studies indicate that diversification of KNOX1 and RCO genes was repeatedly associated with increased leaf complexity. However, whether this gene combination represents a developmentally favored avenue for leaflet formation remains unknown, and the cell-level events through which the combined action of these genes drives leaflet formation are also poorly understood. Here we show, through a genetic screen, that when a C. hirsuta RCO transgene is expressed in A. thaliana, then ectopic KNOX1 expression in leaves represents a preferred developmental path for leaflet formation. Using time-lapse growth analysis, we demonstrate that KNOX1 expression in the basal domain of leaves leads to prolonged and anisotropic cell growth. This KNOX1 action, in synergy with local growth repression by RCO, is instrumental in generating rachises and petiolules, the linear geometrical elements, that bear leaflets in complex leaves. Our results show how the combination of cell-level growth analyses and genetics can help us understand how evolutionary modifications in expression of developmentally important genes are translated into diverse leaf shapes.

Elucidating the biology of transcription factor-DNA interaction for accurate identification of cis-regulatory elements

Transcription factors (TFs) play a critical role in determining cell fate decisions by integrating developmental and environmental signals through binding to specific cis-regulatory modules and regulating spatio-temporal specificity of gene expression patterns. Precise identification of functional TF binding sites in time and space not only will revolutionize our understanding of regulatory networks governing cell fate decisions but is also instrumental to uncover how genetic variations cause morphological diversity or disease. In this review, we discuss recent advances in mapping TF binding sites and characterizing the various parameters underlying the complexity of binding site recognition by TFs.

Club-mosses (Diphasiastrum, Lycopodiaceae) from the Far East - Introgression and possible cryptic speciation

Hybridization occurs often in the genus Diphasiastrum (Lycopodiaceae), which corroborates reports for the two other recognized lycophyte families, Isoëtaceae and Selaginellaceae. Here we investigate the case of D. alpinum and D. sitchense from the Russian Far East (Kamchatka). Their hybrid, D. × takedae, was morphologically recognizable in 16 out of 22 accessions showing molecular signatures of hybridization; the remaining accessions displayed the morphology of either D. alpinum (3) or D. sitchense (3). We sequenced markers for chloroplast microsatellites (cp, 175 accessions from Kamchatka) and for the two nuclear markers RPB and LFY (175 and 152 accessions). A selection of 42 accessions, including all hybrid accessions, was analysed via genotyping by sequencing (GBS). We found multiple, but apparently uniparental hybridization, clearly characterized by a deviating group of haplotypes for D. sitchense and all hybrids. All accessions showing molecular signatures of hybridization in nuclear markers revealed the parental haplotype of D. sitchense, however only the LFY marker differentiated between the parent species. GBS, including 69,819 quality-filtered single nucleotid polymorphisms, unambiguously identified the hybrids and revealed introgression to occur. Most of the hybrids were F₁, but three turned out to be backcrosses with D. alpinum (one) and with D. sitchense (two). These observations are in contrast to prior findings on three European species and their intermediates where all three hybrids turned out to be independent F₁ crosses without evidence of recent backcrossing. In this study, backcrossing was detected, which indicates a limited fertility of the hybrid taxon D. × takedae. A comparison of accessions of Kamchatkian D. alpinum with plants from Europe indicated possible cryptic speciation. Accessions from the Far East had (i) a lower DNA content (7.0 vs. 7.5 pg/2C), (ii) different prevailing cp haplotypes, and (iii) RPB genotypes, and (iv) a clearly different SNP pattern in GBS. Diphasiastrum sitchense and the similar D. nikoënse, for the latter additional accessions from Japan were investigated, appeared as forms of one diverse species, sharing genotypes in both nuclear markers, although chloroplast haplotypes and DNA content show slight variations.

Molecular mechanisms underlying leaf development, morphological diversification, and beyond

The basic mechanisms of leaf development have been revealed through a combination of genetics and intense analyses in select model species. The genetic basis for diversity in leaf morphology seen in nature is also being unraveled through recent advances in techniques and technologies related to genomics and transcriptomics, which have had a major impact on these comparative studies. However, this has led to the emergence of new unresolved questions about the mechanisms that generate the diversity of leaf form. Here, we provide a review of the current knowledge of the fundamental molecular genetic mechanisms underlying leaf development with an emphasis on natural variation and conserved gene regulatory networks involved in leaf development. Beyond that, we discuss open questions/enigmas in the area of leaf development, how recent technologies can best be deployed to generate a unified understanding of leaf diversity and its evolution, and what untapped fields lie ahead.

