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Background Transposable elements (TEs) are fragments of DNA that can insert into new chromosomal locations. They represent a great proportion of eukaryotic genomes. The identification and characterization of TEs facilitates understanding the transpositional activity of TEs with their effects on the orchid genome structure. Results We combined the draft whole-genome sequences of Phalaenopsis equestris with BAC end sequences, Roche 454, and Illumina/Solexa, and identified long terminal repeat (LTR) retrotransposons in these genome sequences by using LTRfinder and classified by using Gepard software. Among the 10 families Gypsy-like retrotransposons, three families Gypsy1, Gypsy2, and Gypsy3, contained the most copies among these predicted elements. In addition, six high-copy retrotransposons were identified according to their reads in the sequenced raw data. The 12-kb Orchid-rt1 contains 18,000 copies representing 220 Mbp of the P. equestris genome. Southern blot and slot blot assays showed that these four retrotransposons Gypsy1, Gypsy2, Gypsy3, and Orchid-rt1 contained high copies in the large-genome-size/large-chromosome species P. violacea and P. bellina. Both Orchid-rt1 and Gypsy1 displayed various ratios of copy number for the LTR sequences versus coding sequences among four Phalaenopsis species, including P. violacea and P. bellina and small-genome-size/small-chromosome P. equestris and P. ahprodite subsp. formosana, which suggests that Orchid-rt1 and Gypsy1 have been through various mutations and homologous recombination events. FISH results showed amplification of Orchid-rt1 in the euchromatin regions among the four Phalaenopsis species. The expression levels of Peq018599 encoding copper transporter 1 is highly upregulated with the insertion of Orchid-rt1, while it is down regulated for Peq009948 and Peq014239 encoding for a 26S proteasome non-ATP regulatory subunit 4 homolog and auxin-responsive factor AUX/IAA-related. In addition, insertion of Orchid-rt1 in these three genes are all in their intron regions. Conclusion Orchid-rt1 and Gypsy1–3 have amplified within Phalaenopsis orchids concomitant with the expanded genome sizes, and Orchid-rt1 and Gypsy1 may have gone through various mutations and homologous recombination events. Insertion of Orchid-rt1 is in the introns and affects gene expression levels.

Hybrid Oncidium orchids, such as Oncidium Gower Ramsey and Oncidium "Honey Angel," are popular cut flowers in Japan and Taiwan. Due to pollen sterility, no new varieties have been created by conventional breeding methods. Recently, we employed RNA interference (RNAi) technology to suppress phytoene synthase and successfully modified floret hue from yellow to white (Liu et al. 2019). Transgenic white Oncidium orchids, Honey Snow MF-1, have been grown to test their genetic stability, and their environmental biosafety was assessed for approximately one year under government regulatory instructions from the Council of Agriculture, Taiwan. In the present study, pollen sterility was demonstrated by cytological observation of the microsporogenesis step, pollen morphology abortion, and failure of pollen germination. Assays on allelopathic effect on the other plants and the soil rhizospheric microbial flora-revealed that transgenic Oncidium orchids are potentially safe with regard to environmental biodiversity. Therefore, the general release permissions have been granted and an application for licensing for commercial production is under way.

In Phalaenopsis, interspecific hybridization has been broadly used for breeding cultivars with new traits of flower colors. Yellow pigments in Phalaenopsis cultivars naturally are derived from the diploid species in subgenus Polychilos, including P. amboinensis, P. fasciata, P. lueddemanniana and P. venosa, etc. Commercial cultivars of yellow Phalaenopsis were made by crossing the diploid species in subgenus Polychilos with tetraploid standard-type cultivars, and this often resulted in the formation of triploid progenies. Here we review the breeding history of yellow Phalaenopsis cultivars from a cytogenetic perspective. Chromosome analyses indicate polyploidization playing an important role in these breeding programs and reveal different chromosome introgression of section Polychilos species in these yellow cultivars. The cytogenetic data of these cultivars could provide basic knowledge for yellow Phalaenopsis breeding.

Additional file 4: Table S2. The expression levels of Orchid-rt1 inserted gene and their paralogs genes among different organs.

Additional file 1: Figure S1. Four native Phalaenopsis species analyzed in the study, including P. aphrodite subsp. formosana (A) and P. equestris (B) with small genome/small chromosomes, and P. bellina (C) and P. violacea (D) with large genome/large chromosomes.

Additional file 2: Table S1. The copy numbers of the predicted Copia-like retrotransposons.

Additional file 3: Figure S2. The global alignment result between Orchid-rt1 full length and predicted insertion region from Peq009948.

To accelerate the mulberry breeding program and examine the genome size and ploidy levels of 27 mulberry accessions of promising lines in Taiwan, nuclei suspensions were prepared from unfolded young leaves and analyzed by a flow cytometer. The genome size of each accession was estimated by referring to the standard genome size of chicken erythrocyte nuclei (CEN, 2.5 pg). Our results indicated that 25 among 27 investigated accessions in M. bombycis, M. alba, M. latifolia, M. australis, M. formosnensis, and M. atropurpurea are diploids with genome sizes ranging from 0.61 to 0.71 pg. ‘Elongated mulberry No. 1’ (M. laevigata) with a genome size of 1.06 pg is a triploid. Two populations were identified in the accession ‘67C001’ (M. australis Poir.) with a genome size of either 0.63 pg or 0.98 pg. Due to their similarity in appearance, we suspected that they are probably from the same origin, thus warranting further investigations. Several important vegetative characters of diploids and triploids have been estimated, including leaf length, leaf width, petiole length, petiole width, leaf thickness, and internode length, to document their correlation using the unpaired t-test. Subsequently, the statistical relationship between diploid and triploid species on some of these important characters, including leaf width, petiole width and internode length, was determined through binary regression analysis. We suggested that the internode length could provide a beneficial index to distinguish individuals with different ploidy levels in the field. Results of this study provide useful information to clarify the taxonomy of Morus and improve breeding programs aiming to advance horticulture and sericulture.

