Plant Genomics Congress: Asia

Global Engage

Plant Genomics Congress: Asia Poster Presentation Abstracts Kuala Lumpur, Malaysia

2016

Poster Titles: Title

Principal Author(s)

Affiliation Functional Genomics Laboratory, Centre of Biotechnology, Siksha O Anusandhan University, Bhubaneswar-751003, India

1

Allium sativum Pathogenesis related protein 5 (AsPR5) Ellojita Rout, Satyabrata Nanda, stimulates the defense response pathway and enhances the Raj Kumar Joshi resistance to necrotrophic fungal infection.

2

Molecular cloning and in silico analysis of nitric oxide associated 1 (NOA1) gene of Elaeis guineensis Jacq.

Yee-Min Kwan, Chai-Ling Ho, Universiti Putra Malaysia Sariah Meon and Mui-Yun Wong*

3

Use of functional genomics to study the response of rice to abiotic stress

Kupusamy UPriya, Gatehouse AMR, Edwards MG

4

Physiological and Proteomic Analysis Reveals Novel Sowbiya Muneer, Byoung Ryong Insights to Adapt temperature stress in Tomato Graft Unions Jeong

5

In situ localization of EgDEF1 variants in mantled oil palm inflorescence.

6

Yen-Yen Kwan, Wei-Yeng Hooi, A third mutation in the oil palm SHELL gene determines fruit Tzer-Ying Seng, Ling- Jiun Leao, FGV Research & Development Sdn forms in some materials of La Me origin. Vengeta Rao and Sharifah Shahrul Bhd Rabiah Syed Alwee

7

Mohd Shahril Firdaus Ab Razak, Mohamad Bahagia Abdul Ghaffar, Application of marker assisted breeding for the improvement Maisarah Mat Saad, Siti Norhayati MARDI of Malaysia Rice variety against Brown Planthopper attacks Ismail, Muhammad Fairuz Mohd Yusof, Azwan Jaafar, Khairun Hisam Nasir & Norzihan Abdullah

8

9

Exploring genomics & genetics information of pineapple using PineappleMart@CMDV

Transcriptome Analysis Across Various Developmental Stages Of Mesocarp Tissues From Angola Based Dura

Analysis of a normalized expressed sequence tag (EST) 10 library and host-mediated gene silencing by disruption of collagen gene in root-knot nematode

Newcastle University, United Kingdom Gyeongsang National University, Jinju, Republic of Korea

Wei-Yeng Hooi, Sharmilah Vetaryan, Estelle Jaligot, Yen-Yen FGV Research & Development Sdn Kwan and Sharifah Shahrul Bhd Rabiah Syed Alwee

Rabiatul Adawiah Z.A., Siti Norhayati I., Azrin A., Norzihan A., Khairun Hisam N., Siti Zainab J. & Umi Kalsom A.B.

Centre for Marker Discovery & Validation (CMDV), Biotechnology & Nanotechnology Research Centre, Malaysian Agricultural Research & Development Institute (MARDI), Selangor, Malaysia

Priscilla Elizabeth Morris; Pek-Lan Chan; Leslie Ooi Cheng-Li; PeiWen Ong; Katialisa Kamaruddin; Malaysian Palm Oil Board Kuang-Lim Chan; Marhalil Marjuni; Leslie Low Eng-Ti and Rajinder Singh Vimalraj Mani, Kang-Hyun Choi, National Institute of Agricultural Parthiban Subramanian, ChangScience, Rural Development Muk Lee, Joon-Soo Sim, and BumAdministration, Korea Soo Hahn

Hasimah Alimon, Syazana Ismail, Syarifah Nur Hidayatul Afifah Syed Response of Malaysian common crops to simulated flooding 11 Mohamed Adnan, Nurmariana Universiti Pendidikan Sultan Idris regime Zulrahman, Nurul Hidayu Asyiqin and Noor Diyana Abdul Rahim

12

Validations of SHELL Markers for Fruit Form Prediction in Oil Palm

Siti Dalila binti Muaz*, Teh Chee Keng, Praveena Tangaya, Fong Po Yee, Ong Ai Ling, Mohaimi Mohamed, Harikrishna Kulaveerasingam & David R. Appleton

Sime Darby Technology Centre Sdn Bhd

13 PROTEOMIC LEADS SNPs DISCOVERY

14

Stable Agrobacterium-mediated transformation in Phalaenopsis aphrodite

Ainul Masni Othman, Jaime Low Yoke Sum, Lim Chin Ming, Chew Fook Tim, Yeap Wan Chin, Tony Eng Keong Ooi, Leona Daniela Jeffery Daim, Lee Fong Chin, Ng Boon Zean, Hirzun Mohd Yusof, Harikrishna Kulaveerasingam, David R. Appleton

Sime Darby

Hong-Xian Hsing, Yi-Jyun Lin, ChiAcademia Sinica Biotechnology Gong Tong, Min-Jeng Li, Yun-Jin Center in Southern Taiwan Chen, and Swee-Suak Rachel Ko* 1The

New Zealand Institute for Plant & Food Research Ltd, (Plant & Food Research), Mt Albert Research Centre, Private Bag 92169, Auckland, New Zealand 2School of Biological Sciences, University of Auckland, Auckland, New Zealand 3 Dipartimento di Scienze Agroalimentari, Ambientali e Animali, University of Udine, Via delle Scienze 206 - 33100 Udine – Italy 4The New Zealand Institute for Plant & Food Research Ltd, (Plant & Food Research), Hawke’s Bay Research Centre, Private Bag 1401, Havelock North, New Zealand

15

Dynamic changes in global gene expression during the apple response to Venturia inaequalis

Kui Lin-Wang1, Cecilia H. Deng1, Scott Wang2, Luigi Falginella3, Guido Cipriani3, Vincent Bus4, Andrew C. Allan1,2, Richard Espley1, Joanna Bowen1

16

Functional analysis of INDETERMINATE DOMAIN family genes mainly expressed in seeds.

