Functional characterization of duplicated B-class MADS-box genes in Japanese gentian

Cloning and Expression Analysis of Onion (Allium cepa L.) MADS-Box Genes and Regulation Mechanism of Cytoplasmic Male Sterility

Flower organ development is one of the most important processes in plant life. However, onion CMS (cytoplasmic male sterility) shows an abnormal development of floral organs. The regulation of MADS-box transcription factors is important for flower development. To further understand the role of MADS-box transcription factors in the regulation of cytoplasmic male sterility onions. We cloned the full-length cDNA of five MADS-box transcription factors from the flowers of onion using RACE (rapid amplification of cDNA ends) technology. We used bioinformatics methods for sequence analysis and phylogenetic analysis. Real-time quantitative PCR was used to detect the expression patterns of these genes in different onion organs. The relative expression levels of five flower development genes were compared in CMS onions and wild onions. The results showed that the full-length cDNA sequences of the cloned MADS-box genes AcFUL, AcDEF, AcPI, AcAG, and AcSEP3 belonged to A, B, C, and E MADS-box genes, respectively. A phylogenetic tree construction analysis was performed on its sequence. Analysis of MADS-box gene expression in wild onion and CMS onion showed that the formation of CMS onion was caused by down-regulation of AcDEF, AcPI, and AcAG gene expression, up-regulation of AcSEP3 gene expression, and no correlation with AcFUL gene expression. This work laid the foundation for further study of the molecular mechanism of onion flower development and the molecular mechanism of CMS onion male sterility.

Identification of a novel viral factor inducing tumorous symptoms by disturbing vascular development in planta

Plant viruses induce various disease symptoms that substantially impact agriculture, but the underlying mechanisms of viral disease in plants are poorly understood. Kobu-sho is a disease in gentian that shows gall formation with ectopic development of lignified cells and vascular tissues such as xylem. Here, we show that a gene fragment of gentian Kobu-sho-associated virus, which is designated as Kobu-sho-inducing factor (KOBU), induces gall formation accompanied by ectopic development of lignified cells and xylem-like tissue in Nicotiana benthamiana. Transgenic gentian expressing KOBU exhibited tumorous symptoms, confirming the gall-forming activity of KOBU. Surprisingly, KOBU expression can also induce differentiation of an additional leaf-like tissue on the abaxial side of veins in normal N. benthamiana and gentian leaves. Transcriptome analysis with Arabidopsis thaliana expressing KOBU revealed that KOBU activates signaling pathways that regulate xylem development. KOBU protein forms granules and plate-like structures and co-localizes with mRNA splicing factors within the nucleus. Our findings suggest that KOBU is a novel pleiotropic virulence factor that stimulates vascular and leaf development. IMPORTANCE While various mechanisms determine disease symptoms in plants depending on virus-host combinations, the details of how plant viruses induce symptoms remain largely unknown in most plant species. Kobu-sho is a disease in gentian that shows gall formation with ectopic development of lignified cells and vascular tissues such as xylem. Our findings demonstrate that a gene fragment of gentian Kobu-sho-associated virus (GKaV), which is designated as Kobu-sho-inducing factor, induces the gall formation accompanied by the ectopic development of lignified cells and xylem-like tissue in Nicotiana benthamiana. The molecular mechanism by which gentian Kobu-sho-associated virus induces the Kobu-sho symptoms will provide new insight into not only plant-virus interactions but also the regulatory mechanisms underlying vascular and leaf development.