Background Termitomyces mushrooms are mutualistically associated with fungus-growing termites, which are widely considered to cultivate a monogenotypic Termitomyces symbiont within a colony. Termitomyces cultures isolated directly from termite colonies are heterokaryotic, likely through mating between compatible homokaryons. Results After pairing homokaryons carrying different haplotypes at marker gene loci MIP and RCB from a Termitomyces fruiting body associated with Odontotermes formosanus, we observed nuclear fusion and division, which greatly resembled meiosis, during each hyphal cell division and conidial formation in the resulting heterokaryons. Surprisingly, nuclei in homokaryons also behaved similarly. To confirm if meiotic-like recombination occurred within mycelia, we constructed whole-genome sequencing libraries from mycelia of two homokaryons and a heterokaryon resulting from mating of the two homokaryons. Obtained reads were aligned to the reference genome of Termitomyces sp. J132 for haplotype reconstruction. After removal of the recombinant haplotypes shared between the heterokaryon and either homokaryons, we inferred that 5.04% of the haplotypes from the heterokaryon were the recombinants resulting from homologous recombination distributed genome-wide. With RNA transcripts of four meiosis-specific genes, including SPO11, DMC1, MSH4, and MLH1, detected from a mycelial sample by real-time quantitative PCR, the nuclear behavior in mycelia was reconfirmed meiotic-like. Conclusion Unlike other basidiomycetes where sex is largely restricted to basidia, Termitomyces maximizes sexuality at somatic stage, resulting in an ever-changing genotype composed of a myriad of coexisting heterogeneous nuclei in a heterokaryon. Somatic meiotic-like recombination may endow Termitomyces with agility to cope with termite consumption by maximized genetic variability. Electronic supplementary material The online version of this article (doi:10.1186/s40529-017-0191-9) contains supplementary material, which is available to authorized users.

Phalaenopsis orchids have a spectacular floral morphology with a highly evolved lip that offers a landing platform for pollinators. The typical morphological orchid lip features are essential for the special pollination mechanism of Phalaenopsis flowers. Previously, we found that in the lip, a member of the AP2/EREBP protein family was highly expressed. Here, we further confirmed its high expression and characterized its function during lip development. Phylogenetic analysis showed that AP2/EREBP belongs to the Va2 subgroup of ERF transcription factors. We named it PeERF1. We found that PeERF1 was only expressed at stage 5, as flowers opened. This coincided with both thickening of the cuticle and development of nanoridges. We performed knockdown expression of PeERF1 using CymMV-based virus-induced gene silencing in either the AP2 conserved domain, producing PeERF1_AP2-silenced plants, or the SHN specific domain, producing PeERF1_SHN-silenced plants. Using cryo-SEM, we found that the number of nanoridges was reduced only in the PeERF1_AP2-silenced group. This change was found on both the abaxial and adaxial surfaces of the central lip lobe. Expression of PeERF1 was reduced significantly in PeERF1_AP2-silenced plants. In cutin biosynthesis genes, expression of both PeCYP86A2 and PeDCR was significantly decreased in both groups. The expression of PeCYP77A4 was reduced significantly only in the PeERF1_AP2-silenced plants. Although PeGPAT expression was reduced in both silenced plants, but to a lesser degree. The expression of PeERF1 was significantly reduced in the petal-like lip of a big-lip variant. PeCYP77A4 and PeGPAT in the lip were also reduced, but PeDCR was not. Furthermore, heterologous overexpression of PeERF1 in the genus Arabidopsis produced leaves that were shiny on the adaxial surface. Taken together, our results show that in Phalaenopsis orchids PeERF1 plays an important role in formation of nanoridges during lip epidermis development.

Background and Aims Although abscisic acid (ABA) is commonly recognized as a primary cause of seed dormancy, there is a lack of information on the role of ABA during orchid seed development. In order to address this issue, the localization and quantification of ABA were determined in developing seeds of Cypripedium formosanum. Methods The endogenous ABA profile of seeds was measured by enzyme-linked immunosorbent assay (ELISA). Temporal and spatial distributions of ABA in developing seeds were visualized by immunohistochemical staining with monoclonal ABA antibodies. Fluoridone was applied to test the causal relationship between ABA content and seed germinability. Key Results ABA content was low at the proembryo stage, then increased rapidly from 120 to 150 days after pollination (DAP), accompanied by a progressive decrease in water content and seed germination. Immunofluorescence signals indicated an increase in fluorescence over time from the proembryo stage to seed maturation. From immunogold labelling, gold particles could be seen within the cytoplasm of embryo-proper cells during the early stages of seed development. As seeds approached maturity, increased localization of gold particles was observed in the periplasmic space, the plasmalemma between embryo-proper cells, the surface wall of the embryo proper, and the inner walls of inner seed-coat cells. At maturity, gold particles were found mainly in the apoplast, such as the surface wall of the embryo proper, and the shrivelled inner and outer seed coats. Injection of fluoridone into capsules resulted in enhanced germination of mature seeds. Conclusions The results indicate that ABA is the key inhibitor of germination in C. formosanum. The distinct accumulation pattern of ABA suggests that it is synthesized in the cytosol of embryo cells during the early stages of seed development, and then exported to the apoplastic region of the cells for subsequent regulatory processes as seeds approach maturity.