Akiko Kozaki

Shizuoka university

De novo Assembly and Transcriptome Analysis of Bulb 17 Onion (Allium cepa L.) during Cold Acclimation using Contrasting Genotypes

Senthil Kumar Thamilarasan, Jeong Suk Hyeon Han, Sathishkumar Natarajan, Jong-In Park and Ill Sup Nou

Sunchon National University

GENOMIC APPROACHES TO UNDERSTANDING 18 DIVERSITY AND GANODERMA RESISTANCE IN OIL PALM (ELAEIS GUINEENSIS JACQ.).

Agnieszka Mudge, Carmel Pilotti and Ian Godwin

University of Queensland (AM & IG) and PNG-OPRA (CP)

Investigation of Phenolic Profiles in Ganoderma Infected 19 Palms

Nalisha Ithnin, Intan Safinar Ismail, Leona Daniela Jeffery Daim, Tony Sime Darby Technology Centre Sdn Ooi Eng Keong, Hirzun Mohd Bhd Yusof, David Ross Appleton 1Department

Unlocking the Transcriptome of the Mature Embryo of 20 Moringa oleifera Lam.: An Oil Rich Plant

21

Dynamics of transcriptome and methylome of rice during regeneration

Vivian A. Panes1, Ai Kitazumi2, Myles Butler2, Reshan D. Baoas1 and Benildo G. de los Reyes2

of Biology, School of Science and Engineering, Ateneo de Manila University, Loyola Heights, Katipunan Avenue, 1108, Quezon City, Philippines 2Plant Molecular Genetics and Functional Genomics Laboratory, 5735 Hitchner Hall, University of Maine, Orono, Maine 04469, USA

Moloya Gohain*, Fei-Man Hsu, Kshitij Tandon, Lin-Yun Kuang, Pao-Yang Chen

Institute of Plant and Microbial Biology, Academia Sinica, Taiwan

Sanimah Simoh, Chandradevan Machap, Mohd Waznul Adly Mohd Metabolomics and gene expression studies to evaluate the Zaidan, Lina Rozano, Fazri Ab 22 anti-cancer activity of Phyllanthus and Curcuma spp extract Rahim, Muhammad Aizuddin mixture Ahmad, Alizah Zainal, Indu Bala Jaganath

Biotechnology & Nanotechnology Research Centre, MARDI, Persiaran MARDI-UPM, 43400, Serdang, Selangor, MALAYSIA

23

24

25

Sime Darby’s High-throughput Marker Deployment In Oil Palm

Nurshazwani Amalina Sudirman*, Arutchelvam Balakrishnan, Khairun Hafizah Mohd Zain, Hafiza Abidin, Airin Niza Za’ba, Fong Po Sime Darby Technology Centre Sdn Yee, Fairuz Farhana Mohd Rodzik, Bhd Mohd Nor Azizi Shabudin, Teh Chee Keng, Sukganah Apparow, David R. Appleton

Soybean Growth and Yield Response in Paddy Field Cultivation with P.E. mulching

Hyeon Jin Park, Won-Young Han, Won Tae Jeon, Jong Soo Ryu, Jin National Institute of Crop Science, Woo Bae, Rural Development Administration Su Min Jo, Jong-Min Ko, In-Jung Lee and Hang Won Kang

Soybean Planting Date and Density for Harvesting with Combine

Jin Woo Bae, Su Min Jo, Hyeon Jin Park, Jong Soo Ryu, WonYoung Han, Won Tae Jeon,

National Institute of Crop Science, Rural Development Administration

Jong-Min Ko and Hang Won Kang Su-Min Jo, Ki-Youl Jung, WonTae Jeon, Jong- Soo Ryu, WonAntioxidant Compounds and Antioxidant Activity of Sorghum National Institute of Crop Science, 26 Young Han, Jin- Woo Bae, Hyeon with Different Drainage Methods Rural Development Administration Jin Park, Jong-Min Ko, Hang-Won Kang

27 Lipases in Oil Palm Fruits

Anusha Nair, Ainul Masni Othman, Katharina Mebus, Koo Ka Loo, Sime Darby Technology Centre Wong Yick Ching, Hirzun Mohd Sdn. Bhd., Sime Darby Plantation, Yusof, David Ross Appleton & Malaysia Harikrishna Kulaveerasingam

28

In silico analysis of phosphate-starvation-inducible PHT1 gene from oil palm

Saeid Kadkhodaei, Siti Nor Akmar Institute of Tropical Agriculture, Abdullah, Farzaneh Ahmadi and Universiti Putra Malaysia Siti Mariyam Ijab

29

Computational prediction on the role of hypothetical genes in papaya during dieback infection.

