MADS-domain transcription factors and the floral quartet model of flower development: linking plant development and evolution

Genomics of Flower Identity in Grapevine (Vitis vinifera L.)

The identity of the four characteristic whorls of typical eudicots, namely, sepals, petals, stamens, and carpels, is specified by the overlapping action of homeotic genes, whose single and combined contributions have been described in detail in the so-called ABCDE model. Continuous species-specific refinements and translations resulted in this model providing the basis for understanding the genetic and molecular mechanisms of flower development in model organisms, such as Arabidopsis thaliana and other main plant species. Although grapevine (Vitis vinifera L.) represents an extremely important cultivated fruit crop globally, studies related to the genetic determinism of flower development are still rare, probably because of the limited interest in sexual reproduction in a plant that is predominantly propagated asexually. Nonetheless, several studies have identified and functionally characterized some ABCDE orthologs in grapevine. The present study is intended to provide a comprehensive screenshot of the transcriptional behavior of 18 representative grapevine ABCDE genes encoding MADS-box transcription factors in a developmental kinetic process, from preanthesis to the postfertilization stage and in different flower organs, namely, the calyx, calyptra, anthers, filaments, ovary, and embryos. The transcript levels found were compared with the proposed model for Arabidopsis to evaluate their biological consistency. With a few exceptions, the results confirmed the expression pattern expected based on the Arabidopsis data.

Identification and characterization of FRUITFULL-like genes from Platanus acerifolia, a basal eudicot tree

The function of euAP1 and euFUL in AP1/FUL lineage have been well characterized in core eudicots, and they play common and distinct roles in plant development. However, the evolution and function of FUL-like genes is poorly understood in basal eudicots. In this study, we identified three FUL-like genes PlacFL1/2/3 from London plane (Platanus acerifolia). Sequence alignment and phylogenetic analysis indicated that PlacFL1/2/3 are AP1/FUL orthologs and encoded proteins containing FUL motif and paleoAP1 motif. Quantitative real-time PCR (qRT-PCR) analysis showed that PlacFL1/2/3 were expressed in both vegetative and reproductive tissues, but with distinct spatiotemporal patterns. In contrast to PlacFL1 and PlacFL3, PlacFL2 exhibited higher expression levels and broader expression regions, and that the expression of PlacFL2 gene showed a decreasing and increasing tendency in subpetiolar buds during dormancy induction and breaking, respectively. Overexpression of PlacFLs in Arabidopsis and PlacFL3 in tobacco resulted in early flowering, as well as early termination of inflorescence meristems for transgenic Arabidopsis plants. The expression changes of flowering time and flower meristem identity genes in transgenic Arabidopsis lines with different PlacFLs suggested that PlacFL2 and PlacFL3 may regulate different downstream genes to perform divergent functions. Yeast two-hybrid analysis indicated that PlacFLs interacted strongly with PlacSEP proteins, and PlacFL3 instead of PlacFL1 and PlacFL2 could also form a homodimer and interact with D-class proteins. Our results suggest that PlacFLs may play conserved functions in regulating flowering and flower development, and PlacFL2 might also be involved in dormancy regulation. The research helps us to understand the functional evolution of FUL-like genes in basal eudicots, especially in perennial woody species.

The MADS-box genes expressed in the inflorescence of Orchis italica (Orchidaceae)

The Orchidaceae family, which is one of the most species-rich flowering plant families, includes species with highly diversified and specialized flower shapes. The aim of this study was to analyze the MADS-box genes expressed in the inflorescence of Orchis italica, a wild Mediterranean orchid species. MADS-box proteins are transcription factors involved in various plant biological processes, including flower development. In the floral tissues of O. italica, 29 MADS-box genes are expressed that are classified as both class I and II. Class I MADS-box genes include one Mβ-type gene, thereby confirming the presence of this type of MADS-box genes in orchids. The class II MIKC* gene is highly expressed in the column, which is consistent with the conserved function of the MIKC* genes in gametophyte development. In addition, homologs of the SOC, SVP, ANR1, AGL12 and OsMADS32 genes are expressed. Compared with previous knowledge on class II MIKC^C genes of O. italica involved in the ABCDE model of flower development, the number of class B and D genes has been confirmed. In addition, 4 class A (AP1/FUL) transcripts, 2 class E (SEP) transcripts, 2 new class C (AG) transcripts and 1 new AGL6 transcript have been identified. Within the AP1/FUL genes, the sequence divergence, relaxation of purifying selection and expression profiles suggest a possible functional diversification within these orchid genes. The detection of only two SEP transcripts in O. italica, in contrast with the 4 genes found in other orchids, suggests that only two SEP genes could be present in the subfamily Orchidoideae. The expression pattern of the MIKC^C genes of O. italica indicates that low levels at the boundary of the domain of a given MADS-box gene can overlap with the expression of genes belonging to a different functional A-E class in the adjacent domain, thereby following a “fading borders” model.

A critical evaluation of the role of ethylene and MADS transcription factors in the network controlling fleshy fruit ripening

Contents Summary 1724 I. Introduction 1725 II. Ripening genes 1725 III. The importance of ethylene in controlling ripening 1727 IV. The importance of MADS-RIN in controlling ripening 1729 V. Interactions between components of the ripening regulatory network 1734 VI. Conclusions 1736 Acknowledgements 1738 Author contributions 1738 References 1738 SUMMARY: Understanding the regulation of fleshy fruit ripening is biologically important and provides insights and opportunities for controlling fruit quality, enhancing nutritional value for animals and humans, and improving storage and waste reduction. The ripening regulatory network involves master and downstream transcription factors (TFs) and hormones. Tomato is a model for ripening regulation, which requires ethylene and master TFs including NAC-NOR and the MADS-box protein MADS-RIN. Recent functional characterization showed that the classical RIN-MC gene fusion, previously believed to be a loss-of-function mutation, is an active TF with repressor activity. This, and other evidence, has highlighted the possibility that MADS-RIN itself is not important for ripening initiation but is required for full ripening. In this review, we discuss the diversity of components in the control network, their targets, and how they interact to control initiation and progression of ripening. Both hormones and individual TFs affect the status and activity of other network participants, which changes overall network signaling and ripening outcomes. MADS-RIN, NAC-NOR and ethylene play critical roles but there are still unanswered questions about these and other TFs. Further attention should be paid to relationships between ethylene, MADS-RIN and NACs in ripening control.

AGLF provides C-function in floral organ identity through transcriptional regulation of AGAMOUS in Medicago truncatula

Floral development is one of the model systems for investigating the mechanisms underlying organogenesis in plants. Floral organ identity is controlled by the well-known ABC model, which has been generalized to many flowering plants. Here, we report a previously uncharacterized MYB-like gene, AGAMOUS-LIKE FLOWER (AGLF), involved in flower development in the model legume Medicago truncatula Loss-of-function of AGLF results in flowers with stamens and carpel transformed into extra whorls of petals and sepals. Compared with the loss-of-function mutant of the class C gene AGAMOUS (MtAG) in M. truncatula, the defects in floral organ identity are similar between aglf and mtag, but the floral indeterminacy is enhanced in the aglf mutant. Knockout of AGLF in the mutants of the class A gene MtAP1 or the class B gene MtPI leads to an addition of a loss-of-C-function phenotype, reflecting a conventional relationship of AGLF with the canonical A and B genes. Furthermore, we demonstrate that AGLF activates MtAG in transcriptional levels in control of floral organ identity. These data shed light on the conserved and diverged molecular mechanisms that control flower development and morphology among plant species.

