Day 1 :
Keynote Forum
Rachel Swee-Suak Ko
Professor, Agricultural Biotechnology Research Center, Taiwan
Keynote: Phalaenopsis aphrodite (moth orchid)- functional genomics and biotechnology
Time : 09:30 AM - 10:15 AM
Biography:
Rachel Swee-Suak Ko works for Academia Sinica Agricultural Biotechnology Research Center/ BCST, Taiwan R.O.C. She got her Ph.D. in National Chung Hsing University in Taiwan. The main focus of her research is to increase double spiking rate and increase flower production in Phalaenopsis orchid by manipulating the best environmental factors of CO2, LED lighting, and temperature. She is interested to understanding and discovers the complex molecular mechanisms that control spiking phenomenon in Phalaenopsis orchid. The basic knowledge gain will facilitate orchid production
Abstract:
Phalaenopsis aphrodite (moth orchid) is one of the most important ornamental crops in the international orchid market. In nature, this epiphytic orchid grows on the surface of trees. Phal. aphrodite has thick, succulent leaves and performs typical Crassulacean acid metabolism (CAM) photosynthesis. CAM orchids evolved to maximize carbon gain and simultaneously minimize water loss by opening their stomates at night under arid conditions, therefore, attaining high water use efficiency. However, several constraints such as slow growth rate, high ploidy levels, and large and complex of genome size might hamper basic study of this orchid.
The availability of next-generation sequencing technologies has greatly advanced the possibility of examination of sequence information in non-model crops. There are two orchid databases, named OrchidBase 2.0 and Orchidstra 2.0 freely available to the public in Taiwan. Notably, Orchidstra 2.0 provides transcriptomic resources for 18 orchid species including gene expression patterns in various tissues. The genome sequence of Phal. equestris was published in 2015, and recently, in April 2018, Academia Sinica further published the genome sequence of Phal. aphrodite. These databases and platforms facilitate functional genomics study and might speed up molecular breeding progress. In addition, several recent molecular technological advances might accelerate basic research, such as virus-induced gene silencing (VIGS) that provides transient, rapid testing for functional validation and screening of functional genes in orchids, and transient protoplast assay technology that can facilitate molecular study. Moreover, we developed a heritable and efficient Agrobacterium- mediated transformation using protocorms that enables functional genomics studies and molecular breeding.
Here, I will present two cases of functional genomics studies of Phal. aphrodite: chloroplast movement and multiple spiking. Plants are sessile; therefore, they have evolved mechanisms to regulate growth and development to cope with ever-changing environments. In general, this orchid is very sensitive to high light irradiation, which can lead to burn spots on the leaves. Phototropins are blue light receptors in plants that function in chloroplast movement, stomatal opening, and affect plant growth and development. We have characterized the function of two PHOTOTROPIN genes in chloroplast movement. For the second case, multiple spike induction and its mechanism in Phal. aphrodite will be discussed.
Keynote Forum
Magdy Montasser
Associate Professor , University of Kuwait, Biological Science
Keynote: Viral Satellite RNA as a Biological Control Agent Against Viral Diseases
Time : 10:15 AM - 11:00 AM
Biography:
Magdy Montasser has his expertise in Molecular Virology and Plant Pathology over the last 30 years of experience in research, evaluation, teaching and supervising graduate students towards M.Sc. He optained his Ph.D. degree from Rutgers University, New Jersey, USA in 1988, and Post Doctor at the University of Maryland. Currently working as an Associate Professor at the University of Kuwait, Biological Science
Abstract:
A naturally occurring satellite RNA possessed by the CMV strain was first characterized and then used as a biological control agent to protect tomato plants against the disease induced by another severe strain. Viability and infectivity of the virus in extracted nucleic acid inoculums was further proved using mechanical transmission method. Tomato plants were pre inoculated or “vaccinated” with the strain containing viral satellite RNA, and then challenge inoculated with the severe strain at different time intervals. All plants challenged three weeks after vaccination showed nearly complete protection from subsequent infection by the severe strain. This biological control technology of plant viruses was effective and could be successfully used as biological control agent at the molecular level.