Efficient double-flowered gentian plant production using the CRISPR/Cas9 system

Japanese cultivated gentians are highly valued ornamental flowers in Japan, but the flower shape is mostly limited to the single-flower type, unlike other flowers such as roses and carnations. To overcome this limitation, we used the CRISPR/Cas9 genome editing system to increase double-flowered genetic resources in gentians. Our approach targeted an AGAMOUS (AG) floral homeotic gene (AG1), which is responsible for the natural mutation that causes double flowers in gentians. We designed two targets in exon 1 of AG1 for genome editing and found that 9 of 12 herbicide-resistant shoots had biallelic mutations in the target regions of AG1. These nine lines all produced double flowers, with stamens converted into petaloid organs, similar to the natural mutant. We also analyzed the off-target effects of AG2, which is homologous to AG1, and found that such effects occurred in gentian genome editing but with low frequency. Furthermore, we successfully produced transgene-free genome-edited plants (null segregants) by crossing with wild-type pollen. F1 seedlings were subjected to PCR analysis to determine whether foreign DNA sequences, two partial regions of the CaMV35S promoter and Cas9 gene, were present in the genome. As a result, foreign genes were segregated at a 1 : 1 ratio, indicating successful null segregant production. Using PCR analysis, we confirmed that four representative null segregants did not contain transfer DNA. In summary, our study demonstrates that the CRISPR/Cas9 system can efficiently produce double-flowered gentians, and null segregants can also be obtained. These genome-edited plants are valuable genetic resources for future gentian breeding programs.

Spatiotemporal profiles of gene activity in stamen delineate nucleo-cytoplasmic interaction in a male-sterile somatic cybrid citrus

Cytoplasmic male sterility (CMS) has long been used to produce seedless fruits in perennial woody crops like citrus. A male-sterile somatic cybrid citrus (G1 + HBP) was generated by protoplast fusion between a CMS callus parent 'Guoqing No. 1' Satsuma mandarin (Citrus unshiu, G1) and a fertile mesophyll parent Hirado Buntan pummelo (Citrus grandis, HBP). To uncover the male-sterile mechanism of G1 + HBP, we compared the transcriptome profiles of stamen organ and cell types at five stages between G1 + HBP and HBP, including the initial stamen primordia, enlarged stamen primordia, pollen mother cells, tetrads, and microspores captured by laser microdissection. The stamen organ and cell types showed distinct gene expression profiles. A majority of genes involved in stamen development were differentially expressed, especially CgAP3.2, which was downregulated in enlarged stamen primordia and upregulated in tetrads of G1 + HBP compared with HBP. Jasmonic acid- and auxin-related biological processes were enriched among the differentially expressed genes of stamen primordia, and the content of jasmonic acid biosynthesis metabolites was higher in flower buds and anthers of G1 + HBP. In contrast, the content of auxin biosynthesis metabolites was lower in G1 + HBP. The mitochondrial tricarboxylic acid cycle and oxidative phosphorylation processes were enriched among the differentially expressed genes in stamen primordia, meiocytes, and microspores, indicating the dysfunction of mitochondria in stamen organ and cell types of G1 + HBP. Taken together, the results indicate that malfunction of mitochondria-nuclear interaction might cause disorder in stamen development, and thus lead to male sterility in the citrus cybrid.

De Novo Transcriptome Analysis Reveals Flowering-Related Genes That Potentially Contribute to Flowering-Time Control in the Japanese Cultivated Gentian Gentiana triflora

Japanese cultivated gentians are perennial plants that flower in early summer to late autumn in Japan, depending on the cultivar. Several flowering-related genes, including GtFT1 and GtTFL1, are known to be involved in regulating flowering time, but many such genes remain unidentified. In this study, we obtained transcriptome profiling data using the Gentiana triflora cultivar ‘Maciry’, which typically flowers in late July. We conducted deep RNA sequencing analysis using gentian plants grown under natural field conditions for three months before flowering. To investigate diurnal changes, the plants were sampled at 4 h intervals over 24 h. Using these transcriptome data, we determined the expression profiles of leaves based on homology searches against the Flowering-Interactive Database of Arabidopsis. In particular, we focused on transcription factor genes, belonging to the BBX and MADS-box families, and analyzed their developmental and diurnal variation. The expression levels of representative BBX genes were also analyzed under long- and short-day conditions using in-vitro-grown seedlings, and the expression patterns of some BBX genes differed. Clustering analysis revealed that the transcription factor genes were coexpressed with GtFT1. Overall, these expression profiles will facilitate further analysis of the molecular mechanisms underlying the control of flowering time in gentians.