Additional file 2. Additional information.

Additional file 1: Table S1. Voucher and GenBank accession number of plant materials used in this study. An asterisk (*) denotes the sequences of species that were obtained from GenBank.

Summary The lily anther-specific gene, LLA1271, encodes an adhesin-like protein found for the first time in higher plants. The protein is deposited on the surface of microspores, moderately affecting exine formation., The anther-specific gene LLA1271 isolated from lily (Lilium longiflorum Thunb.) anthers is novel and exists in two forms. The protein encoded by LLA1271 may represent an adhesin-like protein first found in higher plants. The protein contains a typical N-terminal signal peptide followed by a highly conserved repeat domain. The LLA1271 gene is temporally expressed at the phase of microspore development. RNA blot and RNA in situ hybridization analyses demonstrated that the gene was expressed both in the tapetum and in the microspore. The gene is endo- and exogenously induced by gibberellin. Studies with the gibberellin biosynthesis inhibitor uniconazole and an inhibitor of ethylene activity, 2,5-norbornadien (NBD), revealed that LLA1271 is negatively regulated by ethylene, and a cross-talk of regulation between gibberellin and ethylene occurs in young anthers. The treatment with NBD caused the tapetum to become densely cytoplasmic and highly polarized, whereas uniconazole arrested tapetal development in a state close to that of a tapetum without treatment. The LLA1271 protein is heat stable and heterogeneous. An immunoblot of separated protein fractions of the anther revealed that the LLA1271 protein was detected in protein fraction of the microspore released from the cell wall by treatment with either 0.5% or 2% Triton X-100. Ectopic expression of LLA1271 resulted in impaired stamen and low pollen germination. Scanning electron microscopy of TAP::LLA1271 pollen showed distorted exine formation and patterning. The LLA1271 protein once synthesized in both the tapetum and microspore is secreted and deposited on the surface of microspores, moderately affecting exine formation and patterning.

The Phalaenopsis orchid produces complex flowers that are commercially valuable, which has promoted the study of its flower development. E-class MADS-box genes, SEPALLATA (SEP), combined with B-, C- and D-class MADS-box genes, are involved in various aspects of plant development, such as floral meristem determination, organ identity, fruit maturation, seed formation and plant architecture. Four SEP-like genes were cloned from Phalaenopsis orchid, and the duplicated PeSEPs were grouped into PeSEP1/3 and PeSEP2/4. All PeSEPs were expressed in all floral organs. PeSEP2 expression was detectable in vegetative tissues. The study of protein-protein interactions suggested that PeSEPs may form higher order complexes with the B-, C-, D-class and AGAMOUS LIKE6-related MADS-box proteins to determine floral organ identity. The tepal became a leaf-like organ when PeSEP3 was silenced by virus-induced silencing, with alterations in epidermis identity and contents of anthocyanin and chlorophyll. Silencing of PeSEP2 had minor effects on the floral phenotype. Silencing of the E-class genes PeSEP2 and PeSEP3 resulted in the downregulation of B-class PeMADS2-6 genes, which indicates an association of PeSEP functions and B-class gene expression. These findings reveal the important roles of PeSEP in Phalaenopsis floral organ formation throughout the developmental process by the formation of various multiple protein complexes.

Orchidaceae, one of the largest angiosperm families, has significant commercial value. Isolation of genes involved in orchid floral development and morphogenesis, scent production, and colouration will advance knowledge of orchid flower formation and facilitate breeding new varieties to increase the commercial value. With high-throughput virus-induced gene silencing (VIGS), this study identified five transcription factors involved in various aspects of flower morphogenesis in the orchid Phalaenopsis equestris. These genes are PeMADS1, PeMADS7, PeHB, PebHLH, and PeZIP. Silencing PeMADS1 and PebHLH resulted in reduced flower size together with a pelaloid column containing petal-like epidermal cells and alterations of epidermal cell arrangement in lip lateral lobes, respectively. Silencing PeMADS7, PeHB, and PeZIP alone resulted in abortion of the first three fully developed flower buds of an inflorescence, which indicates the roles of the genes in late flower development. Furthermore, double silencing PeMADS1 and PeMADS6, C- and B-class MADS-box genes, respectively, produced a combinatorial phenotype with two genes cloned in separate vectors. Both PeMADS1 and PeMADS6 are required to ensure the normal development of the lip and column as well as the cuticle formation on the floral epidermal cell surface. Thus, VIGS allows for unravelling the interaction between two classes of MADS transcription factors for dictating orchid floral morphogenesis.