Keynote Forum
Sachiko Isobe
Kazusa DNA Research Institute, Japan
Keynote: Genome sequencing in octoploid strawberry and its application to molecular breeding
Time : 10:45 AM - 11:30 AM
Biography:
Sachiko Isobe started her career as a conventional red clover breeder. Currently she is a plant molecular biologist, lab head of Plant Genomics and Genetics of Kazusa DNA Research Institute. The research group has performed genome sequencing and molecular genetics including DNA marker development, linkage map construction, QTL identification and marker assisted selection. More than 30 model and crop species have been targeted such as strawberry, sweetpotato, tomato, Lotus japonicus, groundnut, and clovers. Of these, strawberry is one of the main species, and comprehensive analysis has been performed such as genome sequencing, RNA-Seq and Genomic Selection.
Abstract:
Strawberry (Fragaria × ananassa) was artificially generated in the 16th century Europe by crossing between two octoploid species, F. chiloensis and F. virginiana. It is cultivated and consumed entire the world. Strawberry is an allo-polyploidy species (2n = 8X = 56) with an estimated genome size of 1C = 708–720 Mb. The complex structure of the polyploid genome has inhibited advances in genomics and genetic analysis We have sequenced a Japanese variety ‘‘Reikou’ with Illumina platform, and constructed subgenome-specific reference sequences by using DenovoMAGIC. A total of 62 (31 × 2 haplotypes) pseudomolecules were developed based on the linkage map in a total length of 1,125 Mb. The large structure differences among the sub-genomes were identified by comparison with the F. vesca genome. By using the constructed pseudomolecules, we have performed RNA-Seq analysis in fruit color. Genomic selection for fruit hardiness has also performed with the four strawberry breeding stations, i.e., National Agricultural Research Organization, Tochigi prefecture, Fukuoka prefecture and Chiba prefecture. The conventional GS requires genome wide genotyping for the both training and breeding populations. To decrease the cost and time for genotyping in the breeding population, we used Ensemble-based Genetic and Genomic Search (EGGS) that enable to make a model with less number of DNA markers. Genomic, genetic analysis and molecular breeding in polyploidy species is still difficult, however, the advance of NGS technologies as well as novel approaches for data analysis has made the challenge possible.
- Plant Genome Science | Agricultural Science | Plant Proteomics | Plant Reproduction | Plant Science | Horticulture | Molecular Plant Breeding |
Chair
Magdy Montasser
University of Biological Science, Kuwait
Co-Chair
Lerma SJ. Maldia
University of the Philippines Los Baños, Philippines
Session Introduction
Alexander Vainstein
The Hebrew University of Jerusalem, Israel
Title: Specialized metabolic pathways: cues controlling floral scent and color production
Time : 11:30 AM - 12:00 PM
Biography:
Alexander Vainstein is the Incumbent of the Wolfson Family Chair in Floriculture and served as a Visiting Professor at USDA and SUNY. He has published more than 140 scientific papers and books, developed 6 patents and has served as the Head of the Hebrew University Graduate Horticulture Program, Graduate Plant Sciences Program and Graduate Biotechnology Program. He was also the Head of The Institute of Plant Sciences and Genetics in Agriculture, Hebrew University of Jerusalem and has served as the President of the Israeli Society of Plant Sciences.
Abstract:
Odor and pigmentation play a prominent role in the location and selection of flowers by insects and hence in the successful production of farmed foods, as well as in maintaining ecological systems. In terms of commercial appeal, scent and color are also extremely important in the food and floriculture industries. Using virus-induced gene silencing/editing and expression approaches for large-scale identification of floral scent genes, we identified and characterized petunia flower-specific regulatory genes named Emission of Benzenoids (EOBs). Their involvement in the biosynthetic cascade leading to the production/emission of floral scent bouquets was detailed. We further demonstrated that PH4, a MYB gene that determines final petal hue through pH homeostasis in the early stages of flower development, is essential for emission, but not production, of the floral volatile bouquet in mature flowers. We also revealed that petunia flowers produce significant amounts of sugar-conjugated scent compounds with a unique diel accumulation pattern that are further catabolized in parallel to scent emission. These phenylpropanoid glycosides are stored in the vacuoles of petunia flowers, providing first evidence of subcellular compartmentalization of scent compounds. We revealed that gibberellin (GA) acts as a developmental cue regulating floral scent production in petunia. GA-dependent timing of the sequential activation of different branches of the phenylpropanoid pathway, products of which are responsible for either color or scent; both necessary for pollinator attraction; may represent an intriguing machinery developed by plants to enable intimate crosstalk between floral pollination syndromes. Integrating knowledge of the structural and regulatory genes involved in floral scent production with the mechanism regulating metabolic flow enabled us to rationally manipulate the pathway toward enhanced production of floral scent compounds and/or pigmentation. Olfactory assay revealed that bees and humans can distinguish the scent of genetically enhanced flowers.