An AGAMOUS MADS-box protein, SlMBP3, regulates the speed of placenta liquefaction and controls seed formation in tomato

AGAMOUS (AG) MADS-box transcription factors have been shown to play crucial roles in floral organ and fruit development in angiosperms. Here, we isolated a tomato (Solanum lycopersicum) AG MADS-box gene SlMBP3 and found that it is preferentially expressed in flowers and during early fruit developmental stages in the wild-type (WT), and in the Nr (never ripe) and rin (ripening inhibitor) mutants. Its transcripts are notably accumulated in the pistils; transcripts abundance decrease during seed and placental development, increasing again during flower development. SlMBP3-RNAi tomato plants displayed fleshy placenta without locular gel and extremely malformed seeds with no seed coat, while SlMBP3-overexpressing plants exhibited advanced liquefaction of the placenta and larger seeds. Enzymatic activities related to cell wall modification, and the contents of cell wall components and pigments were dramatically altered in the placentas of SlMBP3-RNAi compared with the WT. Alterations in these physiological features were also observed in the placentas of SlMBP3-overexpressing plants. The lignin content of mature seeds in SlMBP3-RNAi lines was markedly lower than that in the WT. RNA-seq and qRT-PCR analyses revealed that genes involved in seed development and the biosynthesis of enzymes related to cell wall modification, namely gibberellin, indole-3-acetic acid, and abscisic acid were down-regulated in the SlMBP3-RNAi lines. Taking together, our results demonstrate that SlMBP3 is involved in the regulation of placenta and seed development in tomato.

Genome-wide analysis of BES1 genes in Gossypium revealed their evolutionary conserved roles in brassinosteroid signaling

Brassinosteroids (BRs), which are essential phytohormones for plant growth and development, are important for cotton fiber development. Additionally, BES1 transcription factors are critical for BR signal transduction. However, cotton BES1 family genes have not been comprehensively characterized. In this study, we identified 11 BES1 genes in G. arboreum, 11 in G. raimondii, 16 in G. barbadense, and 22 in G. hirsutum. The BES1 sequences were significantly conserved in the Arabidopsis thaliana, rice, and upland cotton genomes. A total of 94 BES1 genes from 10 different plant species were divided into three clades according to the neighbor-joining and minimum-evolution methods. Moreover, the exon/intron patterns and motif distributions were highly conserved among the A. thaliana and cotton BES1 genes. The collinearity among the orthologs from the At and Dt subgenomes was estimated. Segmental duplications in the At and Dt subgenomes were primarily responsible for the expansion of the cotton BES1 gene family. Of the GhBES1 genes, GhBES1.4_At/Dt exhibited BL-induced expression and was predominantly expressed in fibers. Furthermore, Col-0/mGhBES1.4_At plants produced curled leaves with long and bent petioles. These transgenic plants also exhibited decreased hypocotyl sensitivity to brassinazole and constitutive BR induced/repressed gene expression patterns. The constitutive BR responses of the plants overexpressing mGhBES1.4_At were similar to those of the bes1-D mutant.

Diversification of the Homeotic AP3 Clade MADS-Box Genes in Asteraceae Species Chrysanthemum morifolium L. and Helianthus annuus L

The structure and phylogeny of MADS-box genes HAM91 of sunflower (Helianthus annuus) and CDM115 of chrysanthemum (Chrysanthemum morifolium) were characterized. It is shown that these genes encode MADS-domain transcription factors, which are orthologs of TM6 (Solanum lycopersicum) and APETALA3 (Arabidopsis thaliana), respectively. We obtained two types of transgenic tobacco plants (Nicotiana tabacum) with constitutive expression of HAM91 and CDM115 genes. Both types of plants flowered later than the control plants and formed more flowers and seed pods. The weight of seeds of 35S::CDM115 plants was significantly lower than in the control and 35S::HAM91 plants, which may indicate to a change in the identity of ovules in 35S::CDM115.

Ectopic Expression of the Homeotic MADS-Box Gene HAM31 (Helianthus annuus L.) in Transgenic Plants Nicotiana tabacum L. Affects the Gynoecium Identity

The structure of the MADS-box gene HAM31 of the sunflower (Helianthus annuus) was characterized. It is shown that the product of this gene is an ortholog of the B-class MADS transcription factor PISTILLATA (Arabidopsis thaliana). Two types of transgenic tobacco plants (Nicotiana tabacum) with the constitutive expression of the HAM31 gene in the sense and antisense orientation were obtained. The 35S::HAM31s plants formed flowers with an altered gynoecium identity, whereas 35S::HAM31as plants did not differ from the control.

LEAFY maintains apical stem cell activity during shoot development in the fern Ceratopteris richardii

During land plant evolution, determinate spore-bearing axes (retained in extant bryophytes such as mosses) were progressively transformed into indeterminate branching shoots with specialized reproductive axes that form flowers. The LEAFY transcription factor, which is required for the first zygotic cell division in mosses and primarily for floral meristem identity in flowering plants, may have facilitated developmental innovations during these transitions. Mapping the LEAFY evolutionary trajectory has been challenging, however, because there is no functional overlap between mosses and flowering plants, and no functional data from intervening lineages. Here, we report a transgenic analysis in the fern Ceratopteris richardii that reveals a role for LEAFY in maintaining cell divisions in the apical stem cells of both haploid and diploid phases of the lifecycle. These results support an evolutionary trajectory in which an ancestral LEAFY module that promotes cell proliferation was progressively co-opted, adapted and specialized as novel shoot developmental contexts emerged.

The first plants colonized land around 500 million years ago. These plants had simple shoots with no branches, similar to the mosses that live today. Later on, some plants evolved more complex structures including branched shoots and flowers (collectively known as the “flowering plants”). Ferns are a group of plants that evolved midway between the mosses and flowering plants and have branched shoots but no flowers.

The gradual transition from simple to more complex plant structures required changes to the way in which cells divide and grow within plant shoots. Whereas animals produce new cells throughout their body, most plant cells divide in areas known as meristems. All plants grow from embryos, which contain meristems that will form the roots and shoots of the mature plant. A gene called LEAFY is required for cells in moss embryos to divide. However, in flowering plants LEAFY does not carry out this role, instead it is only required to make the meristems that produce flowers.

