Contents. Foreword. ORCHID BIOTECHNOLOGY II World Scientific Publishing Co. Pte. Ltd.

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1 Foreword Preface v vii 1. Molecular Phylogeny and Biogeography of Phalaenopsis Species Introduction Biogeographical Pattern of Genus Phalaenopsis Molecular Phylogeny and Biogeography of the Phalaenopsis Species Phylogenetics and biogeography of the genus Phalaenopsis Molecular phylogenetics of Phalaenopsis Biogeography Phylogenetics and biogeography of the Phalaenopsis amabilis complex Phylogenetics and biogeography of the Phalaenopsis sumatrana complex Molecular phylogenetics Biogeography and evolutionary trends Phylogenetics and biogeography of the Phalaenopsis violacea complex Phylogenetics, biogeography and evolutionary trends of the Phalaenopsis lueddemanniana complex References ix

2 x Contents 2. Endopolyploidy in Phalaenopsis Orchids and Its Application in Polyploid Breeding Introduction Endopolyploidy and its occurrence in plants Endopolyploidy in orchid species Polyploidy in orchids and its significance in variety improvement Endopolyploidy in Phalaenopsis Endopolyploidy in ovule and seed development Endopolyploidy in different tissues at different stages of plant development Production of Polyploid Plants through Endopolyploidy in Phalaenopsis Previous research on spontaneous chromosome doubling through tissue culture Production of polyploid plants by excision of protocorms or protocorm-like bodies (PLBs) Performance of polyploidy plants developed from protocorm-like bodies Polyploid Breeding in Phalaenopsis Major problems in the breeding of Phalaenopsis orchids Chromosome doubling as a means of solution Comprehensive polyploid breeding program for Phalaenopsis orchids A database for the nuclear DNA content of Phalaenopsis species... 41

3 xi A conversion program of diploid Phalaenopsis species to tetraploid Extension and utilization of polyploid germplasm Conclusion and Prospects References Growth Responses and Changes of Active Components as Influenced by Elevations and Orchid Mycorrhizae on Anoectochilus Formosanus Hayata Introduction The medicinal effect of A. formosanus The propagation of A. formosanus PBCM combined with the inoculation ofomf Results Plastic bag cultivation method (PBCM) Inoculation of OMF for the cultivation of A. formosanus Analysis of the antioxidant capacity Comparison and analysis of phenolic compounds Test of Trolox equivalent antioxidant capacity Analysis of the hepatoprotective components Conclusions References A Practical Method for Monitoring the Fertility of Sphagnum Moss During Phalaenopsis Cultivation Introduction Validation of the Pour-through Method for Phalaenopsis Cultivation with Sphagnum Moss... 67

4 xii Contents 4.3 Establishment of a Standard Pour-through Procedure for Fertility Monitoring of Sphagnum Moss Practical Application and Some Considerations Discussion Conclusion and Perspectives References Compositional Variation in the Polysaccharides of the Pseudobulb of Oncidium Gower Ramsey During Different Stages of Inflorescence Development Introduction Biochemical Characterization of Polysaccharides in the Pseudobulb Extraction of polysaccharide components at various growth stages of the pseudobulb Extraction of mannans Extraction of pectins Polysaccharide hydrolysis procedures and high performance anion exchange chromatography with pulsed amperometric detection (HPAEC-PAD) analysis Mannan and pectin profiles in different developmental stages of the pseudobulb Conclusions Future Prospects References Coloration and Color Patterning in Floral Tissues of Oncidium Gower Ramsey Introduction Color Pattern in Floral Tissues of Oncidium Hybrid

5 xiii HPLC analysis of anthocyanin in Oncidium floral tissues Gene expression pattern of anthocyanin biosynthesis Regulatory analysis of anthocyanin biosynthesis Conclusion References Qualitative and Quantitative Analysis of Pigments in Phalaenopsis Species Introduction Constituents of the Phalaenopsis Species Anthocyanins Flavonoids Others The bioactivity of pigments from Phalaenopsis species and their application Quantification of Pigments in Phalaenopsis Species Analysis of native Phalaenopsis species Analysis of Phalaenopsis cultivars Conclusions and Future Prospects References Biosynthetic Pathway of Pigments in Phalaenopsis Species Introduction Common Biosynthetic Pathway of Anthocyanins Phenylpropanoid metabolism leading to flavonoids and anthocyanins Colors of different anthocyanins Stabilization of anthocyanins