Lerma SJ. Maldia
University of the Philippines Los Baños, Philippines
Title: Genetic diversity and structure of Gmelina arborea Roxb. and Falcataria moluccana (Miq.) Barneby & J.W.Grimes plantations in the Philippines based on microsatellites
Time : 12:00 PM - 12:30 PM
Biography:
Lerma S J Maldia has expertise in tree population genetics and molecular phylogenetics and phylogeography. She has recently established the Forest Genomics Laboratory of the College of Forestry and Natural Resources of UPLB. Currently, she is leading a number of similar genetic studies on various indigenous high value forest trees for their genetic conservation and sustainable utilization.
Abstract:
Statement of the Problem: In the Philippines, industrial tree plantations have the largest share to the country’s current total log production. Gmelina arborea and Falcataria moluccana (Paraserianthes falcataria) are two commercially important plantation species in the northern and southern regions of the Philippines, respectively. But, often the quantity and quality of wood of the species are low and poor. Field testing of planting materials from various plantations has recently been established to determine significant variation in important traits, with aims to select the best possible source(s). However, the lack of information on the origins or seed sources of the introduced materials has posed major limitation that could assist with the selection of materials for economical and faster improved production.
Methodology & Theoretical Orientation: This study assessed the genetic diversity and ascertained the genetic structure of all currently available propagated materials of the two species. The usefulness of molecular markers to assess genetic variation especially in recurrently planted populations has been well demonstrated and in this study the microsatellite markers developed for each species were used.
Findings: Based on structure analysis, without prior information on the location of individuals, the optimum genetic clusters (K) of Gmelina arborea and Falcataria moluccana are four and two, respectively. However, the distribution of the genetic clusters in each species does not correspond to a specific or unique sampling location but was randomly distributed in generally all sampling locations. Compared to the natural populations of Gmelina arborea, there was notable (20-30%) decreased in genetic diversity in the materials available in the Philippines, although modest divergence was found among clusters. For Falcataria moluccana, high genetic variation within-but low differentiation between clusters was observed.
Conclusion & Significance: Genetic diversity and structure of forest tree plantations is a foremost crucial concern to consider in tree breeding and improvement as genetic gain increases with high genetic variation in a species. Therefore, the results of this study should be useful as baseline information for tree breeding and improvement of these species.
Beng-Kah Song
School of Science, Monash University, Malaysia
Title: When East meets West: the origins and spread of weedy rice in Southeast Asia
Time : 01:30 PM - 02:00 PM
Biography:
Song Beng Kah has completed his PhD in Universiti Kebangsaan Malaysia and joined Monash University Malaysia as a Lecturer in Genetics. He was an Honorary Research Scientist at the Washington University in St. Louis, USA, researching population genetics and evolution of rice (2011-2013, 2016). In 2014, he was promoted to Senior Lecturer. He has teaching and research responsibilities in genomics and molecular genetics. His research has won a Gold Medal at the University Malaysia Sabah Research Competition, 2013. His current research investigates the development of genome-wide SNPs for assessment of genetic structure and evolutionary history of Malaysian and Southeast Asian weedy rice. He serves a number of societies including the Genetics Society of Malaysia and the Malaysian Society for Biochemistry and Molecular Biology.
Abstract:
Statement of the Problem: Weedy rice is a conspecific form of cultivated rice (Oryza sativa) that infests the rice fields and causes severe production loss worldwide. There has been on-going study of weedy rice in the western hemisphere and East Asia, but less in the Southeast Asian regions.
Methodology & Theoretical Orientation: Using a combined analysis of 24 neutral Simple Sequence Repeat (SSR) loci, four domestication genes (sh4, Bh4, Rc, and An-1 controlling seed shattering, hull color, pericarp color and awn development, respectively), 45,000 genotyping-by-sequencing-derived SNPs and whole genome sequences, we examined the complex evolutionary dynamics and origins of weedy rice in Southeast Asia.