Intragenomic variability is known to be present in multi-copy gene sequences of several plant species and causes severe problems on molecular phylogenetic analysis. Initial investigation revealed extensive presence of intragenomic variability in nrITS of Camellia. Detailed investigation using 20–30 sequences from each leaf sample of seven species of Camellia revealed considerable sequence variability in terms of Kimura pair-wise distance, nucleotide diversity and Tamura's D parameters. Fluorescence in situ hybridization (FISH) revealed the dispersion of rDNA loci into multiple chromosomes and a small percentage of species in Camellia were allotetraploids. The distribution of rDNA loci into nonhomologous chromosomes along with long generation period and incidence of the interspecific hybridization are considered the major reasons for the failure of complete homogenization of the nrITS repeats by concerted evolution in Camellia. Nevertheless, in the majority diploid species or in the dominant sequence types of the allotetraploids, nrITS sequence variability was not high enough to obliterate the phylogenetic signals. Thus, utilization of nrITS in the phylogeny of Camellia is still possible, if adequate care is taken.

Pollination is composed of cell-cell communication and complicated signaling cascades that regulate pollen tube growth and guidance toward the ovules for double fertilization, and is critical for successful sexual reproduction. Exploring expression profiles of in vivo grown pollen tubes is important. Nevertheless, it is difficult to obtain accessible pollen tubes for profiling studies in most model plants. By taking advantage of the hollow styles of lily (Lilium longiflorum), in vivo pollen tubes harvested from pollinated styles which had been cut open were used here to study their protein and transcript profiles. Pollination quantitatively and qualitatively altered the total protein composition of elongating pollen tubes. cDNAs generated and amplified from total RNAs of 24 h in vivo grown and 12 h in vitro cultured pollen tubes were used for suppression subtractive hybridization analyses and preparation of home-made array chips. Microarray analyses conducted with different probe sets revealed 16 transcripts specifically present and/or enriched in in vivo pollen tubes. Reverse transcription-PCR (RT-PCR), in situ hybridization and Northern blotting were applied to validate their unique pollination-induced expression features. Interestingly, several transcripts were simultaneously detected on the stylar transmitting tract epidermis, where in vivo pollen tubes tightly adhered during pollination. Their deduced amino acid sequences showed that most of them encoded small proteins and could be classified into several families. Transient assay revealed filament-like structures decorated by these proteins and one probably localized in the generative cell. These small peptides might be critical for pollen tube growth during pollination, and further exploration of their biological functions and mechanisms of action are of great interest.

Background and aims Lady's slipper orchids (Paphiopedilum) are of high value in floriculture, and interspecific hybridization has long been used for breeding improved cultivars; however, information regarding the genome affinities of species and chromosome pairing behaviour of the hybrids remains almost unknown. The present work analyses the meiotic behaviour of interspecific hybrids by genomic in situ hybridization and cytologically evaluates the genomic relationships among parental species. Methods Eight interspecific F(1) hybrids of Paphiopedilum species in various subgenera or sections were investigated in this study. The chromosome behaviour in meiosis of these interspecific hybrids was analysed and subjected to genomic in situ hybridization and fluorescent in situ hybridization. Key results Genomic in situ hybridization was demonstrated as an efficient method to differentiate between Paphiopedilum genomes and to visualize the chromosome pairing affinities in interspecific F(1) hybrids, clarifying the phylogenetic distances among these species. Comparatively regular chromosome pairing observed in the hybrids of P. delenatii × P. bellatulum, P. delenatii × P. rothschildianum and P. rothschildianum × P. bellatulum suggested high genomic affinities and close relationships between parents of each hybrid. In contrast, irregular chromosome associations, such as univalents, trivalents and quadrivalents occurred frequently in the hybrids derived from distant parents with divergent karyotypes, such as P. delenatii × P. callosum, P. delenatii × P. glaucophyllum, P. rothschildianum × P. micranthum and P. rothschildianum × P. moquetteanum. The existence of multivalents and autosyndesis demonstrated by genomic in situ hybridization in this study indicates that some micro-rearrangements and other structural alterations may also play a part in differentiating Paphiopedilum species at chromosomal level, demonstrated as different chromosome pairing affinities in interspecific hybrids. Conclusions The results indicate that genome homology and the interaction of genetic factors, but not chromosome number nor karyotype similarity, determine the chromosome pairing behaviour in Paphiopedilum hybrids.

Lycoris species of the Amaryllidaceae are important ornamental and medicinal plants in Asia. Karyotypes of Lycoris species have been studied extensively since the time when their chromosome numbers were first counted over 80 years ago. Based on karyotype, Lycoris taxa can be classified into the monomorphic A group, dimorphic MT group, and the sterile dikaryotype MT-A group. Numerous reports dealing with karyotype analysis and phylogenetic relationship in the genus Lycoris have been published. However, there are disputes and controversies regarding karyotype evolution resulting from lacking efficient and reliable markers for chromosome identification in the genus Lycoris. In this study, we applied fluorescent in situ hybridization (FISH) to visualize the 5S and 45S rDNA loci on chromosomes as landmarks for chromosome identification in Lycoris taxa. In total, 12 accessions of three karyotype groups, including nine species and three artificial dikaryotype hybrids, were investigated. A high degree of variation in the number and position of 5S and 45S rDNA loci was detected among Lycoris taxa. There were four to 14 FISH signals of 5S rDNAs and two to 12 FISH signals of 45S rDNAs observed in each investigated Lycoris accession. Lycoris accessions with the same karyotype 2n = 22A may have different numbers of rDNA loci, which distributed at different chromosomal positions. In an interspecific hybrid, the number and chromosomal position of both 5S and 45S rDNA loci were either the combinations of those in their parental species or considerably modified. Overlapping FISH signals of 5S and 45S rDNAs were colocalized with a 4′, 6-diamidino-2-phenylindole-positive band at the end of the p-arm on almost every T-type chromosome (but not the A-type chromosomes). Based on the features of T-type chromosomes, the possibility of centromeric fission in karyotypic evolution of Lycoris is discussed.