Lina Rozano, Adrain Ling Chieng Kuang, Suhaina Supian, Wee Chien Yeong

Progress on the Molecular Analysis of Wheat Stem Rust Resistance Locus Sr26 Using Mutagenesis and 30 Comparative Genomics

Malaysian Agricultural Research and Development Institute 1CSIRO

Agriculture, GPO Box 1600, Jianping Peng Canberra, 2601 ACT, Australia, Sambasivam Periyannan1, Robert 2The University of Sydney Plant Park2, Evans Lagudah1 Breeding Institute - Cobbitty, 107 Cobbitty Road, NSW 2570, Australia Zhang12,

Zhang2,

31

New generation sequencing reveals potential new targets for improving nitrogen use efficiency in Sorghum bicolor

Karen Massel, Bradley C. Campbell, Emma S. Mace, Shuaishuai Tai, Yongfu Tao, University of Queensland Belinda Worland, David R. Jordan, Ian D. Godwin

32

Genetic Diversity Analysis of Rice Different Anthocyanin Content Based on DNA Microsatellite Markers

A.I. Farkhi, M.A. Muslim, and Suprayogi

DArT genome profiling and KDDart data management solutions for plant research and practice

Katarzyna Heller-Uszynska, Adriane Machado, Cina Vipin, Colleen Hopper, Damian Jaccoud, Faisal Pirzad, Jason Carling, Ling Diversity Arrays Technology Pty. Xia, Vanessa Caig, Grzegorz Ltd. Uszynski, Puthick Hok, Brian Pierce, David Hunter, Stanley Wijoyo, Manil Chaudhary, Alex Spence and Andrzej Kilian

33

Enhancing the Production of Carotenoids from Papaya via 34 UVB stress: A Preliminary Study

M. Chandradevan and M. Aizuddin Ahmad

Agrotechnology, Faculty of Agriculture, Jenderal Soedirman University

Malaysian Agricultural Research and Development Institute (MARDI)

35

De-novo Transcriptome Assembly of Sarawak Local Rice Variety and Discovery of Saline Responsive Genes

Brandon YEO Pei Hui, Mrinal BHAVE, HWANG Siaw San

Swinburne University of Technology Sarawak Campus

Comparative analysis of the protein profiles of soybean 36 seedlings in response to flooding stress

Sung Cheol Koo, Hyun Tae Kim, Sang Ouk Shin, Beom Kyu Kang, National Institute of Crop Science Jeong Hyun Seo, Hong Tai Yun, In Seok Oh, Man Soo Choi

Screening of transgenic Eksotika papaya for resistance to 37 papaya dieback disease

Nazrul Hisham Nazaruddin, Rogayah Sekeli, Noriha Mat Amin, Malaysian Agricultural Research Wee Chien Yeong, Nor'aini and Development Institute (MARDI) Abdullah and Amin Asyraf Tamizi.

A transcriptome next-generation sequencing of Carica papaya

Adrain C.K. Ling, Mohd Waznul Adly Mohd Zaidan, Chien Yeong Wee, Lina Malaysian Agricultural Research Rozano, Suhaina Supian, Muhammad and Development Institute (MARDI) Mustaqi Ab Halim, Nor Hidayah Mohtar, Fazri Abd Rahim, Johari Sarip

38

Yun Shin Sew, Kamariah Mohammed, Salma Idris, Khairun Hisham, Chien

Transcriptome profiling of Lansium domesticum tree bark Young Wee, Maheswary Vellupillai, 39 under regulated deficit irrigation for early flowering induction Rabiatul Adawiah Zainal Abidin and

Malaysian Agricultural Research and Development Institute (MARDI)

Umi Kalsom AbuBakar

40

41

Key factors for the success in genome-wide genotyping with Kenta Shirasawa, Hideki restriction site-associated DNA sequencing. Hirakawa, and Sachiko Isobe

Cnaphalocrocis medinalis resistant/tolerance rice varieties in Taiwan

Characterization of Pathogenesis Related (PR) Genes 42 Expression Associated With Disease Resistance for The Establishment of Systemic Acquired Resistance Marker.

Kazusa DNA Research Institute

Kun-Yu Tu1, Tzu-Wei Guo1, Chung-Ta Liao2 and WenPo Chuang1

1.National Taiwan University, Taipei, Taiwan, 2.Taichung District Agricultural Research and Extension Station, Changhua County, Taiwan

Norliza, A.B., Rafidah,B, Mohd Zulfadli, S

Malaysian Agriculture Research and Development Institute (MARDI)

43

Transcriptome analysis and molecular markers identification G. Veera Singham, Mohamat in different tissues and clones of Hevea brasiliensis Muda, Ahmad Sofiman Othman

Universiti Sains Malaysia

44

Nucleic Acid Extraction From Plant Material Using chemagen Magnetic Separation Technology

Xinyi Ngew, Michael Abdo Ph.D.

