Characterization of HoMADS 1 and its induction by plant hormones during in vitro ovule development in Hyacinthus orientalis L

Genome-Wide Analysis of MADS-Box Gene Family Reveals CjSTK as a Key Regulator of Seed Abortion in Camellia japonica

The plant MADS-box transcription factor family is a major regulator of plant flower development and reproduction, and the AGAMOUS-LIKE11/SEEDSTICK (AGL11/STK) subfamily plays conserved functions in the seed development of flowering plants. Camellia japonica is a world-famous ornamental flower, and its seed kernels are rich in highly valuable fatty acids. Seed abortion has been found to be common in C. japonica, but little is known about how it is regulated during seed development. In this study, we performed a genome-wide analysis of the MADS-box gene the in C. japonica genome and identified 126 MADS-box genes. Through gene expression profiling in various tissue types, we revealed the C/D-class MADS-box genes were preferentially expressed in seed-related tissues. We identified the AGL11/STK-like gene, CjSTK, and showed that it contained a typical STK motif and exclusively expressed during seed development. We found a significant increase in the CjSTK expression level in aborted seeds compared with normally developing seeds. Furthermore, overexpression of CjSTK in Arabidopsis thaliana caused shorter pods and smaller seeds. Taken together, we concluded that the fine regulation of the CjSTK expression at different stages of seed development is critical for ovule formation and seed abortion in C. japonica. The present study provides evidence revealing the regulation of seed development in Camellia.

Carpel-specific down-regulation of GhCKXs in cotton significantly enhances seed and fiber yield

Cytokinin is considered to be an important driver of seed yield. To increase the yield of cotton while avoiding the negative consequences caused by constitutive overproduction of cytokinin, we down-regulated specifically the carpel genes for cytokinin oxidase/dehydrogenase (CKX), a key negative regulator of cytokinin levels, in transgenic cotton. The carpel-specific down-regulation of CKXs significantly enhanced cytokinin levels in the carpels. The elevated cytokinin promoted the expression of carpel- and ovule-development-associated genes, GhSTK2, GhAG1, and GhSHP, boosting ovule formation and thus producing more seeds in the ovary. Field experiments showed that the carpel-specific increase of cytokinin significantly increased both seed yield and fiber yield of cotton, without resulting in detrimental phenotypes. Our study details the regulatory mechanism of cytokinin signaling for seed development, and provides an effective and feasible strategy for yield improvement of seed crops.

Evolution and functional divergence of MADS-box genes in Pyrus

MADS-box transcription factors widely regulate all aspects of plant growth including development and reproduction. Although the MADS-box gene family genes have been extensively characterized in many plants, they have not been studied in closely related species. In this study, 73 and 74 MADS-box genes were identified in European pear (Pyrus communis) and Chinese pear (Pyrus bretschneideri), respectively. Based on the phylogenetic relationship, these genes could be clustered into five groups (Mα, Mβ, Mr, MIKC^C, MIKC*) and the MIKC^C group was further categorized into 10 subfamilies. The distribution of MADS-box genes on each chromosome was significantly nonrandom. Thirty-seven orthologs, twenty-five PcpMADS (P. communis MADS-box) paralogs and nineteen PbrMADS (P. bretschneideri MADS-box) paralogs were predicted. Among these paralogous genes, two pairs arose from tandem duplications (TD), nineteen from segmental duplication (SD) events and twenty-three from whole genome duplication (WGD) events, indicating SD/WGD events led to the expansion of MADS-box gene family. The MADS-box genes expression profiles in pear fruits indicated functional divergence and neo-functionalization or sub-functionalization of some orthologous genes originated from a common ancestor. This study provided a useful reference for further analysis the mechanisms of species differentiation and biodiversity formation among closely related species.

