The Evolution of the KANADI Gene Family and Leaf Development in Lycophytes and Ferns

Genome-Wide Identification and Comprehensive Analysis of the GARP Transcription Factor Superfamily in Populus deltoides

Background/Objectives: The GARP transcription factor superfamily is crucial for plant growth, development, and stress responses. This study systematically identified and analyzed the GARP family genes in Populus deltoides to explore their roles in plant development and abiotic stress responses. Methods: A total of 58 PdGARP genes were identified using bioinformatics tools. Their physicochemical properties, genomic locations, conserved motifs, gene structures, and phylogenetic relationships were analyzed. Expression patterns under phosphorus and nitrogen deficiency, as well as tissue-specific expression, were investigated using RT-qPCR. Transgenic RNAi lines were generated to validate the function of GLK genes in chlorophyll biosynthesis. Results: The 58 PdGARP genes were classified into five subfamilies based on their evolutionary relationships and protein sequence similarity. Segmental duplication was found to be the primary driver of the PdGARP family's expansion. Cis-regulatory elements (CREs) related to light, hormones, and abiotic stresses were identified in the promoters of PdGARP genes. Differential expression patterns were observed for NIGT1/HRS1/HHO and PHR/PHL subfamily members under phosphorus and nitrogen deficiency, indicating their involvement in stress responses. KAN subfamily members exhibited tissue-specific expression, particularly in leaves. Structural analysis of the GLK subfamily revealed conserved α-helices, extended chains, and irregular coils. Transgenic RNAi lines targeting GLK genes showed significant reductions in chlorophyll and carotenoid content. Conclusions: This study provides a comprehensive analysis of the GARP transcription factor superfamily in P. deltoides, highlighting their potential roles in nutrient signaling and stress response pathways. The findings lay the foundation for further functional studies of PdGARP genes and their application in stress-resistant breeding of poplar.

Identification and Candidate Gene Analysis of Brcl1, a Novel Gene Confers a Leaf Curled Phenotype in Brassica rapa L

Leaf shape is an important determinant of photosynthesis, yield and quality in plants. In this study, we obtained a curled leaf mutant, cl1, from an ethyl methanesulfonate (EMS)-induced mutagenesis population. It was designated the Brcl1YS locus. Bulk segregant RNA sequencing combined with recombinant screening identified the candidate interval responsible for Brcl1YS in a 97.5 kb region on chromosome A02. Twelve genes were identified within the candidate region. Sequence differences and co-separation verification confirmed that BraA02g017030.3C was the most promising candidate gene underlying the Brcl1YS locus. It is homologous to Arabidopsis AT1G66350 (RGL1), which has been shown to act as a negative regulator of the gibberellin pathway. Combined with cell morphology observation, it is speculated that the loss of function of Brcl1YS results in differences in cell development, ultimately leading to changes in leaf morphology. The results will contribute to the understanding of the molecular mechanisms underlying leaf curling in B. rapa.

Developmental Morphology, Physiology, and Molecular Basis of the Pentagram Fruit of Averrhoa carambola

Averrhoa carambola, a key tropical and subtropical economic tree in the Oxalidaceae family, is distinguished by its unique pentagram-shaped fruit. This study investigates the developmental processes shaping the polarity of A. carambola fruit and their underlying hormonal and genetic mechanisms. By analyzing the Y1, Y2, and Y3 developmental stages-defined by the fruit diameters of 3-4 mm, 4-6 mm, and 6-12 mm, respectively-we observed that both cell number and cell size contribute to fruit development. Our findings suggest that the characteristic pentagram shape is established before flowering and is maintained throughout development. A hormonal analysis revealed that indole-3-acetic acid (IAA) and abscisic acid (ABA) show differential distribution between the convex and concave regions of the fruit across the developmental stages, with IAA playing a crucial role in polar auxin transport and shaping fruit morphology. A transcriptomic analysis identified several key genes, including AcaGH3.8, AcaIAA20, AcaYAB2, AcaXTH6, AcaYAB3, and AcaEXP13, which potentially regulate fruit polarity and growth. This study advances our comprehension of the molecular mechanisms governing fruit shape, offering insights for improving fruit quality through targeted breeding strategies.