PerkinElmer Inc., Life Sciences Solutions

Suhaina Supian, Mohd Zulhilmi Ramlee, Nazrul Hisham Nazaruddin, Lina Rozano, Wee Chien Yeong, Johari Sarip, Adrain Ling Cheng Kuang

Biotechnology and Nanotechnology Research Centre, Malaysian Agricultural Research and Development Institute (MARDI)

Molecular response of tolerant and non-tolerant papaya 45 plants to dieback disease : a proteomics approach

Gene Expression Profiling of Effector/Virulent Genes Rafidah Badrun, Norliza Tendot, 46 Associated to Erwinia mallotivora Pathogenecity in Papaya Rohaiza Redzuan, Jameah Dieback Disease Baharom & Ariffiah Ahmad

Malaysia Agricultural Research and Development Institute (MARDI) 1

47

Spontaneous production of Arteannuin B in the moss Physcomitrella patens

Nur Kusaira Khairul Ikram1,2,4, Arman Beyraghdar Kashkooli3, Alexander van der Krol3, Harro J. Bouwmeester3, Henrik Toft Simonsen2

48

Genotyping-by-Sequencing (GBS) in Tomato Using Ion Ampliseq™ Technology

Xiaoqing You, Pius Brzoska, Mousumi Rath, Allen Nguyen, Ferrier Le and Garrett Chow

Next Generation Sequencing-Based Molecular Marker 49 Development: A Resource for Breeding Fast Growing Coconut (Cocos nucifera L.) Varieties

University of Copenhagen, Denmark 2 University of Denmarkk 3 Wageningen University, Netherlands 4 University of Malaya, Malaysia Thermofisher Scientific

Edward A. Barlaan1, Ian Kendrich C. 1University of Southern Mindanao, Fontanilla2, Christian John S. Robiso2, Philippines Andrea Danna S. Camiling2, Madel M. 2 University of the Philippines 2 2 Facun and Cynthia P. Saloma

For purposes of conference attendance only. All rights reserved.

-1Contributing Author(s)

Ellojita Rout, Satyabrata Nanda, Raj Kumar Joshi

Organisation

Functional Genomics Laboratory, Centre of Biotechnology, Siksha O Anusandhan University, Bhubaneswar-751003, India

Email Address

[email protected]

Poster Title Abstract

Allium sativum Pathogenesis related protein 5 (AsPR5) stimulates the defense response pathway and enhances the resistance to necrotrophic fungal infection. Pathogenesis-related protein 5 (PR5) are often encoded in a wide variety of plants for the regulation of physiological processes in response to biotic and abiotic stresses. In the present study, we have cloned and characterized a PR5 gene which is induced in response to Fusarium oxysporum f. sp. cepae (FOC) infection in garlic. The predicted protein codes for 223 amino acids and contains 16 conserved cysteine residues along with five additional conserved amino acids related with antifungal activity of most plant thaumatin like proteins. Semi-quantitative RTPCR revealed high accumulation of AsPR5 transcript in stem tissues, the primary site of FOC infection. Temporal expression analysis revealed induced expression of AsPR5 upon infection with FOC as well as various phytohormones (JA, ET and ABA) suggesting its involvement in both biotic and abiotic stresses. The antifungal activity of AsPR5 was detected in in vitro plates, and the purified AsPR5 protein significantly inhibited the hyphal growth of major necrotrophic fungi including Alternaria brassicola, FOC and Colletotrichum gloeosporoides. Furthermore, in order to verify the function of AsPR5, the constitutive plant expression vector of AsPR5 was constructed and transferred into Arabidopsis thaliana. The Southern blot and quantitative reverse transcription-polymerase chain reaction (qRT–PCR) analysis demonstrated that the AsPR5 gene was integrated into the genome of the Arabidopsis transformants and highly expressed in the transgenic lines. Additionally, the ectopic expression of AsPR5 in A. thaliana results in a concomitant and significant activation of defense responsive genes after infection such as Lox3, PDF1.2, PAD3, AOS, and AOC. Thus, the present work suggests that AsPR5 play significant role in activating multiple defense pathways for enhancing resistance against multiple necrotrophic pathogens.


Yee-Min Kwan, Chai-Ling Ho, Sariah Meon and Mui-Yun Wong*

Organisation

Universiti Putra Malaysia

Email Address

[email protected]; *[email protected] (corresponding author)


Molecular cloning and in silico analysis of nitric oxide associated 1 (NOA1) gene of Elaeis guineensis Jacq. Basal stem rot (BSR) of oil palm (Elaeis guineensis Jacq.) is a notorious disease caused by the white rot fungus, Ganoderma boninense. The disease has resulted in the reduction of fresh fruit bunch (FFB) and collapse of standing palms causing severe economic loss. During plantpathogen interaction, the rapid production of reactive nitrogen species (RNS) modulates the signalling networks of plant defence responses. Nitric oxide associated (NOA) protein is implicated in nitric oxide (NO) biosynthesis and hormonal signalling in plants. This study was carried out to isolate and characterize the full-length cDNA encoding NOA protein in oil palm. Two expressed sequence tag (EST) sequences encoding NOA protein were retrieved from the cDNA library of oil palm root followed by primer design. Rapid Amplification of cDNA Ends (RACE) was performed to prepare PCR template from good quality RNA isolated from oil palm root tissues followed by 3’ RACE and 5’ RACE amplification of target genes. The ORF was subjected to homology search, multiple sequence alignment, phylogenetic tree construction, motif analysis, protein molecular weight and isoelectric point analysis, and sub-cellular location prediction. A full-length transcript of NOA was successfully isolated and designated as EgNOA1. The PCR amplicon of 1940 bp has an open reading frame (ORF) of 1674 bp. Homology search has confirmed the amplicon identity as plant NOA1 gene. Multiple sequence alignment of amino acid sequences confirmed the presence of three active domains reported in plant NOA1, arranged in the order: N-terminal zinc-binding domain (ZBD), circularly permuted GTPase (CPG) domain and C-terminal domain (CTD). Phylogenetic analysis revealed the close evolutionary relationship between EgNOA1 and NOA1 of Poaceae family. The polypeptide of 558 amino acids was predicted to have a molecular weight of 61.16 kDa, isoelectric point of 9.42 and targeted to the chloroplast and mitochondria.