How did LEAFY transition from a general role in embryos to a more specialized role in making flowers? To address this question, Plackett, Conway et al. studied the two LEAFY genes in a fern called Ceratopteris richardii. The experiments showed that at least one of these LEAFY genes was active in the meristems of fern shoots throughout the lifespan of the plant. The shoots of ferns with less active LEAFY genes could not form the leaves seen in normal C. richardii plants. This suggests that as land plants evolved, the role of LEAFY changed from forming embryos to forming complex shoot structures.

Most of our major crops are flowering plants. By understanding how the role of LEAFY has changed over the evolution of land plants, it might be possible to manipulate LEAFY genes in crop plants to alter shoot structures to better suit specific environments.

Evolution and genetic control of the floral ground plan

Contents Summary 70 I. Introduction 70 II. What is the floral ground plan? 71 III. Diversity and evolution of the floral ground plan 72 IV. Genetic mechanisms 77 V. What's next? 82 Acknowledgements 83 References 83 SUMMARY: The floral ground plan is a map of where and when floral organ primordia arise. New results combining the defined phylogeny of flowering plants with extensive character mapping have predicted that the angiosperm ancestor had whorls rather than spirals of floral organs in large numbers, and was bisexual. More confidently, the monocot ancestor likely had three organs in each whorl, whereas the rosid and asterid ancestor (Pentapetalae) had five, with the perianth now divided into sepals and petals. Genetic mechanisms underlying the establishment of the floral ground plan are being deduced using model species, the rosid Arabidopsis, the asterid Antirrhinum, and in grasses such as rice. In this review, evolutionary and genetic conclusions are drawn together, especially considering how known genes may control individual processes in the development and evolution of ground plans. These components include organ phyllotaxis, boundary formation, organ identity, merism (the number or organs per whorl), variation in the form of primordia, organ fusion, intercalary growth, floral symmetry, determinacy and, finally, cases where the distinction between flowers and inflorescences is blurred. It seems likely that new pathways of ground plan evolution, and new signalling mechanisms, will soon be uncovered by integrating morphological and genetic approaches.

A Dynamic Co-expression Map of Early Inflorescence Development in Setaria viridis Provides a Resource for Gene Discovery and Comparative Genomics

The morphological and functional diversity of plant form is governed by dynamic gene regulatory networks. In cereal crops, grain and/or pollen-bearing inflorescences exhibit vast architectural diversity and developmental complexity, yet the underlying genetic framework is only partly known. Setaria viridis is a small, rapidly growing grass species in the subfamily Panicoideae, a group that includes economically important cereal crops such as maize and sorghum. The S. viridis inflorescence displays complex branching patterns, but its early development is similar to that of other panicoid grasses, and thus is an ideal model for studying inflorescence architecture. Here we report a detailed transcriptional resource that captures dynamic transitions across six sequential stages of S. viridis inflorescence development, from reproductive onset to floral organ differentiation. Co-expression analyses identified stage-specific signatures of development, which include homologs of previously known developmental genes from maize and rice, suites of transcription factors and gene family members, and genes of unknown function. This spatiotemporal co-expression map and associated analyses provide a foundation for gene discovery in S. viridis inflorescence development, and a comparative model for exploring related architectural features in agronomically important cereals.

Functional Specialization of Duplicated AGAMOUS Homologs in Regulating Floral Organ Development of Medicago truncatula

The C function gene AGAMOUS (AG) encodes for a MADS-box transcription factor required for floral organ identity and floral meristem (FM) determinacy in angiosperms. Unlike Arabidopsis, most legume plants possess two AG homologs arose by an ancient genome duplication event. Recently, two euAGAMOUS genes, MtAGa and MtAGb, were characterized and shown to fulfill the C function activity in the model legume Medicago truncatula. Here, we reported the isolation and characterization of a new mtaga allele by screening the Medicago Tnt1 insertion mutant collection. We found that MtAGa was not only required for controlling the stamen and carpel identity but also affected pod and seed development. Genetic analysis indicated that MtAGa and MtAGb redundantly control Medicago floral organ identity, but have minimal distinct functions in regulating stamen and carpel development in a dose-dependent manner. Interestingly, the stamens and carpels are mostly converted to numerous vexillum-like petals in the double mutant of mtaga mtagb, which is distinguished from Arabidopsis ag. Further qRT-PCR analysis in different mtag mutants revealed that MtAGa and MtAGb can repress the expression of putative A and B function genes as well as MtWUS, but promote putative D function genes expression in M. truncatula. In addition, we found that the abnormal dorsal petal phenotype observed in the mtaga mtagb double mutant is associated with the upregulation of CYCLOIDEA (CYC)-like TCP genes. Taken together, our data suggest that the redundant MtAGa and MtAGb genes of M. truncatula employ a conserved mechanism of action similar to Arabidopsis in determining floral organ identity and FM determinacy but may have evolved distinct function in regulating floral symmetry by coordinating with specific floral dorsoventral identity factors.

Pioneer Factors in Animals and Plants-Colonizing Chromatin for Gene Regulation

Unlike most transcription factors (TF), pioneer TFs have a specialized role in binding closed regions of chromatin and initiating the subsequent opening of these regions. Thus, pioneer TFs are key factors in gene regulation with critical roles in developmental transitions, including organ biogenesis, tissue development, and cellular differentiation. These developmental events involve some major reprogramming of gene expression patterns, specifically the opening and closing of distinct chromatin regions. Here, we discuss how pioneer TFs are identified using biochemical and genome-wide techniques. What is known about pioneer TFs from animals and plants is reviewed, with a focus on the strategies used by pioneer factors in different organisms. Finally, the different molecular mechanisms pioneer factors used are discussed, highlighting the roles that tertiary and quaternary structures play in nucleosome-compatible DNA-binding.

Transcriptomic analysis identifies the key genes involved in stamen petaloid in lotus (Nelumbo nucifera)

Background

Flower morphology, a phenomenon regulated by a complex network, is one of the vital ornamental features in Nelumbo nucifera. Stamen petaloid is very prevalent in lotus flowers. However, the mechanism underlying this phenomenon is still obscure.

Results

Here, the comparative transcriptomic analysis was performed among petal, stamen petaloid and stamen through RNA-seq. Using pairwise comparison analysis, a large number of genes involved in hormonal signal transduction pathways and transcription factors, especially the MADS-box genes, were identified as candidate genes for stamen petaloid in lotus.

Conclusions

Taken together, these results provide an insight into the molecular networks underlying lotus floral organ development and stamen petaloid.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-4950-0) contains supplementary material, which is available to authorized users.

The Evolution of Diverse Floral Morphologies

The angiosperm flower develops through a modular programme which, although ancient and conserved, provides the flexibility that has allowed an almost infinite variety of floral forms to emerge. In this review, we explore the evolution of floral diversity, focusing on our recent understanding of the mechanistic basis of evolutionary change. We discuss the various ways in which flower size and floral organ size can be modified, the means by which flower shape and symmetry can change, and the ways in which floral organ position can be varied. We conclude that many challenges remain before we fully understand the ecological and molecular processes that facilitate the diversification of flower structure.