The genes encoding for 18S-5.8S-28S ribosomal RNA (rDNA) are both conserved and diversified. We used rDNA as probe in the fluorescent in situ hybridization (rDNA-FISH) to localized rDNAs on chromosomes of 15 accessions representing ten Oryza species. These included cultivated and wild species of rice, and four of them are tetraploids. Our results reveal polymorphism in the number of rDNA loci, in the number of rDNA repeats, and in their chromosomal positions among Oryza species. The numbers of rDNA loci varies from one to eight among Oryza species. The rDNA locus located at the end of the short arm of chromosome 9 is conserved among the genus Oryza. The rDNA locus at the end of the short arm of chromosome 10 was lost in some of the accessions. In this study, we report two genome specific rDNA loci in the genus Oryza. One is specific to the BB genome, which was localized at the end of the short arm of chromosome 4. Another may be specific to the CC genome, which was localized in the proximal region of the short arm of chromosome 5. A particular rDNA locus was detected as stretched chromatin with bright signals at the proximal region of the short arm of chromosome 4 in O. grandiglumis by rDNA-FISH. We suggest that chromosomal inversion and the amplification and transposition of rDNA might occur during Oryza species evolution. The possible mechanisms of cyto-evolution in tetraploid Oryza species are discussed.

Changes in endogenous abscisic acid (ABA) concentrations were investigated in developing seeds and the pretreated seeds of Calanthe tricarinata, a hard-to-germinate terrestrial orchid. ABA concentration was as low as 2.16 to 2.26 ng·mg−1 fresh weight at the proembryo stage [60 to 90 days after pollination (DAP)] and then continuously increased to 11.6 ng·mg−1 fresh weight at 210 DAP. Seed maturation was accompanied by a dramatic decrease in water content and a prominent accumulation of protein and lipid bodies within the embryo proper. The optimum time for asymbiotic seed germination was obtained from immature seeds at 150 DAP. At this stage, the embryo proper reached its maximum size, and the seedcoat became dehydrated and gradually shrunk into a thin layer. By 180 DAP, seed germination declined sharply as seed approached maturity. Mature seeds pretreated with ultrasound (45 min), 1% NaOCl (45 to 60 min), or 1N NaOH (45 min) were effective in improving the germination percentage and lowering seed ABA concentrations. Our results suggest that high concentrations of endogenous ABA in orchid seeds may play a critical role in arresting embryo growth and in preventing seed germination.

The repeat sequences occupied more than 50 % of soybean genome. In order to understand where these repeat sequences distributed in soybean genome and its related Glycine species, we examined three new repeat sequences—soybean repeat sequence (SBRS1, SBRS2 and SBRS3), some nonspecific repeat sequences and 45S rDNA on several Glycine species, including annual and perennial accessions in this study. In the annual species, G. soja, signals for SBRS1 and ATT repeat can be found on each chromosome in GG genome, but those for SBRS2 and SBRS3 were located at three specific loci. In perennial Glycine species, these three SBR repeat frequently co-localized with 45S rDNA, two major 45S rDNA loci were found in all tetraploid species. However, an extra minor locus was found in one accession of the G. pescadrensis (Tab074), but not in another accession (Tab004). We demonstrate that some repetitive sequences are present in all Glycine species used in the study, but the abundancy is different in annual or perennial species. We suggest this study may provide additional information in investigations of the phylogeny in the Glycine species. Electronic supplementary material The online version of this article (doi:10.1186/s40529-015-0103-9) contains supplementary material, which is available to authorized users.

Additional file 2. Table S2. Sequence of repeat sequences and probes used in the study.

The immunohistochemical technique enables us to visualize phytohormones, for example, abscisic acid (ABA) in plant cells. The distributions and levels of ABA would fluctuate dramatically in organs or tissues in response to environmental changes or developmental stages. The visualization of the spatial changes of ABA is crucial for understanding its physiological function. Here we present the procedures of ABA immunostaining of the seeds of a terrestrial orchid, Cypripedium formosanum using fluorochrome and immunocolloid gold labelings. Unlike the young and fresh tissues, desiccated mature seeds with strong hydrophobic characteristics of seed coats require a longer duration of prefixation and subsequent processing steps. To prevent artifactitious signals from nonspecific binding of antibodies or autofluorescence from lignified cell wall, procedures including pretreating antibodies, quenching the autofluorescence by Toluidine blue O (TBO) staining, and setting careful control staining conditions need to be implemented. Proper selection of a narrow band-pass filter is also necessary to optimize the detection of emission from conjugated fluorochrome to minimize the autofluorescence from the specimen. Though our protocol uses orchid seeds for demonstrating a complete ABA immunostaining procedure, it can be adapted for other plant seeds, or the hard and dry tissues.