The Shoot Apical Meristem: An Evolutionary Molding of Higher Plants

The shoot apical meristem (SAM) gives rise to the aerial structure of plants by producing lateral organs and other meristems. The SAM is responsible for plant developmental patterns, thus determining plant morphology and, consequently, many agronomic traits such as the number and size of fruits and flowers and kernel yield. Our current understanding of SAM morphology and regulation is based on studies conducted mainly on some angiosperms, including economically important crops such as maize (Zea mays) and rice (Oryza sativa), and the model species Arabidopsis (Arabidopsis thaliana). However, studies in other plant species from the gymnosperms are scant, making difficult comparative analyses that help us understand SAM regulation in diverse plant species. This limitation prevents deciphering the mechanisms by which evolution gave rise to the multiple plant structures within the plant kingdom and determines the conserved mechanisms involved in SAM maintenance and operation. This review aims to integrate and analyze the current knowledge of SAM evolution by combining the morphological and molecular information recently reported from the plant kingdom.

Size regulation of the lateral organ initiation zone and its role in determining cotyledon number in conifers

Introduction

Unlike monocots and dicots, many conifers, particularly Pinaceae, form three or more cotyledons. These are arranged in a whorl, or ring, at a particular distance from the embryo tip, with cotyledons evenly spaced within the ring. The number of cotyledons, n_c, varies substantially within species, both in clonal cultures and in seed embryos. n_c variability reflects embryo size variability, with larger diameter embryos having higher n_c. Correcting for growth during embryo development, we extract values for the whorl radius at each n_c. This radius, corresponding to the spatial pattern of cotyledon differentiation factors, varies over three-fold for the naturally observed range of n_c. The current work focuses on factors in the patterning mechanism that could produce such a broad variability in whorl radius. Molecularly, work in Arabidopsis has shown that the initiation zone for leaf primordia occurs at a minimum between inhibitor zones of HD-ZIP III at the shoot apical meristem (SAM) tip and KANADI (KAN) encircling this farther from the tip. PIN1-auxin dynamics within this uninhibited ring form auxin maxima, specifying primordia initiation sites. A similar mechanism is indicated in conifer embryos by effects on cotyledon formation with overexpression of HD-ZIP III inhibitors and by interference with PIN1-auxin patterning.

Methods

We develop a mathematical model for HD-ZIP III/KAN spatial localization and use this to characterize the molecular regulation that could generate (a) the three-fold whorl radius variation (and associated n_c variability) observed in conifer cotyledon development, and (b) the HD-ZIP III and KAN shifts induced experimentally in conifer embryos and in Arabidopsis.

Results

This quantitative framework indicates the sensitivity of mechanism components for positioning lateral organs closer to or farther from the tip. Positional shifting is most readily driven by changes to the extent of upstream (meristematic) patterning and changes in HD-ZIP III/KAN mutual inhibition, and less efficiently driven by changes in upstream dosage or the activation of HD-ZIP III. Sharper expression boundaries can also be more resistant to shifting than shallower expression boundaries.

Discussion

The strong variability seen in conifer n_c (commonly from 2 to 10) may reflect a freer variation in regulatory interactions, whereas monocot (n_c = 1) and dicot (n_c = 2) development may require tighter control of such variation. These results provide direction for future quantitative experiments on the positional control of lateral organ initiation, and consequently on plant phyllotaxy and architecture.

Assessing diversity and phylogeny of Indonesian breadfruit (Artocarpus spp.) using internal transcribed spacer (ITS) region and leaf morphology

BACKGROUND

Breadfruit (Artocarpus spp.) is the main genus of Moraceae with multipurpose benefits, both ecologically and economically important, e.g., food ingredients, building materials, traditional medicine, and natural insecticides. However, most endemic Artocarpus have been threatened due to natural disasters and habitat degradation. The objective of our study was to determine the genetic diversity and relationships of endemic Artocarpus from South Borneo, Indonesia, using an internal transcribed spacer (ITS) region and leaf morphology.

RESULTS

Morphologically, endemic Artocarpus endemic to South Borneo, Indonesia, has a different leaf shape, i.e., narrow-obovate to broad-elliptic, from simple to deeply dissected. Following the ITS region, this germplasm has a moderate level of nucleotide diversity (0.069). The phylogenetic analysis revealed Artocarpus into four (4) main clades, where the nearest is shown by the 'Puyian' (Artocarpus rigidus) and 'Binturung' (Artocarpus odoratissimus) at a coefficient divergence of 0.027, whereas the furthest by 'Kulur' (A. camansi) and 'Tiwadak' (A. integer) at a coefficient of 0.132.

CONCLUSION

In brief, although an endemic Artocarpus of South Borneo, Indonesia, has a moderate level of nucleotide diversity, this germplasm also shows a unique phylogenetic relationship. Thus, this information is urgent in supporting the future Artocarpus breeding and preservation programs, mainly to save this germplasm from being threatened.