Kupusamy UPriya, Gatehouse AMR, Edwards MG

Organisation

Newcastle University, United Kingdom

Email Address

[email protected]

Poster Title

Use of functional genomics to study the response of rice to abiotic stress

Abstract

Rice Oryza sativa is one of the most important food crops in the world. In order to fulfil the demand for rice, production needs to be increased dramatically from its current level. Rice lines, which are more resistant to biotic and abiotic stress, play an important role in increasing the productivity of rice. This study used functional genomics to link nitrogen input to specific transcription factors (TFs) which play important roles in the induced defence response of plants. Two rice cultivars with different levels of tolerance to Brown planthopper (BPH; TN1, susceptible; IR70 resistant) were grown under four different nitrogen regimes and a range of physiological parameters were measured. The most significant difference was seen in shoot height at the lowest nitrogen input, with average shoot heights of 27.9 cm and 40 cm for IR70 and TN1, respectively. Similarly, at the lowest level of nitrogen input, there were fewer leaves on the susceptible line (6 and 7 respectively for TN1 and IR70). As expected, plants grown on the highest nitrogen level produced the highest number of tillers (with an average of 6 tillers/plant) in both the rice lines. Differentially expressed genes were verified by using q-PCR. q-PCR was carried out on a selected set of TFs known to be involved in response of rice to BPH to investigate whether these same TFs are also involved in nitrogen stress. Out of the 12 TFs investigated, 9 TFs were significantly up-regulated in IR70 and 8 were up-regulated in TN1 in response to increased nitrogen levels. There were 7 TFs which were up-regulated in both the resistant and susceptible line. Keywords: Oryza sativa, Transcription factors, Brown planthopper Nilaparvata lugens


Sowbiya Muneer, Byoung Ryong Jeong

Organisation

Gyeongsang National University, Jinju, Republic of Korea

Email Address

[email protected]

Poster Title

Physiological and Proteomic Analysis Reveals Novel Insights to Adapt temperature stress in Tomato Graft Unions Background: Grafting is an established practice for asexual propagation in horticultural and agricultural crops. The transfer of genetic material during grafting, between root to shoot and vice versa, has recently become of interest for investigating signal transduction pathways in plants using proteomic and microarray techniques. However grafting is known to mitigate abiotic or biotic stress. Using physiological and proteomic analyses, we investigated graft unions (rootstock and scions) of tomato genotypes exposed to standard-normal (23/23 and 25/18 °C day/night) and high-low temperatures (30/15 °C day/night).

Abstract

Results: Graft unions had varied responses to the diverse temperatures. High-low temperature, but not standard-normal temperature, induced the production of reactive oxygen species (ROS) in the form of H2O2 and O2-1 in rootstock and scions. However, the expression of many cell protection molecules was also induced, including antioxidant enzymes and their immunoblots, such as superoxide dismutase (SOD), catalase (CAT), and ascorbate peroxidase (APX). The rootstock and scions thus actively defend against stress by modifying their physiological and proteomic responses to establish a new cellular homeostasis. As a result, many proteins for cellular defence were regulated in graft unions under diverse temperature, in addition to the regulation of photosynthetic proteins, ion binding/transport proteins, and protein synthesis. Moreover, biomass, hardness, and vascular transport activity were evaluated to investigate the basic connectivity between rootstock and scions. Conclusions: Our study provides physiological evidence of the grafted plants’ response to diverse temperature. Most notably, our study provides novel insight into the mechanisms used to adapt the diverse temperature in graft unions (rootstock/scion).


Wei-Yeng Hooi, Sharmilah Vetaryan, Estelle Jaligot, Yen-Yen Kwan and Sharifah Shahrul Rabiah Syed Alwee

Organisation

FGV Research & Development Sdn Bhd

Email Address

[email protected]

Poster Title

In situ localization of EgDEF1 variants in mantled oil palm inflorescence.

Abstract

Mantled somaclonal variation of oil palm (Elaeis guineensis Jacq.) is morphologically similar to B-class MADS-box genes mutants in which stamens are being transformed into a carpel-like structure in flowers of both sexes. EgDEF1, an orthologue of Arabidopsis thaliana’s APETALA3 in oil palm, together with GLOBOSA and SEPALLATA specify petal and stamen identity in flower. Two forms of EgDEF1 variants, cDEF1 and tDEF1, were isolated from oil palm inflorescence. Both variants are detected at the floral meristem, emerging stamen and pollen sacs in mantled male inflorescence. Identical localization of the two variants in the male mantled inflorescence suggests the absence of functional diversification of the two variants. Surprisingly, tDEF generated a stronger signal compared to cDEF. Comparative localization in normal male inflorescence will provide a better understanding of the role played by cDEF and tDEF in oil palm inflorescence development.