BoALG10, an α-1,2 glycosyltransferase, plays an essential role in maintaining leaf margin shape in ornamental kale

The morphological diversity of leaf margin shapes is an identifying characteristic of many plant species. In our previous work, BoALG10 (α-1,2 glycosyltransferase) was predicted to be a key regulator of leaf margin shape in ornamental kale (Brassica oleracea var. acephala). An alanine and a leucine residue in the conserved domain of the smooth-margined S0835 were replaced by an aspartate and a phenylalanine, respectively, in the corresponding positions of the feathered-margined F0819. However, the expression pattern and function of this gene remain unclear. Here, we examined the expression patterns of BoALG10 using quantitative real-time PCR, and found that statistically significant differences in expression existed between F0819 and S0835 in nine developmental stages. The BoALG10 protein localized to the endoplasmic reticulum. The function of BoALG10 was then examined using complementary mutant assays. The overexpression strains phenocopied the smooth leaf margin after introduction of BoALG10 ^S0835 into the feathered-margined inbred line F0819. Simultaneously, irregular dissections appeared in the leaf margins of knockout mutants KO-1 and KO-2, which were generated by CRISPR/Cas9 technology from the smooth-margined inbred line S0835. Microscopic observation showed that the leaf margin cells of the smooth-margined plants S0835 and OE-3 were arranged regularly, while the cells of the feathered-margined plants F0819 and KO-1 were of inconsistent size and distributed in an irregular manner, particularly around the indentations of the leaf. This elucidation of BoALG10 function provides a novel insight into the morphological regulation of leaf margin shape.

A procedure for Dex-induced gene transactivation in Arabidopsis ovules

BACKGROUND

Elucidating the genetic and molecular control of plant reproduction often requires the deployment of functional approaches based on reverse or forward genetic screens. The loss-of-function of essential genes, however, may lead to plant lethality prior to reproductive development or to the formation of sterile structures before the organ-of-interest can be analyzed. In these cases, inducible approaches that enable a spatial and temporal control of the genetic perturbation are extremely valuable. Genetic induction in reproductive organs, such as the ovule, deeply embedded in the flower, is a delicate procedure that requires both optimization and validation.

RESULTS

Here we report on a streamlined procedure enabling reliable induction of gene expression in Arabidopsis ovule and anther tissues using the popular pOP/LhGR Dex-inducible system. We demonstrate its efficiency and reliability using fluorescent reporter proteins and histochemical detection of the GUS reporter gene.

CONCLUSION

The pOP/LhGR system allows for a rapid, efficient, and reliable induction of transgenes in developing ovules without compromising developmental progression. This approach opens new possibilities for the functional analysis of candidate regulators in sporogenesis and gametogenesis, which is otherwise affected by early lethality in conventional, stable mutants.

Impact of Genetic Variation in Gene Regulatory Sequences: A Population Genomics Perspective

The unprecedented rise of high-throughput sequencing and assay technologies has provided a detailed insight into the non-coding sequences and their potential role as gene expression regulators. These regulatory non-coding sequences are also referred to as cis-regulatory elements (CREs). Genetic variants occurring within CREs have been shown to be associated with altered gene expression and phenotypic changes. Such variants are known to occur spontaneously and ultimately get fixed, due to selection and genetic drift, in natural populations and, in some cases, pave the way for speciation. Hence, the study of genetic variation at CREs has improved our overall understanding of the processes of local adaptation and evolution. Recent advances in high-throughput sequencing and better annotations of CREs have enabled the evaluation of the impact of such variation on gene expression, phenotypic alteration and fitness. Here, we review recent research on the evolution of CREs and concentrate on studies that have investigated genetic variation occurring in these regulatory sequences within the context of population genetics.

From genes to networks: The genetic control of leaf development

Substantial diversity exists for both the size and shape of the leaf, the main photosynthetic organ of flowering plants. The two major forms of leaf are simple leaves, in which the leaf blade is undivided, and compound leaves, which comprise several leaflets. Leaves form at the shoot apical meristem from a group of undifferentiated cells, which first establish polarity, then grow and differentiate. Each of these processes is controlled by a combination of transcriptional regulators, microRNAs and phytohormones. The present review documents recent advances in our understanding of how these various factors modulate the development of both simple leaves (focusing mainly on the model plant Arabidopsis thaliana) and compound leaves (focusing mainly on the model legume species Medicago truncatula).