Differential methylation and expression of HUA1 ortholog in three sex types of papaya

Papaya is trioecious and an excellent system for studying sex determination and differentiation in plants. An ortholog of HUA1, CpHUA1, a gene controlling stamen and carpel development in Arabidopsis, was cloned and characterized in papaya. CpHUA1 consists of 12 exons with full genomic length of 19,313 bp in male AU9 and 19,312 bp in hermaphrodite SunUp, whereas the Arabidopsis HUA1 consists of 12 exons with full genomic length of 4300 bp. All the 324 SNPs between male and hermaphrodite varieties are in the 11th intron, which spans 8.5 kb. Quantitative RT-PCR revealed that CpHUA1 expression is highly elevated in carpels, suggesting that CpHUA1 may be involved in sex differentiation gene network. Southern blot analysis revealed a distinct restriction pattern in male AU9 compared to hermaphrodite Kapoho and SunUp, despite high DNA sequence identity and sharing of all but two EcoR I restriction sites in genomic CpHUA1 sequences of AU9 and SunUp. The methylation of cytosine at one restriction site in male but not in other two sex types may result in distinct restriction pattern of EcoR I in southern blot result. Bisulfite sequencing showed differential methylation of CpHUA1 among sex types, particularly the enrichment of sex-specific methylation in 9th and 11th intron. The methylation difference in cold stress induced male to hermaphrodite mutant mostly observed in the CHH context of CpHUA1, but no methylation difference detected in CHH context in other sex types, which may indicate the role of methylation in CHH context of CpHUA1 in temperature-related stress response and sex reversal.

Array of MADS-Box Genes: Facilitator for Rapid Adaptation?

In a world of global warming, the question emerges whether all plants have suitable mechanisms to keep pace with the rapidly changing environment. Most previous studies have focused on either the ability of plants to rapidly acclimatize via physiological and developmental plasticity, or long-term adaptation over thousands of years. However, we wonder whether plants can also adapt to changes in the environment within only a few generations. We hypothesize that rapidly evolving clusters of tandemly duplicated developmental control genes represent a source for fast adaptation. Specifically, we propose that a tandem cluster of FLC-like MADS-box genes involved in the transition to flowering in Arabidopsis functions as a facilitator for rapid adaptation to changes in ambient temperature.

The floral homeotic protein SEPALLATA3 recognizes target DNA sequences by shape readout involving a conserved arginine residue in the MADS-domain

SEPALLATA3 of Arabidopsis thaliana is a MADS-domain transcription factor (TF) and a key regulator of flower development. MADS-domain proteins bind to sequences termed 'CArG-boxes' [consensus 5'-CC(A/T)₆ GG-3']. Because only a fraction of the CArG-boxes in the Arabidopsis genome are bound by SEPALLATA3, more elaborate principles have to be discovered to better understand which features turn CArG-boxes into genuine recognition sites. Here, we investigate to what extent the shape of the DNA is involved in a 'shape readout' that contributes to the binding of SEPALLATA3. We determined in vitro binding affinities of SEPALLATA3 to DNA probes that all contain the CArG-box motif, but differ in their predicted DNA shape. We found that binding affinity correlates well with a narrow minor groove of the DNA. Substitution of canonical bases with non-standard bases supports the hypothesis of minor groove shape readout by SEPALLATA3. Analysis of mutant SEPALLATA3 proteins further revealed that a highly conserved arginine residue, which is expected to contact the DNA minor groove, contributes significantly to the shape readout. Our studies show that the specific recognition of cis-regulatory elements by a plant MADS-domain TF, and by inference probably also of other TFs of this type, heavily depends on shape readout mechanisms.

Changing MADS-Box Transcription Factor Protein-Protein Interactions as a Mechanism for Generating Floral Morphological Diversity

Flowers display fantastic morphological diversity. Despite extreme variability in form, floral organ identity is specified by a core set of deeply conserved proteins-the floral MADS-box transcription factors. This indicates that while core gene function has been maintained, MADS-box transcription factors have evolved to regulate different downstream genes. Thus, the evolution of gene regulation downstream of the MADS-box transcription factors is likely central to the evolution of floral form. Gene regulation is determined by the combination of transcriptional regulators present at a particular cis-regulatory element at a particular time. Therefore, the interactions between transcription factors can be of profound importance in determining patterns of gene regulation. Here, after a short primer on flowers and floral morphology, I discuss the centrality of protein-protein interactions to MADS-box transcription factor function, and review the evidence that the evolution of MADS-box protein-protein interactions is a key driver in the evolution of gene regulation downstream of the MADS-box genes.

Recent Trends in Plant Protein Complex Analysis in a Developmental Context

Because virtually all proteins interact with other proteins, studying protein-protein interactions (PPIs) is fundamental in understanding protein function. This is especially true when studying specific developmental processes, in which proteins often make developmental stage- or tissue specific interactions. However, studying these specific PPIs in planta can be challenging. One of the most widely adopted methods to study PPIs in planta is affinity purification coupled to mass spectrometry (AP/MS). Recent developments in the field of mass spectrometry have boosted applications of AP/MS in a developmental context. This review covers two main advancements in the field of affinity purification to study plant developmental processes: increasing the developmental resolution of the harvested tissues and moving from affinity purification to affinity enrichment. Furthermore, we discuss some new affinity purification approaches that have recently emerged and could have a profound impact on the future of protein interactome analysis in plants.

Identification of genes regulating ovary differentiation after pollination in hazel by comparative transcriptome analysis

BACKGROUND

Hazel (Corylus spp.) exhibits ovary differentiation and development that is initiated from the ovary primordium after pollination, conferring the plant with a unique delayed fertilization. Failure of development of the ovary and ovule after pollination can lead to ovary abortion and blank fruit formation, respectively, with consequent yield loss. However, the genes involved in ovary and ovule differentiation and development are largely unknown.

RESULTS

In unpollinated pistillate inflorescences (stage F), the stigma shows an extension growth pattern. After pollination, a rudimentary ovary begins to form (stage S), followed by ovule differentiation (stage T) and growth (stage FO). Total RNA was obtained from pistillate inflorescences or young ovaries at stage F, S, T and FO, and sequencing was carried out on a HiSeq 4000 system. De novo assembly of sequencing data yielded 62.58 Gb of nucleotides and 90,726 unigenes; 5524, 3468, and 8714 differentially expressed transcripts were identified in F-vs-S, S-vs-T, and T-vs-FO paired comparisons, respectively. An analysis of F-vs-S, S-vs-T, and T-vs-FO paired comparisons based on annotations in the Kyoto Encyclopedia of Genes and Genomes revealed six pathways that were significantly enriched during ovary differentiation, including ko04075 (Plant hormone signal transduction). Auxin level increased after pollination, and an immunohistochemical analysis indicated that auxin was enriched at the growth center of pistillate inflorescences and young ovaries. These results indicate that genes related to auxin biosynthesis, transport, signaling, the floral quartet model, and flower development may regulate ovary and ovule differentiation and development in hazel.