Yen-Yen Kwan, Wei-Yeng Hooi, Tzer-Ying Seng, Ling- Jiun Leao, Vengeta Rao and Sharifah Shahrul Rabiah Syed Alwee

Organisation

FGV Research & Development Sdn Bhd

Email Address

[email protected]


A third mutation in the oil palm SHELL gene determines fruit forms in some materials of La Me origin. The identification and mapping of the oil palm Shell gene, and two separate mutations therein, now allows breeders to be informed a palm’s fruit form at seedling age. Such early determination increases breeding efficiency. Two independent mutations in DNA-binding MADS domain of the Shell gene were reported to be responsible for the shell-less pisifera fruit type, the wild type being the thick-shelled dura and the heterozygote being the thin-shell tenera form. A commercially available diagnostic kit, the SureSawit Gel Kit, designed on the two independent mutations, was tested with FGV’s La Me materials but predictions failed on the tenera and pisifera fruit form in these particular breeding materials. Analysis of the PCR amplicon of the first exon of the Shell gene revealed an unreported third mutation hitherto detected only in La Me materials The single nucleotide substitution results in an alanine-to-aspartic acid amino change in the DNA-binding MADS domain. The novel mutation reported here is essential in assigning teneras and pisiferas fruit form correctly in some La Me materials.


Mohd Shahril Firdaus Ab Razak, Mohamad Bahagia Abdul Ghaffar, Maisarah Mat Saad, Siti Norhayati Ismail, Muhammad Fairuz Mohd Yusof, Azwan Jaafar, Khairun Hisam Nasir & Norzihan Abdullah

Organisation

MARDI

Email Address

[email protected]


Application of marker assisted breeding for the improvement of Malaysia Rice variety against Brown Planthopper attacks The Brown Planthopper (BPH), Nilaparvata lugens (Stal) is one of the most destructive phloemfeeding insect in rice and gave a serious threat to rice production in Asia. In present study, SSR markers that were tightly linked to Bph3 gene and SNP markers that were unlinked to Bph3 gene were used for foreground and background selection, respectively. These markers were applied in backcross generated by crossing between resistant cultivar, Rathu heenathi and the Malaysian widely grown recurrent variety, MR269. The foreground selection was performed on BC1F1, BC2F1 and BC3F1 populations while the background selection was performed on BC2F1 and BC3F1 populations. In foreground and background selection, individuals that showed the presence of heterozygote resistant alleles with highest similarities to MR269 were selected for backcrossing purpose. Currently, we are genotyping the BC3F2 population in order to select individuals with homozygous allele of tightly linked markers to Bph3 gene. The plant harbouring Bph3 gene will be further screened against BPH biotypes to confirm their resistance against BPH. This marker assisted breeding (MAB) approach provides an efficient and effective tool to intogress desired genes or QTLs through molecular breeding.

-8Contributing Author(s) Organisation

Rabiatul Adawiah Z.A., Siti Norhayati I., Azrin A., Norzihan A., Khairun Hisam N., Siti Zainab J. & Umi Kalsom A.B. Centre for Marker Discovery & Validation (CMDV), Biotechnology & Nanotechnology Research Centre, Malaysian Agricultural Research & Development Institute (MARDI), Selangor, Malaysia

Email Address

Poster Title

Exploring genomics & genetics information of pineapple using PineappleMart@CMDV

Abstract

PineappleMart@CMDV is an in house data warehousing system based on BioMart (http://www.biomart.org). The PineappleMart@CMDV is primarily focused on genomics and genetics information retrieved from pineapple genome sequences varieties F153 and MD2 (http://phytozome.jgi.doe.gov/pz/portal.html). It provides robust and versatile data mining tool for molecular biologist, geneticist, and breeders at CMDV for application in the development of pineapple genetic markers. The current PineappleMart@CMDV consists of 54,965 putative SSRs mining from F153 and 43,190 putative SSRs from MD2 ranges from dinucleotide to hexanucleotide repeats. Of these, only 177 putative SSRs from MD2 were anchored onto F153 linkage groups (LG01-LG25). The putative SSRs information includes marker ID, repeat type, repeat motif, repeat length, chromosome location, SSR position and primer sequences. All these information are required for designing of SSRs primer. The annotated SSR markers are also deposited in PineappleMart@CMDV. The ultimate goal of PineappleMart@CMDV is to act as a central hub of pineapple genomics and genetics information where it enables the researchers to browse, search and download the genomics and genetics information that are useful for further genetic study and varietal development in pineapples, such as diversity study, comparative mapping and germplasm fingerprinting.


Priscilla Elizabeth Morris; Pek-Lan Chan; Leslie Ooi Cheng-Li; Pei-Wen Ong; Katialisa Kamaruddin; Kuang-Lim Chan; Marhalil Marjuni; Leslie Low Eng-Ti and Rajinder Singh

Organisation

Malaysian Palm Oil Board

Email Address

[email protected]