Type-B ARRs Control Carpel Regeneration Through Mediating AGAMOUS Expression in Arabidopsis

Plants are known for their capacity to regenerate organs, such as shoot, root and floral organs. Recently, a number of studies contributed to understanding the mechanisms of shoot and root regeneration. However, the mechanisms underlying floral organ regeneration are largely unknown. In this study, we established a carpel regeneration system in which two types of carpels were induced by exogenous cytokinin. For type I, all the floral organs in the regenerated inflorescence were transformed into carpels. For type II, carpels were generated directly from callus. The transcript level of AGAMOUS (AG), the carpel identity gene, was up-regulated during carpel induction. The expression signals of AG were detected in the initiating carpel primordia and regenerating carpels, and co-localized with those of two Type-B ARABIDOPSIS RESPONSE REGULATORs (ARRs), ARR1 and ARR10. Repression of either AG or type-B ARRs reduced carpel regeneration. Binding analyses showed that ARR1 and ARR10 directly bound to transcriptional regulatory regions of AG and positively regulated its expression. In addition, the expression of type-B ARRs overlapped with that of AG in the floral primordia in planta. Defects in type-B ARRs reduced the number of carpels. The results indicate that type-B ARRs control carpel regeneration through activating AG expression. Our results provide new information for understanding the mechanism of carpel formation.

Analysis of the floral MADS-box genes from monocotyledonous Trilliaceae species indicates the involvement of SEPALLATA3-like genes in sepal-petal differentiation

The evolution of greenish sepals from petaloid outer tepals has occurred repeatedly in various lineages of non-grass monocots. Studies in distinct monocot species showed that the evolution of sepals could be explained by the ABC model; for example, the defect of B-class function in the outermost whorl was linked to the evolution of sepals. Here, floral MADS-box genes from three sepal-bearing monocotyledonous Trilliaceae species, Trillium camschatcense, Paris verticillata, and Kinugasa japonica were examined. Unexpectedly, expression of not only A- but also B-class genes was detected in the sepals of all three species. Although the E-class gene is generally expressed across all floral whorls, no expression was detected in sepals in the three species examined here. Overexpression of the E-class SEPALLATA3-like gene from T. camschatcense (TcamSEP) in Arabidopsis thaliana produced phenotypes identical to those reported for orthologs in other monocots. Additionally, yeast hybrid experiments indicated that TcamSEP could form a higher-order complex with an endogenous heterodimer of B-class APETALA3/DEFICIENS-like (TcamDEF) and PISTILLATA/GLOBOSA-like (TcamGLO) proteins. These results suggest a conserved role for Trilliaceae SEPALLATA3-like genes in functionalization of the B-class genes, and that a lack of SEPALLATA3-like gene expression in the outermost whorl may be related to the formation of greenish sepals.

Expression of paralogous SEP-, FUL-, AG- and STK-like MADS-box genes in wild-type and peloric Phalaenopsis flowers

The diverse flowers of Orchidaceae are the result of several major morphological transitions, among them the most studied is the differentiation of the inner median tepal into the labellum, a perianth organ key in pollinator attraction. Type A peloria lacking stamens and with ectopic labella in place of inner lateral tepals are useful for testing models on the genes specifying these organs by comparing their patterns of expression between wild-type and peloric flowers. Previous studies focused on DEFICIENS- and GLOBOSA-like MADS-box genes because of their conserved role in perianth and stamen development. The "orchid code" model summarizes this work and shows in Orchidaceae there are four paralogous lineages of DEFICIENS/AP3-like genes differentially expressed in each floral whorl. Experimental tests of this model showed the conserved, higher expression of genes from two specific DEF-like gene lineages is associated with labellum development. The present study tests whether eight MADS-box candidate SEP-, FUL-, AG-, and STK-like genes have been specifically duplicated in the Orchidaceae and are also differentially expressed in association with the distinct flower organs of Phalaenopsis hyb. "Athens." The gene trees indicate orchid-specific duplications. In a way analogous to what is observed in labellum-specific DEF-like genes, a two-fold increase in the expression of SEP3-like gene PhaMADS7 was measured in the labellum-like inner lateral tepals of peloric flowers. The overlap between SEP3-like and DEF-like genes suggests both are associated with labellum specification and similar positional cues determine their domains of expression. In contrast, the uniform messenger levels of FUL-like genes suggest they are involved in the development of all organs and their expression in the ovary suggests cell differentiation starts before pollination. As previously reported AG-like and STK-like genes are exclusively expressed in gynostemium and ovary, however no evidence for transcriptional divergence was found in the stage investigated. Gene expression suggests a developmental regulatory system based on the combined activity of duplicate MADS-box genes. We discuss its feasibility based on documented protein interactions and patterns of expression.