Results & Conclusion: Comparative analysis between these genotypic datasets from weedy rice collected from Southeast Asian (SEA) countries and regions where no reproductively compatible wild Oryza species occur (US and South Korea) revealed independent evolutionary origins for SEA weeds and US-Korean strains. Wild-to-weed gene flow was observed in SEA weed populations, including adaptive introgression of domestication alleles, whereas de-domestication of cultivated rice is the major cause of weedy rice emergence in regions without wild rice. In Malaysia, modern cultivars played a prominent role in the origin and recent proliferation of weedy rice, with wild rice introgression, although less predominant than in other SEA countries, nonetheless contributing to the weed origin. Genome-wide assessment of nucleotide diversity further demonstrated that Thai and Malaysian weedy strains harbored very few of genomic regions that were supposed to undergo selection and overlapped among these weedy rice strains. Our study provides a genome-wide view of origin and adaptive evolution of weedy rice strains which could shed light on further molecular breeding of cultivated rice. It is also be useful for advising farmers appropriately in strategies for controlling the spread of weedy rice.
Martin Koudela
Czech University of Life Sciences Prague, Czech Republic
Title: Effect of selected factors on growth of Fusarium oxysporum f. sp. conglutinans and evaluation of cabbage cultivar resistance to Fusarium wilt
Time : 02:00 PM - 02:30 PM
Biography:
Martin Koudela – Assistant professor, Czech University of Life Sciences Prague, Czech Republic is responsible for subjects dealing with the production of vegetables and edible/medicinal mushrooms; member of International Society of Horticultural Science and the editorial board of the journal Horticultural Science; study stays: Forschungsanstalt Geisenheim, Germany (2000), Bodenkultur Universität Wien, Austria (2003); expertise: topics – optimization of biotic and abiotic factors influencing the production and yield of vegetables, production of edible and medicinal mushrooms on non-traditional and alternatively treated substrates; author and co-author of 38 scientific papers, numerous presentations at scientific conferences, popular papers dealing with horticulture.
Abstract:
Statement of the Problem: Fusarium wilt is an important disease of cruciferous vegetables caused by soil phytopathogenic fungus Fusarium oxysporum f. sp. conglutinans (Foc). The dangerous character of the pathogen stems from its persistence in the soil and the ability to attack plants at any stage of its development. The aim was to evaluate the effect of temperature and pH on the development of Foc and assess differences between genotypes (breeding line and cultivar) linked with the sensitivity to Fusarium wilt.
Methodology & Theoretical Orientation: Temperature is one of the factors that can significantly influence the occurrence of Fusarium wilt. At temperatures below 17 °C, the rate of the disease is low and explains a lower risk of the occurrence of the disease in the summer period. The optimum temperature and pH for the development of Foc disease are between 20-25 °C (some sources mentioning even a range of 24-29 °C) and pH 8, respectively. As the curative treatment by fungicides is not efficient, the effective protection against this disease remains a prevention consisting in the selection of a suitable cultivar(s) resistant to the disease. In the experiments conducted at the Czech Agriculture University Prague in 2017, the effect of temperature and pH on the growth of Foc mycelium was measured. The differences between breeding lines and cultivars concerning the sensitivity to Fusarium wilt after inoculation with Foc were determined. The visual symptoms of the attack by Foc were confirmed by PCR using specific markers.
Findings: The experiments documented that the most intense growth of Foc was observed at 24 °C. The intensity of Foc development under in vitro conditions corresponded to the intensity of the attack in a situation when the conventional growing substrate was used at a temperature of 24/22 °C and the attack by the fungus resulted in a higher mortality of plants. Using various pH values, small differences in the mycelial colony growth were found. The lowest growth rate of the phytopathogen was observed at pH 5. The sensitivity of a total of 37 varieties and lines of head cabbage against Foc were tested. The following lines were claimed to be resistant to Foc: DC6, MX11, SU2/15, SU10/15. On the other hand, the lines sensitive to Foc included: DS, DP25, HO2 and RM.
Conclusion & Significance: Selection of the agrotechnical term with temperatures outside the optimum range for the growth of Foc can help eliminate the development of the phytopathogen to some extent. On the other hand, the regulation of soil pH is not an efficient tool to control the development of the pathogen since cruciferous vegetables require a much higher pH, compared to the pH values that inhibit the growth of Foc. Preliminary results suggested the existence of significant differences in resistance to Fusarium wilt between various breeding lines and cultivars.