Does integument arise de novo or from pre-existing structures? ── Insights from the key regulatory genes controlling integument development

The origin of seeds is one of the key innovations in land plant evolution. Ovules are the developmental precursors of seeds. The integument is the envelope structure surrounding the nucellus within the ovule and developing into the seed coat when ovules mature upon fertilization. The question of whether the integument arise de novo or evolve from elaboration of pre-existing structures has caused much debate. By exploring the origin and evolution of the key regulatory genes controlling integument development and their functions during both individual and historical developmental processes, we showed the widespread presence of the homologs of ANT, CUC, BEL1, SPL, C3HDZ, INO, ATS, and ETT in seedless plant genomes. All of these genes have undergone duplication-divergence events in their evolutionary history, with most of the descendant paralogous suffering motif gain and/or loss in the coding regions. Expression and functional characterization have shown that these genes are key components of the genetic program that patterns leaf-like lateral organs. Serial homology can thus be postulated between integuments and other lateral organs in terms of the shared master regulatory genes. Given that the genetic program patterning leaf-like lateral organs formed in seedless plants, and was reused during seed origin, the integument is unlikely to arise de novo but evolved from the stem segment-specific modification of pre-existing serially homologous structures. The master 'switches' trigging the modification to specify the integument identity remain unclear. We propose a successive transformation model of integument origin.

EYFP fusions to HD-Zip IV transcription factors enhance their stability and lead to phenotypic changes in Arabidopsis

Green fluorescent protein (GFP) and its derivatives are extensively used for labeling cells, monitoring gene expression and/or tracking the localization or interactions of proteins. Previous reports of detrimental effects of fluorescent protein (FP) expression include cytotoxicity and interference with fusion protein function or localization. Only a few studies have documented the fluorescent tag-specific effects in plants. Here, we show that placing an enhanced yellow FP (EYFP) tag on the amino-terminus of GLABRA2 (GL2) and PROTODERMAL FACTOR2 (PDF2), two developmentally important HD-Zip IV transcription factors from Arabidopsis, enhances their protein stability. Additionally, expression of EYFP:GL2 not only rescued the gl2 null mutant but also resulted in the abnormal development of abaxially curled leaves associated with EYFP-tag induced GL2 overexpression. Our study raises concerns on the use of FPs regarding their effects on the native properties of target proteins as well as biological consequences of fusion protein expression on morphology.

Insight into the formation of trumpet and needle-type leaf in Ginkgo biloba L. mutant

The leaf type of a plant determines its photosynthetic efficiency and adaptation to the environment. The normal leaves of modern Ginkgo biloba, which is known as a "living fossil" in gymnosperm, evolved from needle-like to fan-shaped with obvious dichotomous venation. However, a newly discovered Ginkgo variety "SongZhen" have different leaf types on a tree, including needle-, trumpet-, strip-, and deeply split fan-shaped leaves. In order to explore the mechanism in forming these leaf types, the microscopy of different leaf types and transcriptome analysis of apical buds of branches with normal or abnormal leaves were performed. We found that the normal leaf was in an intact and unfolded fan shape, and the abnormal leaf was basically split into two parts from the petiole, and each exhibited different extent of variation. The needle-type leaves were the extreme, having no obvious palisade and spongy tissues, and the phloem cells were scattered and surrounded by xylem cells, while the trumpet-type leaves with normal vascular bundles curled inward to form a loop from the abaxial to adaxial side. The other type of leaves had the characteristics among needle-type, trumpet-type, or normal leaves. The transcriptome analysis and quantitative PCR showed that the genes related to abaxial domain were highly expressed, while the adaxial domain promoting genes were decreasingly expressed in abnormal-type leaf (ANL) buds and abnormal leaves, which might lead to the obvious abaxialized leaves of "SongZhen." In addition, the low expression of genes related to leaf boundary development in ANL buds indicated that single- or double-needle (trumpet) leaves might also be due to the leaf tissue fusion. This study provides an insight into the mechanism of the development of the abnormal leaves in "SongZhen" and lays a foundation for investigating the molecular mechanism of the leaf development in gymnosperms.

Dynamic genome evolution in a model fern

The large size and complexity of most fern genomes have hampered efforts to elucidate fundamental aspects of fern biology and land plant evolution through genome-enabled research. Here we present a chromosomal genome assembly and associated methylome, transcriptome and metabolome analyses for the model fern species Ceratopteris richardii. The assembly reveals a history of remarkably dynamic genome evolution including rapid changes in genome content and structure following the most recent whole-genome duplication approximately 60 million years ago. These changes include massive gene loss, rampant tandem duplications and multiple horizontal gene transfers from bacteria, contributing to the diversification of defence-related gene families. The insertion of transposable elements into introns has led to the large size of the Ceratopteris genome and to exceptionally long genes relative to other plants. Gene family analyses indicate that genes directing seed development were co-opted from those controlling the development of fern sporangia, providing insights into seed plant evolution. Our findings and annotated genome assembly extend the utility of Ceratopteris as a model for investigating and teaching plant biology.