Transcriptome Analysis Across Various Developmental Stages Of Mesocarp Tissues From Angola Based Dura Angolan germplasm materials are being evaluated for their potential use in the oil palm breeding programmes. Large fruit characteristic of some Angola dura palms has provided breeders with a source of favourable trait for introgression into the current planting materials. It was reported that the fatty acid composition and carotene content of some palms are comparable to the commercial dura x pisifera (DxP) materials. With the aim of understanding the molecular regulation during mesocarp development, maturation and ripening of Angola dura palms; efforts were initiated to profile the expression of transcripts across nine different developmental stages of mesocarp tissues. These tissues consist of 5, 8, 10, 12, 15, 18, 20, 22 and 24 weeks after anthesis. For each developmental stage, RNA sequencing (RNA-seq) was performed on 2 biological and 3 technical replicates using Illumina HiSeq 2000. The quality of raw reads were assessed using FastQC, followed by trimming of low quality bases and reads, and assignment of trimmed reads to pair-end or singletons prior to data analysis using the Tuxedo suite pipeline. The total high quality processed reads obtained ranged from 49 to 133 million reads, with an average of 76 million reads per sample. A total of 89.25% processed reads were mapped to the oil palm Pisifera 6.31 reference genome build. Preliminary data analysis using Cuffdiff resulted in the identification of 36,675 total gene set, with 24,226 transcripts successfully annotated with Plant Reference Sequence Databases using BLASTX at the cut off E-values of 1E-5.Genes associated with fatty acid biosynthesis, lipid metabolism, cell wall metabolism, glycolysis, hormone metabolism and transcription factors were identified and their expression profiles will be further discussed. The availability of these transcriptome datasets has given an insight into the transcriptional mechanisms controlling the dura fruit development, maturation and ripening.

- 10 Contributing Author(s) Organisation Email Address


Vimalraj Mani, Kang-Hyun Choi, Parthiban Subramanian, Chang-Muk Lee, Joon-Soo Sim, and Bum-Soo Hahn National Institute of Agricultural Science, Rural Development Administration, Korea [email protected]

Analysis of a normalized expressed sequence tag (EST) library and host-mediated gene silencing by disruption of collagen gene in root-knot nematode Root-knot nematodes are obligatory sedentary endoparasites that require a plant host to complete their life cycle. To understand the genes function of Meloidogyne incognita, we constructed a M. incognita cDNA library from nematode genes transcribed from eggs and second-stage juveniles (J2), following which analysis of the ESTs was carried out using PendantPro Sequence Analysis Suite. RNA interference (RNAi) technology, widely used for gene silencing, has been studied as an alternative strategy for nematode control, particularly in rootknot nematodes. An RNAi vector targeting the collagen gene of root-knot nematode Meloidogyne incognita was constructed and expressed dsRNA of its gene in transgenic tobacco (Nicotiana benthamiana) plants. Levels of mRNA transcripts of the collagen gene analyzed at different stages of nematode life-cycle (egg, J2, J3, J4 and female) revealed higher transcript levels at J2 (preparasitic) stage compared to other stages (egg, J3, J4 and female) of the nematode. The percentage of root-knots after infection in the transgenic tobacco plants producing dsRNA for collagen gene was reduced up to 47% to 53% depending on different lines studied. A concomitant decrease in the number of egg masses up to 47% to 54% was also observed. This result indicates silencing of nematode collagen gene by RNAi suppression could be potential candidate for generating nematode-resistant crops in future.

- 11 Contributing Author(s)

Hasimah Alimon, Syazana Ismail, Syarifah Nur Hidayatul Afifah Syed Mohamed Adnan, Nurmariana Zulrahman, Nurul Hidayu Asyiqin and Noor Diyana Abdul Rahim

Organisation

Universiti Pendidikan Sultan Idris

Email Address

[email protected]

Poster Title

Response of Malaysian common crops to simulated flooding regime

Abstract

In recent years, climate change has increased the rain fall and cause flooding in many areas across Malaysia. Flooding increases moisture in soil, declines soil oxygen and impedes respiration that lead to root suffocation and dying. Therefore, the aim of this study was to observe the responses of several common crops in Malaysia, namely Cucumis sativus (cucmber), Zingiber officinale (ginger), Capsicum frutescens Linn. (small hot chilli), Brassica Rapa var Chinensis (Japanese mustard), and Plectranthus scutellarioides (coleus), to simulated flooding, particularly on the plant growth, the plant morphology and the water quality. These plants were treated in three different sets of flood regime; Set 1 (The water was at the ground level), Set 2 (water level was at half the height of the plant) and Set 3 (plants were totally submerged). The study was conducted for 14 days and repeated three times with controlled external factors such as temperature, light intensity and soil type. The results show that most of the studied plants could not tolerate to the simulated flood. However, two plant species, Zingiber officinale and Capsicum frutescens, survived throughout the treatment period. Formative of adventitious roots at the internodes near the water surface occurred in a few plants. At the end of treatment, the pH level for all treatments were between pH 6-9, and the dissolved oxygen (DO) for all treatments decreased.


Siti Dalila binti Muaz*, Teh Chee Keng, Praveena Tangaya, Fong Po Yee, Ong Ai Ling, Mohaimi Mohamed, Harikrishna Kulaveerasingam & David R. Appleton

Organisation


Email Address

[email protected]; [email protected]

Poster Title

Validations of SHELL Markers for Fruit Form Prediction in Oil Palm

Abstract

The reported SHELL gene and its two simple point mutations, known as SNPs, enable the oil palm industry to predict the fruit form i.e. dura (D; thick-shelled), tenera (T; thin-shelled) and pisifera (P; shell-less) of seedlings before fruiting. The finding is an initial success in translating oil palm genome data into breeding and seed quality control applications. We conducted a twofold validation on the two SNP markers in our breeding populations. Firstly, 600 samples belonging to two origins (EKONA and AVROS) and their hybrids (AVROS x SP and AVROS-SP x EKONA) maintained in Sime Darby Plantation. The markers were only successfully validated based on single-marker approach (SMA) in the non-hybrid populations and AVROS x SP. The predictability was poor using SMA when two mutations were accumulated in the hybrid population, AVROS-SP x EKONA. However, the predictability improved by measuring allelic dosage effect of the two-SNP combination. The finding was successfully replicated in another independent batch of 760 samples from various backgrounds. The current commercial pollen source is still mainly dependent on AVROS, which is theoretically derived from two palms in the past. To provide future improvements in performance, the genetic base of AVROS is being broadened through inter-crossing with other materials, e.g. EKONA. Hence, prediction algorithms for hybrid populations will be required.