Geraldine P Muncada
University of the Philippines Los Baños, Philippines
Title: Antiviral resistance genes from abaca (Musa textilis Nee) BC2 hybrid: Transcriptome responses that mediate innate immunity against abaca bunchy top virus
Time : 02:30 PM - 03:00 PM
Biography:
Abstract:
Abaca (Musa textilis Nee) is susceptible to Abaca Bunchy Top Virus (ABTV). An Abaca BC2 hybrid derived from a cross between abaca variety Abuab and the ABTV resistant donor parent Pacol (M. balbisiana), was observed to be resistant to ABTV. The molecular mechanism underlying ABTV disease resistance in the hybrid has not been elucidated. Currently, transcriptomic data are available to understand the molecular mechanism of resistance of the abaca BC2 hybrid to ABTV. RNA Seq transcriptome data were obtained from the inner whorl of the pseudostems of Abuab, pacol, BC2-A2 non-inoculated, BC2-A2 two weeks post inoculated and BC2-A2 four weeks post inoculated with ABTV. Transcriptome were assembled using CLC Bio Genomics Workbench based on reference-guided assembly with CDS of M. acuminate and M. balbisiana. There are 349 Differentially Expressed (DEGs), 87 of which were putatively classified as defense response genes. These include: Four Pattern Triggered Immunity (PTI), signal receptor genes/Pattern Recognition Receptors (PRRs), 35 Effector Triggered Immunity (ETI)-based effector genes or R genes; four photosynthetic genes, two ER resident chaperones involved in Unfolded Protein Response (UPR) and ER-mediated program cell death, two genes involved in molecular Ubiquitin Proteasome System (UPS), four regulatory receptors and 31 ABTV responsive transcription factors. It was also observed that some genes have similar patterns of expression in the BC2 hybrid and the donor parent, Pacol. Quantitative real-time PCR analysis validated the RNA-Seq expression results for six genes which include Germin-Like Protein (GLP3), Glutathione S-Transferase F11 (GST), Heat Shock Coat Protein 70-1 (HSCP 70-1), Lipid Transfer Protein (LTP3), Senescence Associated Gene (SAG20) and Thioredoxin Superfamily Protein (TXN). This is the first report on the possible complex molecular mechanisms involved in antiviral defense response in Musa textilis Nee
Federico Martinelli
University of Palermo, Italy
Title: Meta-analysis of RNA-seq data to gain insight into crop responses to environmental stresses
Time : 03:00 PM - 03:30 PM
Biography:
Federico Martinelli has worked as an Assistant Professor of Plant Genetics in The Department of Agricultural and Forest Sciences, University of Palermo, Palermo, Italy (2011). He was the Founder of a research company named Environmental Heredity and Evolution Consulting (2016). He has also been a Visiting Professor to the University of California, Davis, USA in July 2017. His research activity is focused on the discovery of key regulatory mechanisms in plant stress biology.
Abstract:
RNA-Seq analysis is a strong tool to gain insight into the molecular responses to biotic stresses in plants. Transcriptomic studies are usually conducted in a singular time, they do not provide any repetition across different seasons and frequently they are performed in field conditions where environmental variability is high and disturbing factors are frequently present. The identification of up or down-regulated genes is often not enough to draw meaningful biological conclusions because it is hard to identify which gene plays a key role in specific signaling networks in host responses. This issue leads to high difficulties in deriving conclusive models for understanding disease symptomatology. For these reasons, more meta-analysis is needed to validate singular transcriptomic works with other similar studies performed with same research purposes. Meta-analysis of transcriptomic data identifies commonalities and differences between differentially regulated gene lists and allows screen which genes are key players in gene-gene and protein-protein interaction networks. These analyses allow delivering important information on how a specific environmental factor affects plant molecular responses and how plants activate general stress responses to environmental stresses. An early stress condition in plants is like the inflammatory response occurring in animals in response to pathogen-associated factors. The objective of this work is to identify specific and common molecular features (genes, proteins, gene sets and pathways) linked to both abiotic and biotic stress resistances among key crops. The identification of common genes between different biotic stress allow to gain insight into these general responses and help the diagnosis of an early “stress state” of the plants. These analyses help in monitoring stressed plants to start early specific management procedures for each disease or disorder.