Developmental regulation of leaf venation patterns: monocot versus eudicots and the role of auxin

Organisation and patterning of the vascular network in land plants varies in different taxonomic, developmental and environmental contexts. In leaves, the degree of vascular strand connectivity influences both light and CO₂ harvesting capabilities as well as hydraulic capacity. As such, developmental mechanisms that regulate leaf venation patterning have a direct impact on physiological performance. Development of the leaf venation network requires the specification of procambial cells within the ground meristem of the primordium and subsequent proliferation and differentiation of the procambial lineage to form vascular strands. An understanding of how diverse venation patterns are manifest therefore requires mechanistic insight into how procambium is dynamically specified in a growing leaf. A role for auxin in this process was identified many years ago, but questions remain. In this review we first provide an overview of the diverse venation patterns that exist in land plants, providing an evolutionary perspective. We then focus on the developmental regulation of leaf venation patterns in angiosperms, comparing patterning in eudicots and monocots, and the role of auxin in each case. Although common themes emerge, we conclude that the developmental mechanisms elucidated in eudicots are unlikely to fully explain how parallel venation patterns in monocot leaves are elaborated.

KANADI promotes thallus differentiation and FR-induced gametangiophore formation in the liverwort Marchantia

In angiosperms, KANADI transcription factors have roles in the sporophyte generation regulating tissue polarity, organogenesis and shade avoidance responses, but are not required during the gametophyte generation. Whether these roles are conserved in the gametophyte-dominant bryophyte lineages is unknown, which we examined by characterising the sole KANADI ortholog, MpKAN, in the liverwort Marchantia polymorpha. In contrast to angiosperm orthologs, MpKAN functions in the gametophyte generation in Marchantia, where it regulates apical branching and tissue differentiation, but does not influence tissue polarity in either generation. MpKAN can partially rescue the sporophyte polarity defects of kanadi mutants in Arabidopsis, indicating that MpKAN has conserved biochemical activity to its angiosperm counterparts. Mpkan loss-of-function plants display defects in far-red (FR) light responses. Mpkan plants have reduced FR-induced growth tropisms, have a delayed transition to sexual reproduction and fail to correctly form gametangiophores. Our results indicate that MpKAN is a modulator of FR responses, which may reflect a conserved role for KANADI across land plants. Under FR, MpKAN negatively regulates MpDELLA expression, suggesting that MpKAN and MpDELLA act in a pathway regulating FR responses, placing MpKAN in a gene regulatory network exhibiting similarities with those of angiosperms.

Fossils and plant evolution: structural fingerprints and modularity in the evo-devo paradigm

Fossils constitute the principal repository of data that allow for independent tests of hypotheses of biological evolution derived from observations of the extant biota. Traditionally, transformational series of structure, consisting of sequences of fossils of the same lineage through time, have been employed to reconstruct and interpret morphological evolution. More recently, a move toward an updated paradigm was fueled by the deliberate integration of developmental thinking in the inclusion of fossils in reconstruction of morphological evolution. The vehicle for this is provided by structural fingerprints-recognizable morphological and anatomical structures generated by (and reflective of) the deployment of specific genes and regulatory pathways during development. Furthermore, because the regulation of plant development is both modular and hierarchical in nature, combining structural fingerprints recognized in the fossil record with our understanding of the developmental regulation of those structures produces a powerful tool for understanding plant evolution. This is particularly true when the systematic distribution of specific developmental regulatory mechanisms and modules is viewed within an evolutionary (paleo-evo-devo) framework. Here, we discuss several advances in understanding the processes and patterns of evolution, achieved by tracking structural fingerprints with their underlying regulatory modules across lineages, living and fossil: the role of polar auxin regulation in the cellular patterning of secondary xylem and the parallel evolution of arborescence in lycophytes and seed plants; the morphology and life history of early polysporangiophytes and tracheophytes; the role of modularity in the parallel evolution of leaves in euphyllophytes; leaf meristematic activity and the parallel evolution of venation patterns among euphyllophytes; mosaic deployment of regulatory modules and the diverse modes of secondary growth of euphyllophytes; modularity and hierarchy in developmental regulation and the evolution of equisetalean reproductive morphology. More generally, inclusion of plant fossils in the evo-devo paradigm has informed discussions on the evolution of growth patterns and growth responses, sporophyte body plans and their homology, sequences of character evolution, and the evolution of reproductive systems.