CONCLUSIONS

Our findings provide insight into the molecular mechanisms of ovary differentiation and development after pollination in this economically valuable plant.

Genome-wide analysis of GRAS transcription factor gene family in Gossypium hirsutum L

BACKGROUND

Cotton is a major fiber and oil crop worldwide. Cotton production, however, is often threatened by abiotic environmental stresses. GRAS family proteins are among the most abundant transcription factors in plants and play important roles in regulating root and shoot development, which can improve plant resistance to abiotic stresses. However, few studies on the GRAS family have been conducted in cotton. Recently, the G. hirsutum genome sequences have been released, which provide us an opportunity to analyze the GRAS family in G. hirsutum.

RESULTS

In total, 150 GRAS proteins from G. hirsutum were identified. Phylogenetic analysis showed that these GRAS protins could be classified into 14 subfamilies including SCR, DLT, OS19, LAS, SCL4/7, OS4, OS43, DELLA, PAT1, SHR, HAM, SCL3, LISCL and G_GRAS. The gene structure and motif distribution analysis of the GRAS members in G. hirsutum revealed that many genes of the SHR subfamily have more than one intron, which maybe a kind of form in the evolution of plant by obtaining or losing introns. Chromosomal location and duplication analysis revealed that segment and tandem duplication maybe the reasons of the expension of the GRAS family in cotton. Gene expression analysis confirmed the expression level of GRAS members were up-regulated under different abiotic stresses, suggesting that their possible roles in response to stresses. What's more, higher expression level in root, stem, leaf and pistil also indicated these genes may have effect on the development and breeding of cotton.

CONCLUSIONS

This study firstly shows the comprehensive analysis of GRAS members in G. hirsutum. Our results provide important information about GRAS family and a framework for stress-resistant breeding in G. hirsutum.

Quantitative Changes in the Transcription of Phytohormone-Related Genes: Some Transcription Factors Are Major Causes of the Wheat Mutant dmc Not Tillering

Tiller number is an important agronomic trait for grain yield of wheat (Triticum aestivum L.). A dwarf-monoculm wheat mutant (dmc) was obtained from cultivar Guomai 301 (wild type, WT). Here, we explored the molecular basis for the restrained tiller development of the mutant dmc. Two bulked samples of the mutant dmc (T1, T2 and T3) and WT (T4, T5 and T6) with three biological replicates were comparatively analyzed at the transcriptional level by bulked RNA sequencing (RNA-Seq). In total, 68.8 Gb data and 463 million reads were generated, 80% of which were mapped to the wheat reference genome of Chinese Spring. A total of 4904 differentially expressed genes (DEGs) were identified between the mutant dmc and WT. DEGs and their related major biological functions were characterized based on GO (Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) categories. These results were confirmed by quantitatively analyzing the expression profiles of twelve selected DEGs via real-time qRT-PCR. The down-regulated gene expressions related to phytohormone syntheses of auxin, zeatin, cytokinin and some transcription factor (TF) families of TALE, and WOX might be the major causes of the mutant dmc, not tillering. Our work provides a foundation for subsequent tiller development research in the future.

Interactions between transcription factors and chromatin regulators in the control of flower development

Chromatin modifiers and remodelers are involved in generating dynamic changes at the chromatin, which allow differential and specific readouts of the genome. While genetic evidence indicates that several chromatin factors play a key role in controlling basic developmental programs for inflorescence and flower morphogenesis, it remained unknown until recently how they exert their specificity toward gene expression, both temporally and spatially. An emerging topic is the recruitment or eviction of chromatin factors through the activity of sequence-specific DNA-binding domains, present in the chromatin factors themselves or in partnering transcription factors. Here we summarize recent progress that has been made in this regard in the model plant Arabidopsis thaliana. We further outline the different possible modes through which chromatin complexes specifically target genes involved in flower development.

A conserved leucine zipper-like motif accounts for strong tetramerization capabilities of SEPALLATA-like MADS-domain transcription factors

The development of angiosperm flowers is regulated by homeotic MIKC-type MADS-domain transcription factors that activate or repress target genes via the formation of DNA-bound, organ-specific tetrameric complexes. The protein-protein interaction (PPI) capabilities differ considerably between different MIKC-type proteins. In Arabidopsis thaliana the floral homeotic protein SEPALLATA3 (SEP3) acts as a hub that incorporates numerous other MADS-domain proteins into tetrameric complexes that would otherwise not form. However, the molecular mechanisms that underlie these promiscuous interactions remain largely unknown. In this study, we created a collection of amino acid substitution mutants of SEP3 to quantify the contribution of individual residues on protein tetramerization during DNA-binding, employing methods of molecular biophysics. We show that leucine residues at certain key positions form a leucine-zipper structure that is essential for tetramerization of SEP3, whereas the introduction of physicochemically very similar residues at respective sites impedes the formation of DNA-bound tetramers. Comprehensive molecular evolutionary analyses of MADS-domain proteins from a diverse set of flowering plants revealed exceedingly high conservation of the identified leucine residues within SEP3-subfamily proteins throughout angiosperm evolution. In contrast, MADS-domain proteins that are unable to tetramerize among themselves exhibit preferences for other amino acids at homologous sites. Our findings indicate that the subfamily-specific conservation of amino acid residues at just a few key positions accounts for subfamily-specific interaction capabilities of MADS-domain transcription factors and this has shaped the present-day structure of the PPI network controlling flower development.

Identification and Characterization of the MADS-Box Genes and Their Contribution to Flower Organ in Carnation (Dianthus caryophyllus L.)

Dianthus is a large genus containing many species with high ornamental economic value. Extensive breeding strategies permitted an exploration of an improvement in the quality of cultivated carnation, particularly in flowers. However, little is known on the molecular mechanisms of flower development in carnation. Here, we report the identification and description of MADS-box genes in carnation (DcaMADS) with a focus on those involved in flower development and organ identity determination. In this study, 39 MADS-box genes were identified from the carnation genome and transcriptome by the phylogenetic analysis. These genes were categorized into four subgroups (30 MIKC^c, two MIKC*, two Mα, and five Mγ). The MADS-box domain, gene structure, and conserved motif compositions of the carnation MADS genes were analysed. Meanwhile, the expression of DcaMADS genes were significantly different in stems, leaves, and flower buds. Further studies were carried out for exploring the expression of DcaMADS genes in individual flower organs, and some crucial DcaMADS genes correlated with their putative function were validated. Finally, a new expression pattern of DcaMADS genes in flower organs of carnation was provided: sepal (three class E genes and two class A genes), petal (two class B genes, two class E genes, and one SHORT VEGETATIVE PHASE (SVP)), stamen (two class B genes, two class E genes, and two class C), styles (two class E genes and two class C), and ovary (two class E genes, two class C, one AGAMOUS-LIKE 6 (AGL6), one SEEDSTICK (STK), one B sister, one SVP, and one Mα). This result proposes a model in floral organ identity of carnation and it may be helpful to further explore the molecular mechanism of flower organ identity in carnation.