- YRF PRESENTATION
Location: Osaka, Japan
Session Introduction
Umme Qulsum
Japan Advanced Institute of Science and Technology, Japan
Title: Investigation of tissue-specific alternative splicing of RNA editing related family genes in Arabidopsis thaliana
Time : 03:20 PM - 03:50 PM
Biography:
Umme Qulsum is a Doctoral candidate in School of Materials Science, Japan Advanced Institute of Science and Technology. She is also affiliated to Department of Botany, University of Rajshahi, Bangladesh as an Assistant Professor. Her main interests include research on alternative splicing of RNA editing related family proteins and their effect on RNA editing in plants. She has experimental knowledge in plant molecular biology.
Abstract:
Arabidopsis is the most useful model plants in molecular biology. RNA editing is a post-transcriptional modification of genes that commonly occur in plant plastids and mitochondria. Alternative splicing is a post and co-transcriptional regulation of gene expression. In recent studies, it is found that the PPR family proteins are involved in RNA editing in plants. In flowering plants, not only PPR but also non-PPR proteins like MORF, ORRM and OZ participate in multiple RNA editing events. The PPR–RNA complex is organized into the editosome with several additional non-PPR protein factors. The aim of this study is to find out the frequency and extends of tissue-specific RNA editing events and expression of alternative splicing of these genes and their effect on protein structure and functionality. We collected samples of different tissues of different developmental stages of Arabidopsis. Gene expression analysis and sequencing were performed. I-TASSER was used for protein modulation study. We found editing events in eleven genes out of twelve of PPR family genes and only one genes out of nine of ZNF family genes. We found nine types of RNA editing events these events included possible intra-base transitions: C-to-U, U-to-C, A-to-I, A-to-C, A-to-U, G-to-A, G-to-C, U-to-A and U-to-G in targeted genes. Most of the editing events in seedling and leaf and less in stem tissues. In our study, most of the alternative splicing events were found in seedling and leaf. We also detected seven unannotated and new alternatively spliced isoforms among these five PPR and two ZNF genes that were confirmed by PCR and sequencing. RNA editing machinery may play important role in proteins diversity and functionality thus ultimately affecting plant physiology. This study suggests that tissue-specific expression of different alternatively spliced transcript happen even in different developmental stages.
Subhankar Bera
Osaka Prefecture University, Japan
Title: Mobile small RNA: Implication for common function during interaction between different hostparasitic plant complexes
Time : 03:50 PM - 04:20 PM
Biography:
Subhankar Bera is pursuing his PhD degree on plant science in Osaka Prefecture University. His PhD work is based on small RNA analyses trace the movement of small RNAs. He is building his experience in research and educational institution. He want's to devote and dedicate himself in dynamic and creative academic interest and to utilize his logical sense, analytical power, potentiality and skills those provide steady growth.
Abstract:
Parasitic plants are grown on hosts through haustorial formation to uptake water and nutrients for their survival and growth. During host-parasitic interaction plant endogenous mRNA and proteins also moved bi-directionally through parasitic interface tissue. Recent studies shown that parasitic plant accumulate miRNA in interphase tissue of host-parasitic complex to control/or regulate host gene through secondary siRNA production. However, there is no direct evidence of host-derived small RNAs moved to long distance tissue of parasite. The purpose of this study is to find out commonly shared long-distance moved small RNAs in both host and parasitic plants which may have functional regulation during and after host-parasitic interaction. We design experiments on (Cuscuta japonica-Glycine max) and (Cuscuta campestris-Arabidopsis thaliana) as different species of parasitic plants grow on different family of host plants. Small RNA-seq analyses and comparison of non-parasitic and parasitic tissue of both parasite and host plants showed that several small RNAs are produced from common gene family of hosts moved to long distance tissue of parasitic plant. Similarly, there are some orthologous genes of different parasitic plant species produced small RNAs from and moved to long distance tissues of hosts. Small RNA candidates target common of orthologous hosts genes also. By stem-loop PCR followed by Sanger sequencing validate small RNAs. Long distance movement was proved by cross-species detection of sRNAs. These results suggest that small RNAs are moved in bidirectional manner to control trans-species gene regulation.