A Historical Perspective of Bladderworts (Utricularia): Traps, Carnivory and Body Architecture

The genus Utricularia includes around 250 species of carnivorous plants, commonly known as bladderworts. The generic name Utricularia was coined by Carolus Linnaeus in reference to the carnivorous organs (Utriculus in Latin) present in all species of the genus. Since the formal proposition by Linnaeus, many species of Utricularia were described, but only scarce information about the biology for most species is known. All Utricularia species are herbs with vegetative organs that do not follow traditional models of morphological classification. Since the formal description of Utricularia in the 18th century, the trap function has intrigued naturalists. Historically, the traps were regarded as floating organs, a common hypothesis that was maintained by different botanists. However, Charles Darwin was most likely the first naturalist to refute this idea, since even with the removal of all traps, the plants continued to float. More recently, due mainly to methodological advances, detailed studies on the trap function and mechanisms could be investigated. This review shows a historical perspective on Utricularia studies which focuses on the traps and body organization.

Integration of Core Mechanisms Underlying Plant Aerial Architecture

Over the last decade or so important progress has been made in identifying and understanding a set of patterning mechanisms that have the potential to explain many aspects of plant morphology. These include the feedback loop between mechanical stresses and interphase microtubules, the regulation of plant cell polarity and the role of adaxial and abaxial cell type boundaries. What is perhaps most intriguing is how these mechanisms integrate in a combinatorial manner that provides a means to generate a large variety of commonly seen plant morphologies. Here, I review our current understanding of these mechanisms and discuss the links between them.

Expression analyses in Ginkgo biloba provide new insights into the evolution and development of the seed

Although the seed is a key morphological innovation, its origin remains unknown and molecular data outside angiosperms is still limited. Ginkgo biloba, with a unique place in plant evolution, being one of the first extant gymnosperms where seeds evolved, can testify to the evolution and development of the seed. Initially, to better understand the development of the ovules in Ginkgo biloba ovules, we performed spatio-temporal expression analyses in seeds at early developing stages, of six candidate gene homologues known in angiosperms: WUSCHEL, AINTEGUMENTA, BELL1, KANADI, UNICORN, and C3HDZip. Surprisingly, the expression patterns of most these ovule homologues indicate that they are not wholly conserved between angiosperms and Ginkgo biloba. Consistent with previous studies on early diverging seedless plant lineages, ferns, lycophytes, and bryophytes, many of these candidate genes are mainly expressed in mega- and micro-sporangia. Through in-depth comparative transcriptome analyses of Ginkgo biloba developing ovules, pollen cones, and megagametophytes we have been able to identify novel genes, likely involved in ovule development. Finally, our expression analyses support the synangial or neo-synangial hypotheses for the origin of the seed, where the sporangium developmental network was likely co-opted and restricted during integument evolution.

The evolutionary emergence of land plants

There can be no doubt that early land plant evolution transformed the planet but, until recently, how and when this was achieved was unclear. Coincidence in the first appearance of land plant fossils and formative shifts in atmospheric oxygen and CO2 are an artefact of the paucity of earlier terrestrial rocks. Disentangling the timing of land plant bodyplan assembly and its impact on global biogeochemical cycles has been precluded by uncertainty concerning the relationships of bryophytes to one another and to the tracheophytes, as well as the timescale over which these events unfolded. New genome and transcriptome sequencing projects, combined with the application of sophisticated phylogenomic modelling methods, have yielded increasing support for the Setaphyta clade of liverworts and mosses, within monophyletic bryophytes. We consider the evolution of anatomy, genes, genomes and of development within this phylogenetic context, concluding that many vascular plant (tracheophytes) novelties were already present in a comparatively complex last common ancestor of living land plants (embryophytes). Molecular clock analyses indicate that embryophytes emerged in a mid-Cambrian to early Ordovician interval, compatible with hypotheses on their role as geoengineers, precipitating early Palaeozoic glaciations.

Taxon sampling and alternative hypotheses of relationships in the euphyllophyte plexus that gave rise to seed plants: insights from an Early Devonian radiatopsid

An abrupt transition in the fossil record separates Early Devonian euphyllophytes with a simple structure from a broad diversity of structurally complex Middle-Late Devonian plants. Morphological evolution and phylogeny across this transition are poorly understood due to incomplete sampling of the fossil record. We document a new Early Devonian radiatopsid and integrate it in analyses addressing euphyllophyte relationships. Anatomically preserved Emsian fossils (402-394 Ma) from the Battery Point Formation (Gaspé, Quebec, Canada) are studied in serial sections. The phylogenetic analysis is based on a matrix of 31 taxa and 50 characters emphasising vegetative morphology (41 discrete, nine continuous). The new plant, Kenrickia bivena gen. et sp. nov., is one of very few structurally complex euphyllophytes documented in the Early Devonian. Inclusion of Kenrickia overturns previously established phylogenetic relationships among Radiatopses, reiterating the need for increased density of Early Devonian taxon sampling. Kenrickia is recovered as the sister lineage to all other radiatopsids, a clade in which paraphyletic Stenokoleales led to a lignophyte clade where archaeopterids and seed plants fall into sister clades. Our results shed light on early euphyllophyte relationships and evolution, indicating early exploration of structural complexity by multiple lineages and reiterating the potential of a single origin of secondary growth in euphyllophytes.