Isolation and Functional Analysis of EPHEMERAL1-LIKE (EPH1L) Genes Involved in Flower Senescence in Cultivated Japanese Gentians

The elongation of flower longevity increases the commercial value of ornamental plants, and various genes have been identified as influencing flower senescence. Recently, EPHEMERAL1 (EPH1), encoding a NAC-type transcription factor, was identified in Japanese morning glory as a gene that promotes flower senescence. Here we attempted to identify an EPH1 homolog gene from cultivated Japanese gentians and characterized the same with regard to its flower senescence. Two EPH1-LIKE genes (EPH1La and EPH1Lb), considered as alleles, were isolated from a gentian cultivar (Gentiana scabra × G. triflora). Phylogenetic analyses revealed that EPH1L belongs to the NAM subfamily. The transcript levels of EPH1L increased along with its senescence in the field-grown flowers. Under dark-induced senescence conditions, the gentian-detached flowers showed the peak transcription level of EPH1L earlier than that of SAG12, a senescence marker gene, suggesting the involvement of EPH1L in flower senescence. To reveal the EPH1L function, we produced eph1l-knockout mutant lines using the CRISPR/Cas9 system. When the flower longevity was evaluated using the detached flowers as described above, improved longevity was recorded in all genome-edited lines, with delayed induction of SAG12 transcription. The degradation analysis of genomic DNA matched the elongation of flower longevity, cumulatively indicating the involvement of EPH1L in the regulation of flower senescence in gentians.

Identification of Candidate Chromosome Region Related to Melon (Cucumis melo L.) Fruit Surface Groove Trait Through Biparental Genetic Mapping and Genome-Wide Association Study

The melon fruit surface groove (fsg) not only affects peel structure and causes stress-induced fruit cracking but also fits consumers' requirements in different regions. In this study, genetic inheritance analysis of three F₂ populations derived from six parental lines revealed that the fsg trait is controlled by a simple recessive inherited gene. Through bulked segregant analysis sequencing (BSA-seq), the Cmfsg locus was detected in an 8.96 Mb interval on chromosome 11 and then initially mapped to a region of approximately 1.15 Mb. Further fine mapping with a large F₂ population including 1,200 plants narrowed this region to 207 kb containing 11 genes. A genome-wide association study (GWAS) with 187 melon accessions also produced the same chromosome region for the Cmfsg locus. Due to the rare molecular markers and lack of mutations in the coding and promoter regions of the 11 candidate genes in the fine-mapped interval, we conducted in silico BSA to explore the natural melon panel to predict candidate genes for the Cmfsg locus. A 1.07 kb segment upstream of MELO3C019694.2 (annotated as the AGAMOUS MADS-box transcription factor) exhibited a correlation with the grooved and non-grooved accessions among the F₂ individuals, and a natural panel consisted of 17 melon accessions. The expression level of MELO3C019694.2 in the pericarp was higher in grooved lines than in non-grooved lines and was specifically expressed in fruit compared with other tissues (female flower, male flower, root, and leaf). This work provides fundamental information for further research on melon fsg trait formation and molecular markers for melon breeding.

Isolation and Characterization of APETALA3 Orthologs and Promoters from the Distylous Fagopyrum esculentum