Evolution of fruit development genes in flowering plants

The genetic mechanisms regulating dry fruit development and opercular dehiscence have been identified in Arabidopsis thaliana. In the bicarpellate silique, valve elongation and differentiation is controlled by FRUITFULL (FUL) that antagonizes SHATTERPROOF1-2 (SHP1/SHP2) and INDEHISCENT (IND) at the dehiscence zone where they control normal lignification. SHP1/2 are also repressed by REPLUMLESS (RPL), responsible for replum formation. Similarly, FUL indirectly controls two other factors ALCATRAZ (ALC) and SPATULA (SPT) that function in the proper formation of the separation layer. FUL and SHP1/2 belong to the MADS-box family, IND and ALC belong to the bHLH family and RPL belongs to the homeodomain family, all of which are large transcription factor families. These families have undergone numerous duplications and losses in plants, likely accompanied by functional changes. Functional analyses of homologous genes suggest that this network is fairly conserved in Brassicaceae and less conserved in other core eudicots. Only the MADS box genes have been functionally characterized in basal eudicots and suggest partial conservation of the functions recorded for Brassicaceae. Here we do a comprehensive search of SHP, IND, ALC, SPT, and RPL homologs across core-eudicots, basal eudicots, monocots and basal angiosperms. Based on gene-tree analyses we hypothesize what parts of the network for fruit development in Brassicaceae, in particular regarding direct and indirect targets of FUL, might be conserved across angiosperms.

The MADS and the Beauty: Genes Involved in the Development of Orchid Flowers

Since the time of Darwin, biologists have studied the origin and evolution of the Orchidaceae, one of the largest families of flowering plants. In the last two decades, the extreme diversity and specialization of floral morphology and the uncoupled rate of morphological and molecular evolution that have been observed in some orchid species have spurred interest in the study of the genes involved in flower development in this plant family. As part of the complex network of regulatory genes driving the formation of flower organs, the MADS-box represents the most studied gene family, both from functional and evolutionary perspectives. Despite the absence of a published genome for orchids, comparative genetic analyses are clarifying the functional role and the evolutionary pattern of the MADS-box genes in orchids. Various evolutionary forces act on the MADS-box genes in orchids, such as diffuse purifying selection and the relaxation of selective constraints, which sometimes reveals a heterogeneous selective pattern of the coding and non-coding regions. The emerging theory regarding the evolution of floral diversity in orchids proposes that the diversification of the orchid perianth was a consequence of duplication events and changes in the regulatory regions of the MADS-box genes, followed by sub- and neo-functionalization. This specific developmental-genetic code is termed the "orchid code."

Cytokinin and auxin regulates WUS induction and inflorescence regeneration in vitro in Arabidopsis