Deciphering the evolution of the ovule genetic network through expression analyses in Gnetum gnemon

BACKGROUND AND AIMS

The ovule is a synapomorphy of all seed plants (gymnosperms and angiosperms); however, there are some striking differences in ovules among the major seed plant lineages, such as the number of integuments or the orientation of the ovule. The genetics involved in ovule development have been well studied in the model species Arabidopsis thaliana, which has two integuments and anatropous orientation. This study is approached from what is known in arabidopsis, focusing on the expression patterns of homologues of four genes known to be key for the proper development of the integuments in arabidopsis: AINTEGUMENTA (ANT), BELL1, (BEL1), KANADIs (KANs) and UNICORN (UCN).

METHODS

We used histology to describe the morphoanatomical development from ovules to seeds in Gnetum gnemon. We carried out spatiotemporal expression analyses in G. gnemon, a gymnosperm, which has a unique ovule morphology with an integument covering the nucellus, two additional envelopes where the outermost becomes fleshy as the seed matures, and an orthotropous orientation.

KEY RESULTS

Our anatomical and developmental descriptions provide a framework for expression analyses in the ovule of G. gnemon. Our expression results show that although ANT, KAN and UCN homologues are expressed in the inner integument, their spatiotemporal patterns differ from those found in angiosperms. Furthermore, all homologues studied here are expressed in the nucellus, revealing major differences in seed plants. Finally, no expression of the studied homologues was detected in the outer envelopes.

CONCLUSIONS

Altogether, these analyses provide significant comparative data that allows us to better understand the functional evolution of these gene lineages, providing a compelling framework for evolutionary and developmental studies of seeds. Our findings suggest that these genes were most likely recruited from the sporangium development network and became restricted to the integuments of angiosperm ovules.

YABBY Genes in the Development and Evolution of Land Plants

Mounting evidence from genomic and transcriptomic studies suggests that most genetic networks regulating the morphogenesis of land plant sporophytes were co-opted and modified from those already present in streptophyte algae and gametophytes of bryophytes sensu lato. However, thus far, no candidate genes have been identified that could be responsible for "planation", a conversion from a three-dimensional to a two-dimensional growth pattern. According to the telome theory, "planation" was required for the genesis of the leaf blade in the course of leaf evolution. The key transcription factors responsible for leaf blade development in angiosperms are YABBY proteins, which until recently were thought to be unique for seed plants. Yet, identification of a YABBY homologue in a green alga and the recent findings of YABBY homologues in lycophytes and hornworts suggest that YABBY proteins were already present in the last common ancestor of land plants. Thus, these transcriptional factors could have been involved in "planation", which fosters our understanding of the origin of leaves. Here, we summarise the current data on functions of YABBY proteins in the vegetative and reproductive development of diverse angiosperms and gymnosperms as well as in the development of lycophytes. Furthermore, we discuss a putative role of YABBY proteins in the genesis of multicellular shoot apical meristems and in the evolution of leaves in early divergent terrestrial plants.

All type II classic MADS-box genes in the lycophyte Selaginella moellendorffii are broadly yet discretely expressed in vegetative and reproductive tissues

The MADS-box genes constitute a large transcription factor family that appear to have evolved by duplication and diversification of function. Two types of MADS-box genes are distinguished throughout eukaryotes, types I and II. Type II classic MADS-box genes, also known as MIKC-type, are key developmental regulators in flowering plants and are particularly well-studied for their role in floral organ specification. However, very little is known about the role that these genes might play outside of the flowering plants. We investigated the evolution of type II classic MADS-box genes across land plants by performing a maximum likelihood analysis with a particular focus on lycophytes. Here, we present the expression patterns of all three type II classic MADS-box homologs throughout plant development in the lycophyte Selaginella moellendorffii: SmMADS1, SmMADS3, and SmMADS6. We used scanning electron microscopy and histological analyses to define stages of sporangia development in S. moellendorffii. We performed phylogenetic analyses of this gene lineage across land plants and found that lycophyte sequences appeared before the multiple duplication events that gave rise to the major MADS-box gene lineages in seed plants. Our expression analyses by in situ hybridization show that all type II classic MADS-box genes in S. moellendorffii have broad but distinct patterns of expression in vegetative and reproductive tissues, where SmMADS1 and SmMADS6 only differ during late sporangia development. The broad expression during S. moellendorffii development suggests that MADS-box genes have undergone neofunctionalization and subfunctionalization after duplication events in seed plants.