6 xiv Contents 8.3 Biosynthesis of Anthocyanins in Phalaenopsis Species Role of glucosyltransferase (GT) in anthocyanin formation Genes involved in color formation in plants Expression of UFGT genes in Phalaenopsis species Proposed pathway for the pigments in Phalaenopsis species Conclusions and Future Prospects References Biosynthetic Regulation of Floral Scent in Phalaenopsis Introduction Significance of the floral/orchid scent Floral scent of Phalaenopsis Difficulty of orchid scent research Reasons for studying P. bellina Scent Biosynthesis Pathway Strategy to isolate scent biosynthesis pathway in P. bellina Scent biosynthesis pathway and related pathway Scent biosynthesis pathway Scent related gene Critical enzyme for scent biosynthesis Characterization and Significance of Geranyl Diphosphate Synthase Gene in Phalaenopsis The role of PbGDPS Molecular cloning and sequence analysis of PbGDPS Functional characterization of recombinant PbGDPS

7 xv Expression patterns of PbGDPS in Phalaenopsis PbGDPS protein behaviors Homology modeling of the PbGDPS structure Site-directed mutagenesis of the Glu-rich motif Phylogenetic relationships of PbGDPS Conclusions Perspectives References Warm- and Cool-Night Temperatures Alter Carbon Dioxide Fixation Pattern and Biochemical Metabolism in Phalaenopsis aphrodite Introduction Different Night Temperature Affects Photosynthesis Chlorophyll a fluorescence Gas exchange Different Night Temperature Affects Biochemical Metabolisms Organic acids Metabolizable carbohydrates Related-enzyme activities The Relationship between Spike Induction and Diurnal Changes in Carbohydrates Conclusion References Flower Development in the Oncidium Orchid Introduction The ABCDE model for flower development

8 xvi Contents Flower development in nongrass monocots The Oncidium flower as a model system Characterization of Oncidium MADS Box Genes A/E class genes and flower transition B class genes and perianth formation C, D class genes and sexual organ formation Flower Modification Modification of the perianth of the Oncidium flower Other applications of Oncidum MADS box genes Conclusions and Future Prospects References The Relationship Between Ethylene and Orchid Ovule Development Introduction Ethylene biosynthesis and ethylene signal transduction Orchid reproductive biology The Unique Control System for Orchid Ovule Development Categories of ovule development in Orchidaceae Orchid ovule morphogenesis Benefit of a unique control system for orchid ovule development Ethylene is Involved in Orchid Ovule Development Ethylene function in plant physiology and development Evidence of ethylene involved in orchid ovule development

9 xvii Expression of Phal-ACS is regulated by pollination Phosphorylation status of Phal-ACS correlated with ethylene production in the ovary Orchid GLOBOSA-like Gene, PeMADS6, Involved in Ovary/ovule Development via a Mode of Action by Auxin/ethylene Expression of PeMADS6 is correlated to pollination Expression of PeMADS6 is regulated by auxin and ethylene Future Prospects References The Application of the Chloroplast Genome of Oncidium in Plant Identification and Breeding in Oncidiinae Introduction Plant identification and breeding in Oncidium PCR is a simple method for chloroplast genome sequencing The Chloroplast Genome of Oncidium Gower Ramsey The structure and characterization of the chloroplast genome of Oncidium Grower Ramsey Broad phylogenetic analysis Analysis of Variability in ndh Genes of 15 Oncidium Species The ndh gene deletion in Oncidiinae cpdna Chloroplast genome deletion in plants Phylogenetic Analysis of 15 Oncidium Species Phylogenetic analysis of orchids