Inflorescence regeneration in vitro provides a simplified approach for the study of inflorescence development. In this study, high frequency of regenerated inflorescences was established using Arabidopsis stage-10 pistil as the explants on the inducing medium containing the 2 mg/L zeatin and 0.01 mg/L indole-3-acetic acid. TERMINAL FLOWER 1 (TFL1) expression was detected in callus at 6 days after transferred to inducing medium, and LEAFY (LFY) expression was detectable subsequently, suggesting that both genes play important roles as they function on inflorescence development in the plant. To investigate the formation of the stem cell organizing center, we examined the WUSCHEL (WUS) and CLAVATA3 (CLV3) expression within callus during inflorescence regeneration. WUS signals start to accumulate on callus at 4 days after induction, and then, the CLV3 signals are induced on callus at 5 days on the inflorescence-inducing medium. The expression domain of WUS is below that of CLV3, indicating that the patterns of the organizing center and stem cell formation are similar to that in zygotic and somatic embryogenesis. However, more cells of the organizing center were observed within callus than pro-embryo, suggesting that inflorescence differentiation requires more cells of the organizing center. Furthermore, it was found that the WUS expression is controlled by the ratio of cytokinin with auxin. The results suggest that other factors besides WUS and CLV3 are required for inflorescence regeneration.

Functional analysis of GbAGL1, a D-lineage gene from cotton (Gossypium barbadense)

Cotton fibres originate from the outer ovule integument and D-lineage genes are essential for ovule development and their roles can be described by the 'ABCDE' model of flower development. To investigate the role of D-lineage genes during ovule and fibre development, GbAGL1 (GenBank accession number: FJ198049) was isolated from G. barbadense by using the SMART RACE strategy. Sequence and phylogenetic analyses revealed that GbAGL1 was a member of the D-lineage gene family. Southern blot analysis showed that GbAGL1 belonged to a low-copy gene family. Semi-quantitative RT-PCR and RNA in situ hybridization analyses revealed that the GbAGL1 gene in G. barbadense was highly expressed in whole floral bud primordia and the floral organs including ovules and fibres, but the signals were barely observed in vegetative tissues. GbAGL1 expression increased gradually with the ovule developmental stages. Over-expression of GbAGL1 in Arabidopsis caused obvious homeotic alternations in the floral organs, such as early flowering, and an extruded stigma, which were the typical phenotypes of the D-lineage gene family. In addition, a complementation test revealed that GbAGL1 could rescue the phenotypes of the stk mutant. Our study indicated that GbAGL1 was a D-lineage gene that was involved in ovule development and might play key roles in fibres development.

Involvement of a banana MADS-box transcription factor gene in ethylene-induced fruit ripening

To investigate the regulation of MADS-box genes in banana (Musa acuminata L. AAA group cv. Brazilian) fruit development and postharvest ripening, we isolated from banana fruit a MADS-box gene designated MuMADS1. Amino acid alignment indicated MuMADS1 belongs to the AGAMOUS subfamily, and phylogenetic analysis indicates that this gene is most similar to class D MADS-box genes. Reverse transcriptase-polymerase chain reaction (RT-PCR) analysis showed that MuMADS1 is expressed in the stamen and pistil of male and female flowers and in the rhizome, the vegetative reproductive organ of the banana plant. In preharvest banana fruit, MuMADS1 is likely expressed throughout banana fruit development. In postharvest banana ripening, MuMADS1 is associated with ethylene biosynthesis. Expression patterns of MuMADS1 during postharvest ripening as determined by real-time RT-PCR suggest that differential expression of MuMADS1 may not only be induced by ethylene biosynthesis associated with postharvest banana ripening, but also may be induced by exogenous ethylene.

Molecular analysis of hormone-regulated petal regeneration in Petunia

The petal is an important floral organ of higher plants. To study the mechanism of petal development, the in vitro regeneration system of petals was established in Petunia. High-frequency induction of petals occurred directly from explants on the media containing the combination of N6-benzyladenine (6-BA) and indole-3-acetic acid (IAA). Expression analysis of genes involved in flower development indicated that these genes were classified into three types. ABERRANT LEAF AND FLOWER (ALF) gene was induced during petal regeneration. Whereas, B-class and E-class genes, and genes involved in cell division were constitutively upregulated. In contrast, C-class and D-class genes were not expressed in explants and regenerated tissues. Further, in situ hybridization analysis showed that both ALF and GREEN PETAL (GP) expression were spatially regulated. The results suggest that differential regulation of gene expression occurs in the presence of hormones during petal regeneration, and hormone-regulated gene expression might be required for petal regeneration. This study provides the preliminary information to understand the mechanism of petal regeneration.