Development and Cell Cycle Activity of the Root Apical Meristem in the Fern Ceratopteris richardii

Ferns are a representative clade in plant evolution although underestimated in the genomic era. Ceratopteris richardii is an emergent model for developmental processes in ferns, yet a complete scheme of the different growth stages is necessary. Here, we present a developmental analysis, at the tissue and cellular levels, of the first shoot-borne root of Ceratopteris. We followed early stages and emergence of the root meristem in sporelings. While assessing root growth, the first shoot-borne root ceases its elongation between the emergence of the fifth and sixth roots, suggesting Ceratopteris roots follow a determinate developmental program. We report cell division frequencies in the stem cell niche after detecting labeled nuclei in the root apical cell (RAC) and derivatives after 8 h of exposure. These results demonstrate the RAC has a continuous mitotic activity during root development. Detection of cell cycle activity in the RAC at early times suggests this cell acts as a non-quiescent organizing center. Overall, our results provide a framework to study root function and development in ferns and to better understand the evolutionary history of this organ.

Leaf dorsoventrality candidate gene CpARF4 has conserved expression pattern but divergent tasiR-ARF regulation in the water fern Ceratopteris pteridoides

PREMISE

Leaves are traditionally classified into microphylls and megaphylls, and recently have been regarded as independently originating in lycophytes, ferns, and seed plants. The developmental genetics of leaf dorsoventrality, a synapomorphy in vascular plants, has been extensively studied in flowering plants. AUXIN RESPONSE FACTOR4 (ARF4) genes are key to leaf abaxial identity in flowering plants, but whether they exist in ferns is still an open question.

METHODS

ARF4 genes from Ceratopteris pteridoides, Cyrtomium guizhouense, and Parathelypteris nipponica were mined from transcriptomes and investigated in terms of evolutionary phylogeny and sequence motifs, with a focus on the tasiR-ARF binding site. In situ hybridization was used to localize expression of CpARF4 in Ceratopteris pteridoides. 5'RNA ligase-mediated-RACE was employed to verify whether CpARF4 transcripts were sliced by tasiR-ARF.

RESULTS

ARF4 genes exist in ferns, and this lineage originates from a gene duplication in the common ancestor of ferns and seed plants. ARF4 genes are of a single copy in the ferns studied here, and they contain divergent and, at most, one tasiR-ARF binding site. CpARF4 is expressed in the abaxial but not the adaxial domain of leaf primordia at various developmental stages. Transcript slicing guided by tasiR-ARF is active in C. pteridoides, but CpARF4 probably has not been affected by it.

CONCLUSIONS

Fern ARF4 genes differ in copy number and tasiR-ARF regulation relative to flowering plants, though they can be similarly expressed in the abaxial domain of leaves, revealing a key role for ARF4 genes in the evolution of leaf dorsoventrality of vascular plants.

Patterning a Leaf by Establishing Polarities

Leaves are the major organ for photosynthesis in most land plants, and leaf structure is optimized for the maximum capture of sunlight and gas exchange. Three polarity axes, the adaxial-abaxial axis, the proximal-distal axis, and the medial-lateral axis are established during leaf development to give rise to a flattened lamina with a large area for photosynthesis and blades that are extended on petioles for maximum sunlight. Adaxial cells are elongated, tightly packed cells with many chloroplasts, and their fate is specified by HD-ZIP III and related factors. Abaxial cells are rounder and loosely packed cells and their fate is established and maintained by YABBY family and KANADI family proteins. The activities of adaxial and abaxial regulators are coordinated by ASYMMETRIC LEAVES2 and auxin. Establishment of the proximodistal axis involves the BTB/POZ domain proteins BLADE-ON-PETIOLE1 and 2, whereas homeobox genes PRESSED FLOWER and WUSCHEL-RELATED HOMEOBOX1 mediate leaf development along the mediolateral axis. This review summarizes recent advances in leaf polarity establishment with a focus on the regulatory networks involved.