10 xviii Contents Multiple sequence combination is a good method for phylogenetic analysis Conclusions Future Prospects References Analysis of Chloroplast RNA Editing Sites in Phalaenopsis aphrodite Introduction RNA editing and regulation of gene function Cis-elements surrounding the editing sites Protein factors involved in RNA editing Determination of Chloroplast RNA Editing Sites in P. aphrodite RNA extraction and RT-PCR Determination of RNA editing sites Chloroplast RNA Editing Patterns in P. aphrodite Overall properties of chloroplast RNA editing in P. aphrodite RNA editing in transcripts encoding for genetic apparatuses RNA editing in transcripts encoding for photosynthetic apparatuses RNA editing in transcripts encoding for miscellaneous proteins Future Prospects References Molecular Characterization of the Early Response of Orchid Phalaenopsis amabilis to Erwinia Chrysanthemi Infection Introduction Pathogenesis of E. chrysanthemi in Orchids

11 xix 15.3 Signaling Transduction in Orchids During Early Infection with E. chrysanthemi Strategy for isolating genes encoding protein kinases and phosphatases Calcium-dependent protein kinases Sequence analysis of PaCDPK1 from P. amabilis Expression of the PaCDPK1 gene in response to E. chrysanthemi Promoter activity of the PaCDPK1 gene in response to E. chrysanthemi Protein Tyrosine Phosphatases Sequence analysis of PaPTP1 from P. amabilis Expression of the PaPTP1 gene in response to wounding and E. chrysanthemi The PaPTP1 gene encoded a functional PTP Genome-Wide Responses of Orchid Plants to E. chrysanthemi Infection Strategy for studying transcriptional regulation during the pathogenesis Pathogen-responsive expressed sequence tags (ESTs) in orchids Functional significance of the pathogen-responsive ESTs Conclusions and Future Prospects References Identification and Characterization of New Phalaenopsis Orchid-Infecting Viruses Orchid-Infecting Viruses Orchid-infecting viruses Phalaenopsis orchid-infecting viruses

12 xx Contents Challenges of the identification of new Phalaenopsis orchid-infecting viruses Capsicum Chlorosis Virus (CaCV-Ph) Virus isolation and serological test Virus identification Back-inoculation Significance of CaCV-Ph Phalaenopsis Chlorotic Spot Virus (PhCSV) Virus isolation and serological test Virus identification Back-inoculation Significance of PhCSV Carnation Mottle Virus (CarMV) Virus isolation and serological test Virus identification Significance of CarMV The Virus Causing a New Disease with Flower Crinkle in Phalaenopsis Virus isolation and serological test Virus identification Back-inoculation Significance of the virus Conclusion and Future Prospects References What We have Learned from Studies of the Differential Movement Mechanism of Cymbidium Mosaic Virus Introduction Two Distinct Isolates of CymMV Move Differentially Between Hosts Two Control Modes are Involved in CymMV Movement and CP Plays a Dominant Role in Movement The Movement Ability of CymMV is Associated with the Binding Affinity of CP and Viral RNA

13 xxi 17.5 Sequence Analysis Revealed that Orchids May Not be the Natural Hosts of CymMV Functional Diversity Generated by Potexviruses Through a Combination of Mutated Proteins from CymMV Quasi-Species Conclusions References Transgenic Protection Against Virus Infection in Orchids Introduction Viruses occurring naturally in orchids Isolates of CymMV and ORSV Control of orchid viruses Transgenic resistance to CymMV in orchids Generating Transgenic Orchids Preparation of transgene Transformation of orchids Molecular Characterization of Transgene Viral Resistance of Transgenic Plants Conclusions Future Prospects Application of CP-mediated protection for resistance against CymMV and ORSV in other orchids Integration of virus-derived fragments in transgenic orchids for virus resistance References Index 355

BIOLOGY YEAR AT A GLANCE RESOURCE ( )

BIOLOGY YEAR AT A GLANCE RESOURCE (2016-17) DATES TOPIC/BENCHMARKS QUARTER 1 LAB/ACTIVITIES 8/22 8/25/16 I. Introduction to Biology Lab 1: Seed Germination A. What is Biology B. Science in the real world