Fluorescence in situ hybridization (FISH) enables us to visualize the physical position of specific DNA sequences in chromosomes spread on a slide, making it possible to study cytogenetics at the molecular level. It involves hybridization of a specific DNA sequence with the complementary DNA spread on a slide and the immunological detection and visualization of those hybridization sites. Genome in situ hybridization (GISH) is a modified version of FISH to use total genomic DNA labeled as a probe. It is often used to differentiate the parental chromosomes in an interspecific hybrid and to reveal the genome components of a polyploid. FISH to plant chromosomes is thought to be more difficult than to animal species mainly because of the cell wall and viscous cytoplasm. Therefore, preparation of chromosome spreads is crucial for satisfactory FISH/GISH results with plant materials. Here we share our experience in preparing plant chromosome spreads for FISH analysis. We also provide a brief FISH procedure for beginners who want to perform FISH analysis of their materials. With the principles described here, a routine FISH/GISH protocol to obtain high-quality FISH images for publication can be established with continuous practice and modification.

The anti-microbial protein was frequently used to control the plant bacterial disease. In this study, it was investigated that the anti-microbial activity of recombinant plant ferredoxin-like protein (PFLP) both in vitro and in vivo. The in vitro assay demonstrated that PFLP produced by transformed Escherichia coli exhibited an anti-microbial activity against several bacteria strain including E. coli, Erwinia carotovora and Pseudomonas syringae. The effectiveness of this anti-microbial activity was depending on the FeSO4 that was applied in the cultivated medium. PFLP lost its anti-microbial activity when it was mutated in the 86th cysteine residue that responding for iron binding. Besides, soft-rot symptom of tobacco plants infected by E. carotovora was reduced by application of recombinant PFLP. Transgenic tobacco ectopically over expressing PFLP in the cytoplasm protected plant from the infection of E. carotovora during the initial stage. These results indicate that PFLP is an anti-microbial protein that might be able to control the plant diseases via reducing the growth of bacterial pathogen. # 2006 Elsevier Ireland Ltd. All rights reserved.

The developments of molecular marker-based genetic linkage maps are now routine. Physical maps based on contigs of large insert genomic clones have been established in several plant species. However, integration of genetic, physical, and cytological maps is still a challenge for most plant species. Here we present an integrated map of rice (Oryza sativa L.) chromosome 5, developed by fluorescence in situ hybridization mapping of 18 bacterial artificial chromosome (BAC) clones or PI-derived artificial chromosome (PAC) clones on meiotic pachytene chromosomes. Each BAC/PAC clone was anchored by a restriction fragment length polymorphism marker mapped to the rice genetic linkage map. This molecular cytogenetic map shows the genetic recombination and sequence information of a physical map, correlated to the cytological features of rice chromosome 5. Detailed comparisons of the distances between markers on genetic, cytological, and physical maps, revealed the distributions of recombination events and molecular organization of the chromosomal features of rice chromosome 5 at the pachytene stage. Discordance of distances between the markers was found among the different maps. Our results revealed that neither the recombination events nor the degree of chromatin condensation were evenly distributed along the entire length of chromosome 5. Detailed comparisons of the correlative positions of markers on the genetic, cytological, and physical maps of rice chromosome 5 provide insight into the molecular architecture of rice chromosome 5, in relation to its cytological features and recombination events on the genetic map. The prospective applications of such an integrated cytogenetic map are discussed.

A fine physical map of the rice (Oryza sativa spp. Japonica var. Nipponbare) chromosome 5 with bacterial artificial chromosome (BAC) and PI-derived artificial chromosome (PAC) clones was constructed through integration of 280 sequenced BAC/PAC clones and 232 sequence tagged site/expressed sequence tag markers with the use of fingerprinted contig data of the Nipponbare genome. This map consists of five contigs covering 99% of the estimated chromosome size (30.08 Mb). The four physical gaps were estimated at 30 and 20 kb for gaps 1-3 and gap 4, respectively. We have submitted 42.2-Mb sequences with 29.8 Mb of nonoverlapping sequences to public databases. BAC clones corresponding to telomere and centromere regions were confirmed by BAC-fluorescence in situ hybridization (FISH) on a pachytene chromosome. The genetically centromeric region at 54.6 cM was covered by a minimum tiling path spanning 2.1 Mb with no physical gaps. The precise position of the centromere was revealed by using three overlapping BAC/PACs for approximately 150 kb. In addition, FISH results revealed uneven chromatin condensation around the centromeric region at the pachytene stage. This map is of use for positional cloning and further characterization of the rice functional genomics.

This investigation documents the key anatomical features in embryo development of Cypripedium formosanum Hayata, in association with the ability of embryos to germinate in vitro, and examines the effects of culture media and seed pretreatments on seed germination. A better understanding of zygotic embryogenesis for the Cypripedium L. species would provide insights into subsequent germination events and aid in the in vitro propagation of these endangered species. In seeds collected at 60 days after pollination (DAP), soon after fertilization, no germination was recorded. The best overall germination was found at 90 DAP (≈70%), at which time early globular to globular embryos with a single-celled suspensors can be observed. After 135 DAP, the seeds germinated poorly. At this time the inner integument shrinks and forms a tight layer, which encloses the embryo, the so-called “carapace.” Using Nile red stain, a cuticular substance was detected in the carapace, which may play a role in the impermeability of the mature seed and may help the seeds survive in the stringent environment. At maturity (after 210 DAP), the embryo proper has an average size of eight cells along its length and six cells across the width. Lipids and proteins are the main storage products within the embryo. To improve seed germination, experiments were conducted to test the suitability of various media and pretreatments of seeds. When different media were used, except for the Harvais medium at 120 DAP, there was no significant difference in seed germination at three different developmental stages tested. Soaking mature seeds in 1% NaOCl or treating them with ultrasound may slightly increase the germination percentage. For seed germination, our results indicate that the timing of seed collection outweighs the composition of medium and the seed pretreatments.