Leaf Shape Diversity: From Genetic Modules to Computational Models

Plant leaves display considerable variation in shape. Here, we introduce key aspects of leaf development, focusing on the morphogenetic basis of leaf shape diversity. We discuss the importance of the genetic control of the amount, duration, and direction of cellular growth for the emergence of leaf form. We highlight how the combined use of live imaging and computational frameworks can help conceptualize how regulated cellular growth is translated into different leaf shapes. In particular, we focus on the morphogenetic differences between simple and complex leaves and how carnivorous plants form three-dimensional insect traps. We discuss how evolution has shaped leaf diversity in the case of complex leaves, by tinkering with organ-wide growth and local growth repression, and in carnivorous plants, by modifying the relative growth of the lower and upper sides of the leaf primordium to create insect-digesting traps.

Coordinating the morphogenesis-differentiation balance by tweaking the cytokinin-gibberellin equilibrium

Morphogenesis and differentiation are important stages in organ development and shape determination. However, how they are balanced and tuned during development is not fully understood. In the compound leaved tomato, an extended morphogenesis phase allows for the initiation of leaflets, resulting in the compound form. Maintaining a prolonged morphogenetic phase in early stages of compound-leaf development in tomato is dependent on delayed activity of several factors that promote differentiation, including the CIN-TCP transcription factor (TF) LA, the MYB TF CLAU and the plant hormone Gibberellin (GA), as well as on the morphogenesis-promoting activity of the plant hormone cytokinin (CK). Here, we investigated the genetic regulation of the morphogenesis-differentiation balance by studying the relationship between LA, CLAU, TKN2, CK and GA. Our genetic and molecular examination suggest that LA is expressed earlier and more broadly than CLAU and determines the developmental context of CLAU activity. Genetic interaction analysis indicates that LA and CLAU likely promote differentiation in parallel genetic pathways. These pathways converge downstream on tuning the balance between CK and GA. Comprehensive transcriptomic analyses support the genetic data and provide insights into the broader molecular basis of differentiation and morphogenesis processes in plants.

Morphogenesis and differentiation are crucial steps in the formation and shaping of organs in both plants and animals. A wide array of transcription factors and hormones were shown to act together to support morphogenesis or promote differentiation. However, a comprehensive molecular and genetic understating of how morphogenesis and differentiation are coordinated during development is still missing. We addressed these questions in the context of the development of the tomato compound leaf, for which many regulators have been described. Investigating the coordination among these different actors, we show that several discrete genetic pathways promote differentiation. Downstream of these separate pathways, two important plant hormones, cytokinin and gibberellin, act antagonistically to tweak the morphogenesis-differentiation balance.

Mechanisms of the Morphological Plasticity Induced by Phytohormones and the Environment in Plants

Plants adapt to environmental changes by regulating their development and growth. As an important interface between plants and their environment, leaf morphogenesis varies between species, populations, or even shows plasticity within individuals. Leaf growth is dependent on many environmental factors, such as light, temperature, and submergence. Phytohormones play key functions in leaf development and can act as molecular regulatory elements in response to environmental signals. In this review, we discuss the current knowledge on the effects of different environmental factors and phytohormone pathways on morphological plasticity and intend to summarize the advances in leaf development. In addition, we detail the molecular mechanisms of heterophylly, the representative of leaf plasticity, providing novel insights into phytohormones and the environmental adaptation in plants.

BnA10.RCO, a homeobox gene, positively regulates leaf lobe formation in Brassica napus L