MADS-box genes and crop domestication: the jack of all traits

MADS-box genes are key regulators of virtually every aspect of plant reproductive development. They play especially prominent roles in flowering time control, inflorescence architecture, floral organ identity determination, and seed development. The developmental and evolutionary importance of MADS-box genes is widely acknowledged. However, their role during flowering plant domestication is less well recognized. Here, we provide an overview illustrating that MADS-box genes have been important targets of selection during crop domestication and improvement. Numerous examples from a diversity of crop plants show that various developmental processes have been shaped by allelic variations in MADS-box genes. We propose that new genomic and genome editing resources provide an excellent starting point for further harnessing the potential of MADS-box genes to improve a variety of reproductive traits in crops. We also suggest that the biophysics of MADS-domain protein-protein and protein-DNA interactions, which is becoming increasingly well characterized, makes them especially suited to exploit coding sequence variations for targeted breeding approaches.

Molecular cloning, characterization and expression analysis of MADS-box genes associated with reproductive development in Momordica dioica Roxb

The repertoire and functions of MADS-box family transcription factors (TFs) largely remains unexplored with respect to floral organogenesis of Momordica dioica Roxb. Degenerative PCR followed by rapid amplification of cDNA ends was employed in the present study to clone and characterize 17 MADS-box genes (designated as MdMADS01 to MdMADS17) from the floral buds of M. dioica. The cloned genes were clustered into three subgroups (11 MIKC^C, 4 MIKC* and 2 Mα) based on phylogenetic relationships with the MADS-box genes from Cucumis sativus, Cucumis melo and Arabidopsis thaliana. Southern hybridization showed that all the isolated genes were represented by single copy locus in the M. dioica genome. Gene structure analysis revealed 1-8 exons in MdMADS-box genes with the number of exons in MIKC greatly exceeding from that in M-type genes. Motif elicitation of the MdMADS-box genes indicated the presence of additional domains with MIKC type, suggesting that they had more complex structures. Expression analysis of MdMADS genes in six M. dioica transcriptome suggested that, 11 MIKC^C-type genes are associated with floral homeotic functions, 4 MIKC*-type genes (MdMADS12 to MdMADS15) controlled the growth of male gametophyte, while the two M-type genes (MdMADS16 and MdMADS17) played significant role in female gametogenesis and seed development. Overall, these are the first set of MADS-box genes from M. dioica exhibiting a differential expression pattern during floral development. The results from this study will provide valuable information for further functional studies of candidate MADS-box genes in the sexual dimorphism of this economically important dioecious cucurbit.

Glass promotes the differentiation of neuronal and non-neuronal cell types in the Drosophila eye

Transcriptional regulators can specify different cell types from a pool of equivalent progenitors by activating distinct developmental programs. The Glass transcription factor is expressed in all progenitors in the developing Drosophila eye, and is maintained in both neuronal and non-neuronal cell types. Glass is required for neuronal progenitors to differentiate as photoreceptors, but its role in non-neuronal cone and pigment cells is unknown. To determine whether Glass activity is limited to neuronal lineages, we compared the effects of misexpressing it in neuroblasts of the larval brain and in epithelial cells of the wing disc. Glass activated overlapping but distinct sets of genes in these neuronal and non-neuronal contexts, including markers of photoreceptors, cone cells and pigment cells. Coexpression of other transcription factors such as Pax2, Eyes absent, Lozenge and Escargot enabled Glass to induce additional genes characteristic of the non-neuronal cell types. Cell type-specific glass mutations generated in cone or pigment cells using somatic CRISPR revealed autonomous developmental defects, and expressing Glass specifically in these cells partially rescued glass mutant phenotypes. These results indicate that Glass is a determinant of organ identity that acts in both neuronal and non-neuronal cells to promote their differentiation into functional components of the eye.

Laser Capture Micro-Dissection Coupled to RNA Sequencing: A Powerful Approach Applied to the Model Legume Medicago truncatula in Interaction with Sinorhizobium meliloti

Understanding the development of multicellular organisms requires the identification of regulators, notably transcription factors, and specific transcript populations associated with tissue differentiation. Laser capture microdissection (LCM) is one of the techniques that enable the analysis of distinct tissues or cells within an organ. Coupling this technique with RNA sequencing (RNAseq) makes it extremely powerful to obtain a genome-wide and dynamic view of gene expression. Moreover, RNA sequencing allows two or potentially more interacting organisms to be analyzed simultaneously. In this chapter, a LCM-RNAseq protocol optimized for root and symbiotic root nodule analysis is presented, using the model legume Medicago truncatula (in interaction with Sinorhizobium meliloti in the nodule samples). This includes the description of procedures for plant material fixation, embedding, and micro-dissection; it is followed by a presentation of techniques for RNA extraction and amplification, adapted for the simultaneous analysis of plant and bacterial cells in interaction or, more generally, polyadenylated and non-polyadenylated RNAs. Finally, step-by-step statistical analyses of RNAseq data are described. Those are critical for quality assessment of the whole procedure and for the identification of differentially expressed genes.

I Want to (Bud) Break Free: The Potential Role of DAM and SVP-Like Genes in Regulating Dormancy Cycle in Temperate Fruit Trees

Bud dormancy is an adaptive process that allows trees to survive the hard environmental conditions that they experience during the winter of temperate climates. Dormancy is characterized by the reduction in meristematic activity and the absence of visible growth. A prolonged exposure to cold temperatures is required to allow the bud resuming growth in response to warm temperatures. In fruit tree species, the dormancy cycle is believed to be regulated by a group of genes encoding MADS-box transcription factors. These genes are called DORMANCY-ASSOCIATED MADS-BOX (DAM) and are phylogenetically related to the Arabidopsis thaliana floral regulators SHORT VEGETATIVE PHASE (SVP) and AGAMOUS-LIKE 24. The interest in DAM and other orthologs of SVP (SVP-like) genes has notably increased due to the publication of several reports suggesting their role in the control of bud dormancy in numerous fruit species, including apple, pear, peach, Japanese apricot, and kiwifruit among others. In this review, we briefly describe the physiological bases of the dormancy cycle and how it is genetically regulated, with a particular emphasis on DAM and SVP-like genes. We also provide a detailed report of the most recent advances about the transcriptional regulation of these genes by seasonal cues, epigenetics and plant hormones. From this information, we propose a tentative classification of DAM and SVP-like genes based on their seasonal pattern of expression. Furthermore, we discuss the potential biological role of DAM and SVP-like genes in bud dormancy in antagonizing the function of FLOWERING LOCUS T-like genes. Finally, we draw a global picture of the possible role of DAM and SVP-like genes in the bud dormancy cycle and propose a model that integrates these genes in a molecular network of dormancy cycle regulation in temperate fruit trees.