What can lycophytes teach us about plant evolution and development? Modern perspectives on an ancient lineage

All Evo-Devo studies rely on representative sampling across the tree of interest to elucidate evolutionary trajectories through time. In land plants, genetic resources are well established in model species representing lineages including bryophytes (mosses, liverworts, and hornworts), monilophytes (ferns and allies), and seed plants (gymnosperms and flowering plants), but few resources are available for lycophytes (club mosses, spike mosses, and quillworts). Living lycophytes are a sister group to the euphyllophytes (the fern and seed plant clade), and have retained several ancestral morphological traits despite divergence from a common ancestor of vascular plants around 420 million years ago. This sister relationship offers a unique opportunity to study the conservation of traits such as sporophyte branching, vasculature, and indeterminacy, as well as the convergent evolution of traits such as leaves and roots which have evolved independently in each vascular plant lineage. To elucidate the evolution of vascular development and leaf formation, molecular studies using RNA Seq, quantitative reverse transcription polymerase chain reaction, in situ hybridisation and phylogenetics have revealed the diversification and expression patterns of KNOX, ARP, HD-ZIP, KANADI, and WOX gene families in lycophytes. However, the molecular basis of further trait evolution is not known. Here we describe morphological traits of living lycophytes and their extinct relatives, consider the molecular underpinnings of trait evolution and discuss future research required in lycophytes to understand the key evolutionary innovations enabling the growth and development of all vascular plants.

Fine mapping of the BnUC2 locus related to leaf up-curling and plant semi-dwarfing in Brassica napus

Background

Studies of leaf shape development and plant stature have made important contributions to the fields of plant breeding and developmental biology. The optimization of leaf morphology and plant height to improve lodging resistance and photosynthetic efficiency, increase planting density and yield, and facilitate mechanized harvesting is a desirable goal in Brassica napus.

Results

Here, we investigated a B. napus germplasm resource exhibiting up-curled leaves and a semi-dwarf stature. In progeny populations derived from NJAU5737 and Zhongshuang 11 (ZS11), we found that the up-curled leaf trait was controlled by a dominant locus, BnUC2. We then fine mapped the BnUC2 locus onto an 83.19-kb interval on chromosome A05 using single nucleotide polymorphism (SNP) and simple sequence repeat (SSR) markers. We further determined that BnUC2 was a major plant height QTL that explained approximately 70% of the phenotypic variation in two BC₅F₃ family populations derived from NJAU5737 and ZS11. This result implies that BnUC2 was also responsible for the observed semi-dwarf stature. The fine mapping interval of BnUC2 contained five genes, two of which, BnaA05g16700D (BnaA05.IAA2) and BnaA05g16720D, were revealed by comparative sequencing to be mutated in NJAU5737. This result suggests that the candidate gene mutation (BnaA05g16700D, encoding Aux/IAA2 proteins) in the conserved Degron motif GWPPV (P63S) was responsible for the BnUC2 locus. In addition, investigation of agronomic traits in a segregated population indicated that plant height, main inflorescence length, and branching height were significantly reduced by BnUC2, whereas yield was not significantly altered. The determination of the photosynthetic efficiency showed that the BnUC2 locus was beneficial to improve the photosynthetic efficiency. Our findings may provide an effective foundation for plant type breeding in B. napus.

Conclusions

Using SNP and SSR markers, a dominant locus (BnUC2) related to up-curled leaves and semi-dwarf stature in B. napus has been fine mapped onto an 83.19-kb interval of chromosome A05 containing five genes. The BnaA05.IAA2 is inferred to be the candidate gene responsible for the BnUC2 locus.

Phylogenetic analyses of key developmental genes provide insight into the complex evolution of seeds

Gene duplication plays a decisive role in organismal diversification and in the appearance of novel structures. In plants the megagametophyte covered by the integuments, which after fertilization becomes the seed constitutes a novel structure: the ovule. In Arabidopsis thaliana, genetic mechanisms regulating ovule development, including the genetics underlying ovule initiation, ovule patterning and integument development, have been identified. Among seed plants, integuments are not only a novelty in evolution, but integuments also present an enormous morphological variation. This study is focused on the evolution of gene families that play a role in the proper morphological development of the integuments, BELL1 (BEL1), KANADIs (KAN1, KAN2, and KAN4/ATS), UNICORN (UCN) and SHORT INTEGUMENTS1 (SIN1). In Arabidopsis, BEL1 establishes the initiation of integument development. KAN1 and 2 act in the proper development of the outer integument. While ABERRANT TESTA SHAPE (ATS), is involved in the correct separation of both integuments. UCN acts in planar growth of the outer integument repressing ATS. SIN1 is involved in cell elongation in the integuments. The results of our analyses show that each of these genes has a different evolutionary history and that while gymnosperms appear to have a simpler ovule morphology, they have more homologues of these candidate genes than angiosperms. In addition, we present the conserved and novel motifs for each of these genes among seed plants and their selection constraints, which may be related to functional changes and to the diversity of ovule morphologies.