Rice, one of the world's most important food plants, has important syntenic relationships with the other cereal species and is a model plant for the grasses. Here we present a map-based, finished quality sequence that covers 95% of the 389 Mb genome, including virtually all of the euchromatin and two complete centromeres. A total of 37,544 non-transposable-element-related protein-coding genes were identified, of which 71% had a putative homologue in Arabidopsis. In a reciprocal analysis, 90% of the Arabidopsis proteins had a putative homologue in the predicted rice proteome. Twenty-nine per cent of the 37,544 predicted genes appear in clustered gene families. The number and classes of transposable elements found in the rice genome are consistent with the expansion of syntenic regions in the maize and sorghum genomes. We find evidence for widespread and recurrent gene transfer from the organelles to the nuclear chromosomes. The map-based sequence has proven useful for the identification of genes underlying agronomic traits. The additional single-nucleotide polymorphisms and simple sequence repeats identified in our study should accelerate improvements in rice production.

Overexpression of bacterial-derived starch metabolic enzymes in plant starch storage organs represents a valuable strategy for improving starch quality, bioprocessing and nutritional value. Transgenic rice seeds producing a thermostable and bifunctional starch hydrolase, amylopullulanase (APU) from Thermoanaerobacter ethanolicus 39E, were generated. Starch in these seeds could be hydrolyzed with optimal temperatures between 85 and 95 °C, which resulted in complete conversion of starch into soluble sugars and production of protein-enriched flour within a few hours. By expressing various levels of APU, rice seeds containing reduced amounts of amylose, which is an important factor affecting starch quality, were obtained without a significant impact on grain yield. Elevation in granule-bound pullulanase activity correlates with the reduction of amylose in developing APU-containing rice seeds. APU was found to be localized within amyloplasts and in cell walls, which could be the result of overexpression of APU with a signal peptide. This study establishes novel approaches to alter starch properties, accelerate bioprocessing of starch and production of protein-enriched flour from rice seeds, and could significantly impact the industrial and food uses of cereals.

Rice oil bodies enclosed by unique structural proteins, oleosins, are found in the embryo and the aleurone layer, but not the starchy endosperm where starch and storage proteins are accumulated. To examine oleosin promoter specificity, a sesame storage protein, 2S albumin, was expressed in transgenic rice seeds under the control of a rice oleosin promoter. In all transgenic rice seeds, the sesame 2S albumin was found exclusively in the bran fraction after milling. Immunological staining revealed that the sesame 2S albumin was also located in the embryo and the outermost cells of the starchy endosperm. Furthermore, immunogold labeling showed that the transgenic 2S albumin was deposited in both type-I and type-II protein bodies of the outermost cells of the endosperm as well as in the type-II protein bodies of the embryo. The methionine and cysteine contents in the bran from four homozygous transgenic lines were elevated by 24–38 and 50–62%, respectively, compared with those of wild-type plants. The results suggest that the rice oleosin promoter is bran-specific and could be used to add value to rice bran, an abundant by-product of rice polishing, by genetic engineering.

The hypersensitive response (HR) is a form of cell death associated with plant resistance to pathogen infection. Harpinpss, an elicitor from the bacterium Pseudomonas syringae pv. syringae, induces a HR in non-host plants. Previously, we reported an amphipathic protein from sweet pepper interfering with harpinpss-mediated HR. In this report, we isolated and characterized a cDNA clone encoded that amphipathic protein from sweet pepper. This protein is designated as PFLP (plant ferredoxin-like protein) by virtue of its high homology with plant ferredoxin protein containing an N-terminal signal peptide responsible for chloroplast targeting and a putative 2Fe-2S domain responsible for redox activity. Recombinant PFLP obtained from Escherichia coliwas able to significantly increase active oxygen species (AOS) generation when mixed with harpinpss in tobacco suspension cells. It also showed enhanced HR when co-infiltrated with harpinpss in tobacco leaves. We used a transgenic tobacco suspension cells system that constitutively expresses the Pflpgene driven by the CaMV 35S promoter to study the function of PFLP in enhancing harpinpss-mediated hypersensitive cell death in vivo. In response to harpinpss, suspension cells derived from Pflptransgenic tobacco showed a significant increase both in the generation of AOS and in cell death as compared to the wild type. AOS inhibitors diphenylene iodonium chloride (DPI) and lanthanum chlorate (LaCl3) were used to study the involvement of AOS in harpinpss-induced cell death. Our results demonstrate enhanced generation of AOS is necessary to cause enhanced hypersensitive cell death in Pflp transgenic tobacco cells and it is plasma membrane-bound NADPH-oxidase-dependent. Sub-cellular localization studies showed that PFLP is present in the cytoplasm and chloroplast of Pflp transgenic tobacco cells, but only in the chloroplast, not in the cytoplasm, of wild-type tobacco cells. It is possible that PFLP can change the redox state of the cell upon harpinpss inoculation to increase AOS generation and hypersensitive cell death. Overall, this study will provide a new insight in the functional properties of ferredoxin in hypersensitive cell death.