Utilization of transcription factors for controlling floral morphogenesis in horticultural plants

Transcription factors play important roles not only in the development of floral organs but also in the formation of floral characteristics in various plant species. Therefore, transcription factors are reasonable targets for modifying these floral traits and generating new flower cultivars. However, it has been difficult to control the functions of transcription factors because most plant genes, including those encoding transcription factors, exhibit redundancy. In particular, it has been difficult to understand the functions of these redundant genes by genetic analysis. Thus, a breakthrough silencing method called chimeric repressor gene silencing technology (CRES-T) was developed specifically for plant transcription factors. This method transforms transcriptional activators into dominant repressors, and the artificial chimeric repressors suppress the function of transcription factors regardless of their redundancy. Among these chimeric repressors, some were found to be inappropriate for expression throughout the plant body because they resulted in deformities. For these chimeric repressors, utilization of floral organ-specific promoters overcomes this problem by avoiding expression throughout the plant body. In contrast, attachment of viral activation domain VP16 to transcriptional repressors effectively alters into transcriptional activators. This review presents the importance of transcription factors for characterizing floral traits, describes techniques for controlling the functions of transcription factors.

Dissecting functions of SEPALLATA-like MADS box genes in patterning of the pseudanthial inflorescence of Gerbera hybrida

The pseudanthial inflorescences of the sunflower family, Asteraceae, mimic a solitary flower but are composed of multiple flowers. Our studies in Gerbera hybrida indicate functional diversification for SEPALLATA (SEP)-like MADS box genes that often function redundantly in other core eudicots. We conducted phylogenetic and expression analysis for eight SEP-like GERBERA REGULATOR OF CAPITULUM DEVELOPMENT (GRCD) genes, including previously unstudied gene family members. Transgenic gerbera plants were used to infer gene functions. Adding to the previously identified stamen and carpel functions for GRCD1 and GRCD2, two partially redundant genes, GRCD4 and GRCD5, were found to be indispensable for petal development. Stepwise conversion of floral organs into leaves in the most severe RNA interference lines suggest redundant and additive GRCD activities in organ identity regulation. We show conserved and redundant functions for several GRCD genes in regulation of flower meristem maintenance, while functional diversification for three SEP1/2/4 clade genes in regulation of inflorescence meristem patterning was observed. GRCD genes show both specialized and pleiotropic functions contributing to organ differentiation and flower meristem fate, and uniquely, to patterning of the inflorescence meristem. Altogether, we provide an example of how plant reproductive evolution has used conserved genetic modules for regulating the elaborate inflorescence architecture in Asteraceae.

Genetics of flower development in Ranunculales - a new, basal eudicot model order for studying flower evolution

Contents 361 I. 361 II. 362 III. 363 IV. 364 V. 364 Acknowledgements 365 References 365 SUMMARY: Ranunculales, the sister group to all other eudicots, encompasses species with a remarkable floral diversity, which are currently emerging as new model organisms to address questions relating to the genetic architecture of flower morphology and its evolution. These questions concern either traits only found in members of the Ranunculales or traits that have convergently evolved in other large clades of flowering plants. We present recent results obtained on floral organ identity and number, symmetry evolution and spur formation in Ranunculales species. We discuss benefits and future prospects of evo-devo studies in Ranunculales, which can provide the opportunity to decipher the genetic architecture of novel floral traits and also to appraise the degree of conservation of genetic mechanisms involved in homoplasious traits.

Role of floral organ identity genes in the development of unisexual flowers of Quercus suber L

Monoecious species provide an excellent system to study the specific determinants that underlie male and female flower development. Quercus suber is a monoecious species with unisexual flowers at inception. Despite the overall importance of this and other tree species with a similar reproductive habit, little is known regarding the mechanisms involved in the development of their male and female flowers. Here, we have characterised members of the ABCDE MADS-box gene family of Q. suber. The temporal expression of these genes was found to be sex-biased. The B-class genes, in particular, are predominantly, or exclusively (in the case of QsPISTILLATA), expressed in the male flowers. Functional analysis in Arabidopsis suggests that the B-class genes have their function conserved. The identification of sex-biased gene expression plus the identification of unusual protein-protein interactions suggest that the floral organ identity of Q. suber may be under control of specific changes in the dynamics of the ABCDE model. This study constitutes a major step towards the characterisation of the mechanisms involved in reproductive organ identity in a monoecious tree with a potential contribution towards the knowledge of conserved developmental mechanisms in other species with a similar sex habit.

Recent advances in understanding the roles of whole genome duplications in evolution

Ancient whole-genome duplications (WGDs)- paleopolyploidy events-are key to solving Darwin's 'abominable mystery' of how flowering plants evolved and radiated into a rich variety of species. The vertebrates also emerged from their invertebrate ancestors via two WGDs, and genomes of diverse gymnosperm trees, unicellular eukaryotes, invertebrates, fishes, amphibians and even a rodent carry evidence of lineage-specific WGDs. Modern polyploidy is common in eukaryotes, and it can be induced, enabling mechanisms and short-term cost-benefit assessments of polyploidy to be studied experimentally. However, the ancient WGDs can be reconstructed only by comparative genomics: these studies are difficult because the DNA duplicates have been through tens or hundreds of millions of years of gene losses, mutations, and chromosomal rearrangements that culminate in resolution of the polyploid genomes back into diploid ones (rediploidisation). Intriguing asymmetries in patterns of post-WGD gene loss and retention between duplicated sets of chromosomes have been discovered recently, and elaborations of signal transduction systems are lasting legacies from several WGDs. The data imply that simpler signalling pathways in the pre-WGD ancestors were converted via WGDs into multi-stranded parallelised networks. Genetic and biochemical studies in plants, yeasts and vertebrates suggest a paradigm in which different combinations of sister paralogues in the post-WGD regulatory networks are co-regulated under different conditions. In principle, such networks can respond to a wide array of environmental, sensory and hormonal stimuli and integrate them to generate phenotypic variety in cell types and behaviours. Patterns are also being discerned in how the post-WGD signalling networks are reconfigured in human cancers and neurological conditions. It is fascinating to unpick how ancient genomic events impact on complexity, variety and disease in modern life.

Genotype-specific physiological and transcriptomic responses to drought stress in Setaria italica (an emerging model for Panicoideae grasses)

Understanding drought-tolerance mechanisms and identifying genetic dominance are important for crop improvement. Setaria italica, which is extremely drought-tolerant, has been regarded as a model plant for studying stress biology. Moreover, different genotypes of S. italica have evolved various drought-tolerance/avoidance mechanisms that should be elucidated. Physiological and transcriptomic comparisons between drought-tolerant S. italica cultivar 'Yugu1' and drought-sensitive 'An04' were conducted. 'An04' had higher yields and more efficient photosystem activities than 'Yugu1' under well-watered conditions, and this was accompanied by positive brassinosteroid regulatory actions. However, 'An04's growth advantage was severely repressed by drought, while 'Yugu1' maintained normal growth under a water deficiency. High-throughput sequencing suggested that the S. italica transcriptome was severely remodelled by genotype × environment interactions. Expression profiles of genes related to phytohormone metabolism and signalling, transcription factors, detoxification, and other stress-related proteins were characterised, revealing genotype-dependent and -independent drought responses in different S. italica genotypes. Combining our data with drought-tolerance-related QTLs, we identified 20 candidate genes that contributed to germination and early seedling' drought tolerance in S. italica. Our analysis provides a comprehensive picture of how different S. italica genotypes respond to drought, and may be used for the genetic improvement of drought tolerance in Poaceae crops.