BnA10.RCO positively regulates the development of leaf lobes in Brassica napus, and cis-regulatory divergences cause the different allele effects. The functional importance of lobed leaves in rapeseed (Brassica napus L.) has been identified with potential advantages for high-density planting and hybrid production. Our previous studies indicated that the tandemly duplicated LMI1-like genes BnA10. RCO and BnA10.LMI1 are candidate genes of an incompletely dominant locus, which is responsible for the lobed-leaf shape in rapeseed. We provided strong evidence that BnA10.LMI1 positively regulates leaf lobe formation. Here, we show that BnA10.RCO is a nucleus-specific protein, encoding an HD-ZIP I transcription factor, which is responsible for the lobed-leaf shape in rapeseed. Sequence analysis of parental alleles revealed that no vital sequence variation was detected in the coding sequence of BnA10.RCO, whereas abundant variations were identified in the regulatory regions. Consistent with this finding, the expression level of BnRCO was substantially elevated in the lobed-leaved parent HY compared with its near-isogenic line. Moreover, the altered expression of BnA10.RCO in transgenic lines showed a positive connection with leaf complexity without a substantial change in BnLMI1 transcript level. Furthermore, CRISPR/Cas9-induced null mutations of BnA10.RCO in the lobed-leaved parent HY were sufficient to produce an unlobed leaf without alteration in BnLMI1 transcript level. Our results indicate that BnA10.RCO functions together with BnA10.LMI1 to positively determine the lobed-leaf development, providing a fundamental basis for crop improvement by targeting leaf shape in rapeseed.

Mutation bias interacts with composition bias to influence adaptive evolution

Mutation is a biased stochastic process, with some types of mutations occurring more frequently than others. Previous work has used synthetic genotype-phenotype landscapes to study how such mutation bias affects adaptive evolution. Here, we consider 746 empirical genotype-phenotype landscapes, each of which describes the binding affinity of target DNA sequences to a transcription factor, to study the influence of mutation bias on adaptive evolution of increased binding affinity. By using empirical genotype-phenotype landscapes, we need to make only few assumptions about landscape topography and about the DNA sequences that each landscape contains. The latter is particularly important because the set of sequences that a landscape contains determines the types of mutations that can occur along a mutational path to an adaptive peak. That is, landscapes can exhibit a composition bias—a statistical enrichment of a particular type of mutation relative to a null expectation, throughout an entire landscape or along particular mutational paths—that is independent of any bias in the mutation process. Our results reveal the way in which composition bias interacts with biases in the mutation process under different population genetic conditions, and how such interaction impacts fundamental properties of adaptive evolution, such as its predictability, as well as the evolution of genetic diversity and mutational robustness.

Mutation is often depicted as a random process due its unpredictable nature. However, such randomness does not imply uniformly distributed outcomes, because some DNA sequence changes happen more frequently than others. Mutation bias can be an orienting factor in adaptive evolution, influencing the mutational trajectories populations follow toward higher-fitness genotypes. Because these trajectories are typically just a small subset of all possible mutational trajectories, they can exhibit composition bias—an enrichment of a particular kind of DNA sequence change, such as transition or transversion mutations. Here, we use empirical data from eukaryotic transcriptional regulation to study how mutation bias and composition bias interact to influence adaptive evolution.

Lateral Leaflet Suppression 1 (LLS1), encoding the MtYUCCA1 protein, regulates lateral leaflet development in Medicago truncatula

In species with compound leaves, the positions of leaflet primordium initiation are associated with local peaks of auxin accumulation. However, the role of auxin during the late developmental stages and outgrowth of compound leaves remains largely unknown. Using genome resequencing approaches, we identified insertion sites at four alleles of the LATERAL LEAFLET SUPPRESSION1 (LLS1) gene, encoding the auxin biosynthetic enzyme YUCCA1 in Medicago truncatula. Linkage analysis and complementation tests showed that the lls1 mutant phenotypes were caused by the Tnt1 insertions that disrupted the LLS1 gene. The transcripts of LLS1 can be detected in primordia at early stages of leaf initiation and later in the basal regions of leaflets, and finally in vein tissues at late leaf developmental stages. Vein numbers and auxin content are reduced in the lls1-1 mutant. Analysis of the lls1 sgl1 and lls1 palm1 double mutants revealed that SGL1 is epistatic to LLS1, and LLS1 works with PALM1 in an independent pathway to regulate the growth of lateral leaflets. Our work demonstrates that the YUCCA1/YUCCA4 subgroup plays very important roles in the outgrowth of lateral leaflets during compound leaf development of M. truncatula, in addition to leaf venation.

Evolution: How a Homeobox Gene Cuts the Mustard Leaf

Gene duplication and cis-regulatory divergence created the growth-repressing RCO homeobox gene and facilitated evolution of dissected crucifer leaves. Identification of RCO targets reveals that auto-repression evolved to fine-tune RCO activity and that RCO dissects leaves by increasing cytokinin signalling to inhibit growth locally.