In many eukaryotic organisms, homeobox genes are important regulators that specify the cell fate and body plan in early embryogenesis. In this study, a gene designated OSTF1 (Oryza sativa transcription factor 1) encoding a homeodomain protein in rice was isolated and characterized. The encoded OSTF1, although sharing only approximately 51% sequence identity with other HD-GL2 members, contains four characteristic motifs (an N-terminal acidic region, a homeodomain, a truncated leucine zipper, and a START domain). OSTF1 was detected as a single copy gene in rice. The transcripts were absent in young panicle or mature spikelet before anthesis, but appeared very early in the pollinated grain with a transient profile. In vegetative tissues examined, expression was only detectable in root. In situ hybridization analysis on developing grains revealed that OSTF1 was strongly and uniformly expressed in the embryo at the globular stage and preferentially localized to the protoderm at 3–6 d after pollination. Expression was also detectable in the integument and throughout the endosperm. Although OSTF1 is not closely related to the remaining HD-GL2 members in sequences, this gene exhibits an analogous epidermis-preferential expression pattern.

1-Aminocyclopropane-1-carboxylic acid (ACC) oxidase catalyzes the oxidation of ACC to the gaseous plant hormone, ethylene. Although the enzyme does not contain a typical N-terminal consensus sequence for the transportation across the endoplasmic reticulum (ER), it has recently been shown to locate extracellularly by immunolocalization study. It was of interest to examine whether the enzyme contains a signal peptide that is overlooked by structure prediction. We observed that the in vitro translated apple ACC oxidase was not co-processed or imported by the canine pancreatic rough microsomes, a system widely used to identify signal peptide for protein translocation across ER, suggesting that apple ACC oxidase does not contain a signal peptide for ER transport. A highly specific polyclonal antibody raised against the recombinant apple ACC oxidase was used to examine the subcellular localization of the enzyme in apple fruit (Malus domestica, var. Golden Delicious). The location of ACC oxidase appeared to be mainly in the cytosol of the apple fruit pericarp tissue as was demonstrated by electron microscopy using immunogold-labeled antibodies. The pre-immune serum or pre-climacteric fruit control gave essentially no positive signal. Based on these observations, we conclude that ACC oxidase is a cytosolic protein.

A wounded gene WI12 was used as a marker to examine the interaction between biotic stress (wounding) and abiotic stress (high salt) in the facultative halophyte ice plant (Mesembryanthemum crystallinum). The deduced WI12 amino acid sequence has 68% similarity to WUN1, a known potato (Solanum tuberosum) wound-induced protein. Wounding, methyl jasmonate, and pathogen infection induced localWI12 expression. Upon wounding, the expression ofWI12 reached a maximum level after 3 h in 4-week-old juvenile leaves, whereas the maximum expression was after 24 h in 8-week-old adult leaves. The temporal expression ofWI12 in salt-stressed juvenile leaves was similar to that of adult leaves. The result suggests that a salt-induced switch from C3 to Crassulacean acid metabolism has a great influence on the ice plant's response to wounding. The expression ofWI12 and the accumulation of WI12 protein were constitutively found in phloem and in wounded mesophyll cells. At the reproductive stage, WI12 was constitutively found in petals and styles, and developmentally regulated in the placenta and developing seeds. The histochemical analysis showed that the appearance of WI12 is controlled by both environmental and developmental factors. Immunogold labeling showed WI12 preferentially accumulates in the cell wall, suggesting its role in the reinforcement of cell wall composition after wounding and during plant development.

The chromosomal instability described herein occurred spontaneously among the progenies of Triplo 1 and Triplo 4, which are two of the twelve rice trisomic lines established at IRRI. In Triplo 1, some trisomic plants have been identified to have an extra chromosome 8 instead of extra chromosome 1. Cytological evidence revealed that the instability found in Triplo 1 was originated from the breakage of chromosome 8. The resulting chromosomal fragment carrying mainly heterochromatin could provoke chromosome non-disjunction at meiosis. We suggest that the appearance of non-parental trisomics was resulted from the event of non-disjunction of chromosomes 8. Since the longer chromosomes would cause more imbalance than the shorter ones, chromosome 8 is much smaller than chromosome 8 and greatly favored its transmission over chromosome 1 as extra chromosome found among the trisomic progenies of Triplo 1. Triplo 4 had been previously designated as Triplo 12 for having a very short extra chromosome. In this study, we present the evidence indicating that the instability of Triplo 4 was induced by two subsequent breaks of chromosome 4.

During the past three decades, Nishimura's reciprocal translocation lines of rice have been used in rice cytogenetics to locate genes on chromosomes, to number extra chromosomes of trisomic series and to associate individual linkage groups with specific chromosomes. In this report, we present our identification of the chromosomes involved in 11 of Nishimura's translocation lines using both meiotic pachytene and mitotic prometaphase chromosome analysis. In addition, the numbering of the 12 linkage groups suggested by Nagao and Takahashi, and modified later by many workers, has been revised to agree with the numbering of the identified chromosomes.