Two C3H Type Zinc Finger Protein Genes, CpCZF1 and CpCZF2, from Chimonanthus praecox Affect Stamen Development in Arabidopsis

Wintersweet (Chimonanthus praecox) is a popular garden plant because of its flowering time, sweet fragrance, and ornamental value. However, research into the molecular mechanism that regulates flower development in wintersweet is still limited. In this study, we sought to investigate the molecular characteristics, expression patterns, and potential functions of two C3H-type zinc finger (CZF) protein genes, CpCZF1 and CpCZF2, which were isolated from the wintersweet flowers based on the flower developmental transcriptome database. CpCZF1 and CpCZF2 were more highly expressed in flower organs than in vegetative tissues, and during the flower development, their expression profiles were associated with flower primordial differentiation, especially that of petal and stamen primordial differentiation. Overexpression of either CpCZF1 or CpCZF2 caused alterations on stamens in transgenic Arabidopsis. The expression levels of the stamen identity-related genes, such as AGAMOUS (AG), PISTILLATA (PI), SEPALLATA1 (SEP1), SEPALLATA2 (SEP2), SEPALLATA3 (SEP3), APETALA1 (AP1), APETALA2 (AP2), and boundary gene RABBIT EAR (RBE) were significantly up-regulated in CpCZF1 overexpression lines. Additionally, the transcripts of AG, PI, APETALA3SEP1-3, AP1, and RBE were markedly increased in CpCZF2 overexpressed plant inflorescences. Moreover, CpCZF1 and CpCZF2 could interact with each other by using yeast two-hybrid and bimolecular fluorescence complementation assays. Our results suggest that CpCZF1 and CpCZF2 may be involved in the regulation of stamen development and cause the formation of abnormal flowers in transgenic Arabidopsis plants.

Bypassing Negative Epistasis on Yield in Tomato Imposed by a Domestication Gene

Selection for inflorescence architecture with improved flower production and yield is common to many domesticated crops. However, tomato inflorescences resemble wild ancestors, and breeders avoided excessive branching because of low fertility. We found branched variants carry mutations in two related transcription factors that were selected independently. One founder mutation enlarged the leaf-like organs on fruits and was selected as fruit size increased during domestication. The other mutation eliminated the flower abscission zone, providing "jointless" fruit stems that reduced fruit dropping and facilitated mechanical harvesting. Stacking both beneficial traits caused undesirable branching and sterility due to epistasis, which breeders overcame with suppressors. However, this suppression restricted the opportunity for productivity gains from weak branching. Exploiting natural and engineered alleles for multiple family members, we achieved a continuum of inflorescence complexity that allowed breeding of higher-yielding hybrids. Characterizing and neutralizing similar cases of negative epistasis could improve productivity in many agricultural organisms. VIDEO ABSTRACT.

Phytoplasma-conserved phyllogen proteins induce phyllody across the Plantae by degrading floral MADS domain proteins

ABCE-class MADS domain transcription factors (MTFs) are key regulators of floral organ development in angiosperms. Aberrant expression of these genes can result in abnormal floral traits such as phyllody. Phyllogen is a virulence factor conserved in phytoplasmas, plant pathogenic bacteria of the class Mollicutes. It triggers phyllody in Arabidopsis thaliana by inducing degradation of A- and E-class MTFs. However, it is still unknown whether phyllogen can induce phyllody in plants other than A. thaliana, although phytoplasma-associated phyllody symptoms are observed in a broad range of angiosperms. In this study, phyllogen was shown to cause phyllody phenotypes in several eudicot species belonging to three different families. Moreover, phyllogen can interact with MTFs of not only angiosperm species including eudicots and monocots but also gymnosperms and a fern, and induce their degradation. These results suggest that phyllogen induces phyllody in angiosperms and inhibits MTF function in diverse plant species.

Network approaches for plant phylogenomic synteny analysis

Network analysis approaches have been widely applied across disciplines. In biology, network analysis is now frequently adopted to organize protein-protein interactions, organize pathways and/or to interpret gene co-expression patterns. However, comparative genomic analyses still largely rely on pairwise comparisons and linear visualizations between genomes. In this article, we discuss the challenges and prospects for establishing a generalized plant phylogenomic synteny network approach needed to interpret the wealth of new and emerging genomic data. We illustrate our approach with an example synteny network of B-class floral MADS-box genes. A broad synteny network approach holds great promise for understanding the evolutionary history of genes and genomes across broad phylogenetic groups and divergence times.

Expression patterns of Passiflora edulis APETALA1/FRUITFULL homologues shed light onto tendril and corona identities

BACKGROUND

Passiflora (passionflowers) makes an excellent model for studying plant evolutionary development. They are mostly perennial climbers that display axillary tendrils, which are believed to be modifications of the inflorescence. Passionflowers are also recognized by their unique flower features, such as the extra whorls of floral organs composed of corona filaments and membranes enclosing the nectary. Although some work on Passiflora organ ontogeny has been done, the developmental identity of both Passiflora tendrils and the corona is still controversial. Here, we combined ultrastructural analysis and expression patterns of the flower meristem and floral organ identity genes of the MADS-box AP1/FUL clade to reveal a possible role for these genes in the generation of evolutionary novelties in Passiflora.

RESULTS

We followed the development of structures arising from the axillary meristem from juvenile to adult phase in P. edulis. We further assessed the expression pattern of P. edulis AP1/FUL homologues (PeAP1 and PeFUL), by RT-qPCR and in situ hybridization in several tissues, correlating it with the developmental stages of P. edulis. PeAP1 is expressed only in the reproductive stage, and it is highly expressed in tendrils and in flower meristems from the onset of their development. PeAP1 is also expressed in sepals, petals and in corona filaments, suggesting a novel role for PeAP1 in floral organ diversification. PeFUL presented a broad expression pattern in both vegetative and reproductive tissues, and it is also expressed in fruits.

CONCLUSIONS

Our results provide new molecular insights into the morphological diversity in the genus Passiflora. Here, we bring new evidence that tendrils are part of the Passiflora inflorescence. This points to the convergence of similar developmental processes involving the recruitment of genes related to flower identity in the origin of tendrils in different plant families. The data obtained also support the hypothesis that the corona filaments are likely sui generis floral organs. Additionally, we provide an indication that PeFUL acts as a coordinator of passionfruit development.

Petal, Sepal, or Tepal? B-Genes and Monocot Flowers

In petaloid monocots expansion of B-gene expression into whorl 1 of the flower results in two whorls of petaloid organs (tepals), as opposed to sepals in whorl 1 of typical eudicot flowers. Recently, new gene-silencing technologies have provided the first functional data to support this, in the genus Tricyrtis (Liliaceae).