Cell fate switch during in vitro plant organogenesis

Plant mature cells have the capability to reverse their state of differentiation and produce new organs under cultured conditions. Two phases, dedifferentiation and redifferentiation, are commonly characterized during in vitro organogenesis. In these processes, cells undergo fate switch several times regulated by both extrinsic and intrinsic factors, which are associated with reentry to the cell cycle, the balance between euchromatin and heterochromatin, reprogramming of gene expression, and so forth. This short article reviews the advances in the mechanism of organ regeneration from plant somatic cells in molecular, genomic and epigenetic aspects, aiming to provide important information on the mechanism underlying cell fate switch during in vitro plant organogenesis.

Hormone-regulated inflorescence induction and TFL1 expression in Arabidopsis callus in vitro

To study hormone-regulated inflorescence development, we established the in vitro regeneration system of Arabidopsis inflorescences in the presence of cytokinin and auxin. Media containing a combination of thidiazuron (TDZ) and 2,4-dichlorophenoxyacetic acid (2,4-D) were used to induce callus formation. Higher frequencies of calli were obtained by using the inflorescence stems as explants. After transferring the calli to media containing a combination of zeatin and indole-3-acetic acid (IAA), the inflorescences were induced from the calli. The morphology of regenerated inflorescences was similar to that of inflorescences in plants; however, flowers of regenerated inflorescences often lacked a few floral organs. Furthermore, TFL1, a gene involved in floral transition in Arabidopsis, was activated during the inflorescence induction. Our results suggest that the TFL1 gene plays an important role in hormone-regulated inflorescence formation.

Spatiotemporal expression of duplicate AGAMOUS orthologues during floral development in Phalaenopsis

The AGAMOUS (AG) family of MADS-box genes plays important roles in controlling the development of the reproductive organs of flowering plants. To understand the molecular mechanisms behind the floral development in the orchid, we isolated and characterized two AG-like genes from Phalaenopsis that we denoted PhalAG1 and PhalAG2. Phylogenetic analysis indicated that PhalAG1 and PhalAG2 fall into different phylogenetic positions in the AG gene family as they belong to the C- and D-lineages, respectively. Reverse transcription-polymerase chair reaction (RT-PCR) analyses showed that PhalAG1 and PhalAG2 transcripts were detected in flower buds but not in vegetative organs. Moreover, in situ hybridization experiments revealed that PhalAG1 and PhalAG2 hybridization signals were observed in the lip, column, and ovule during the floral development of Phalaenopsis, with little difference between the expression patterns of the two genes. These results suggest that both AG-like genes in Phalaenopsis act redundantly with each other in floral development.

Cloning and transcription analysis of an AGAMOUS- and SEEDSTICK ortholog in the orchid Dendrobium thyrsiflorum (Reichb. f.)

Studies have shown that several plant species possess AGAMOUS (AG) and SEEDSTICK (STK) orthologs. These genes are part of the so-called C- and D MADS-box gene lineages and play key roles in ovule development in Arabidopsis thaliana. We have cloned an AG- and STK ortholog in the orchid Dendrobium thyrsiflorum, named DthyrAG1 and DthyrAG2, respectively, and analyzed their expression patterns. Quantification by real-time RT-PCR analysis shows that both are transcribed in the mature flowers and during ovule development. Localization of the transcripts by in situ hybridization analysis in flowers reveals that both genes are transcribed in the rostellum, stigma, and stylar canal. Expression analysis during ovule development shows that DthyrAG1 is expressed only in the initial periods of placenta- and ovule development, whereas the DthyrAG2 is transcribed throughout ovule development. These results suggest that both C- and D lineage orthologs are involved in various aspects of flower development and that DthyrAG2 have a more prominent role than DthyrAG1 in late ovule development in D. thyrsiflorum.