Common buckwheat (Fagopyrum esculentum) produces distylous flowers with undifferentiated petaloid tepals, which makes it obviously different from flowers of model species. In model species Arabidopsis, APETALA3 (AP3) is expressed in petal and stamen and specifies petal and stamen identities during flower development. Combining with our previous studies, we found that small-scale gene duplication (GD) event and alternative splicing (AS) of common buckwheat AP3 orthologs resulted in FaesAP3_1, FaesAP3_2 and FaesAP3_2a. FaesAP3_2 and FaesAP3_2a were mainly expressed in the stamen of thrum and pin flower. Promoters functional analysis suggested that intense GUS staining was observed in the whole stamen in pFaesAP3_2::GUS transgenic Arabidopsis, while intense GUS staining was observed only in the filament of stamen in pFaesAP3_1::GUS transgenic Arabidopsis. These suggested that FaesAP3_1 and FaesAP3_2 had overlapping functions in specifying stamen filament identity and work together to determine normal stamen development. Additionally, FaesAP3_2 and FaesAP3_2a owned the similar ability to rescue stamen development of Arabidopsis ap3-3 mutant, although AS resulted in a frameshift mutation and consequent omission of the complete PI-derived motif and euAP3 motif of FaesAP3_2a. These suggested that the MIK region of AP3-like proteins was crucial for determining stamen identity, while the function of AP3-like proteins in specifying petal identity was gradually obtained after AP3 Orthologs acquiring a novel C-terminal euAP3 motif during the evolution of core eudicots. Our results also provide a clue to understanding the early evolution of the functional specificity of euAP3-type proteins involving in floral organ development in core eudicots, and also suggested that FaesAP3_2 holds the potential application for biotechnical engineering to develop a sterile male line of F. esculentum.

Morphological and cytological observations of corolla green spots reveal the presence of functional chloroplasts in Japanese gentian

Gentian is an important ornamental flower in Japan. The corolla of the majority of cultivated Japanese gentians have green spots, which are rarely encountered in flowers of other angiosperms. Little information is available on the functional traits of the green spots. In this study, we characterized the green spots in the Japanese gentian corolla using a number of microscopic techniques. Opto-digital microscopy revealed that a single visible green spot is composed of approximately 100 epidermal cells. The epidermal cells of a green spot formed a dome-like structure and the cell lumen contained many green structures that were granular and approximately 5 μm in diameter. The green structures emitted red autofluorescence when irradiated with 488 nm excitation light. Transmission electron microscopy revealed that the green structures contained typical thylakoids and grana, thus indicating they are chloroplasts. No grana were observed and the thylakoids had collapsed in the plastids of epidermal cells surrounding green spots. To estimate the rate of photosynthetic electron transfer of the green spots, we measured chlorophyll fluorescence using the MICROSCOPY version of an Imaging-PAM (pulse-amplitude-modulated) fluorometer. Under actinic light of 449 μmol m-2 s-1, substantial electron flow through photosystem II was observed. Observation of green spot formation during corolla development revealed that immature green spots formed at an early bud stage and developed to maturity associated with chloroplast degradation in the surrounding epidermal cells. These results confirmed that the Japanese gentian corolla contains functional chloroplasts in restricted areas of epidermal cells and indicated that a sophisticated program for differential regulation of chloroplast formation and degradation is operative in the epidermis.

Negative feedback loop between BpAP1 and BpPI/BpDEF heterodimer in Betula platyphylla × B. pendula

MADS-box genes encode transcription factors involved in the control of many important developmental processes, especially the flower development of angiosperms. Analysis on gene regulatory relationship between MADS-box genes is useful for understanding the molecular mechanism of flower development. In this study, we focused on the regulatory relationship between MADS-box transcription factors APETALA1 (AP1) and PISTILLATA(PI)/DEFICIENS (DEF) in birch. We found that BpPI was an authentic target gene of BpAP1, and BpAP1 activated the expression of BpPI via directly binding to the CArG box motif. Functional analysis of BpPI showed that overexpression of BpPI may delay flowering via restricting flowering activators, in which BpAP1 was significantly down-regulated. We further investigated the regulatory of BpAP1 by BpPI, and found that BpPI could directly bind to the promoter of BpAP1 to restrict BpAP1 expression. In addition, we also found that BpPI could interact with its hypothetical partner BpDEF to co-regulate BpAP1 in birch. Our results suggested that overexpression of BpPI may delay flowering via restricting flowering activators, and there is a negative feedback loop between BpAP1 and BpPI/BpDEF heterodimer in birch. Our results will bring new evidences for further analysis of the molecular mechanism of flower formation in plants that produced unisexual flowers.

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.