Ainul Masni Othman, Jaime Low Yoke Sum, Lim Chin Ming, Chew Fook Tim, Yeap Wan Chin, Tony Eng Keong Ooi, Leona Daniela Jeffery Daim, Lee Fong Chin, Ng Boon Zean, Hirzun Mohd Yusof, Harikrishna Kulaveerasingam, David R. Appleton

Organisation

Sime Darby

Email Address

[email protected]

Poster Title

Proteomic Leads SNPS Discovery

Abstract

Oil yield is a trait of economic interest to the palm oil industry. Many studies have focused on characterization of lipid biosynthesis pathway genes contributing to high oil content in oil palm mesocarp and these genes have been widely used as selection markers in oil palm breeding programmes. A total of 37 proteins involved in the fatty acid biosynthesis pathway (plastid) and TAG assembly pathway (endoplasmic reticulum) were identified from literature reviews. Their expression levels were analyzed in 8 high- and 8 low-yielding oil palms using protein immunoassays. Proteins that showed significant differential expression in high- and low-yielding oil palms were considered as leads and further characterized for their functions. Three proteomic leads, β-ketoacyl-ACP synthase II (KAS 2) fatty acid desaturase II (FADS 2), acyl-thioesterase A (FATA) were functionally characterized in yeast and evaluated further in an association studies. Yeast overexpressing oil palm homologues coding for EgFATA and EgFADS2 showed significant increase in total oil content (TOC) by 24.9% and 101.98% respectively except overexpression of EgKAS2, compared with the wild type yeast. We have also examined the association between single nucleotide polymorphism (SNP) markers within these target genes and the oil to dry mesocarp (O/DM) trait. Interestingly, two SNPs in EgFATA gene were found to be significantly associated with O/DM trait in the selected oil palm populations. Individuals harboring GG genotype in both SNPs exhibited higher O/DM value while the absence of a single genotype G led to lower O/DM value. The tagged SNPs in EgFADS2 were insignificantly associated with O/DM trait in the selected oil palm populations. Complementation of EgFADS2 in Arabidopsis thaliana (unpublished data) showed enhanced tolerance of transgenic plant towards abiotic stresses, and data from association studies indicated that genotype C in EgFADS2 may contribute to the tolerance in bad soil condition in estates. Echoing findings from yeast, EgKAS2 tagged SNP was insignificantly associated with O/DM trait, but was found to be significantly associated with fruit characteristic including mesocarp to fruit (M/F), kernel to fruit (K/F) and shell to fruit (S/F). In conclusion, this study provides a better understanding on the functions of three fatty acid biosynthesis pathway genes and their association to oil palm traits.


Hong-Xian Hsing, Yi-Jyun Lin, Chi-Gong Tong, Min-Jeng Li, Yun-Jin Chen, and Swee-Suak Rachel Ko*

Organisation

Academia Sinica Biotechnology Center in Southern Taiwan

Email Address

[email protected]

Poster Title

Stable Agrobacterium-mediated transformation in Phalaenopsis aphrodite

Abstract

Phalaenopsis aphrodite (moth orchid) is visually attractive and it is one of the most important floriculture species in economic aspect. A stable transformation system was generated in this study enables to yield new plant type as well as novel functional genomic studies. Here, we develop a stable and efficient Agrobacterium-mediated transformation using protocorm derived from tetraploid and diploid Phalaenopsis orchids. T-DNA vector construct containing eGFP driven by Ubiquitin promoter was subjected for transformation eventually with approximate 2.6% transformation rate. Genomic PCR confirmed hygromycin selection marker, HptII gene and target gene eGFP are integrated in orchid genome. Southern blotting indicated that low T-DNA insertion number in orchid genome of the transformants. Western blot further confirmed the expression of eGFP protein in the transgenic orchids. Furthermore, fluorescent GFP signal was visualized in the transgenic orchid under microscopy. Backcrossing transgenic pollinia to the stigma of four different Phalaenopsis orchid varieties, the BCF1 progenies showed hygromycin resistance and susceptible in 1:1 ratio. In additions, all survival BCF1 explants showed HptII positive in PCR and expressed GFP protein using Western blot. Herein, a stable, efficient, and inheritable transformation method in Phalaenopsis orchid is demonstrated.


Organisation

Email Address


Kui Lin-Wang1, Cecilia H. Deng1, Scott Wang2, Luigi Falginella3, Guido Cipriani3, Vincent Bus4, Andrew C. Allan1,2, Richard Espley1, Joanna Bowen1 1The New Zealand Institute for Plant & Food Research Ltd, (Plant & Food Research), Mt Albert Research Centre, Private Bag 92169, Auckland, New Zealand 2School of Biological Sciences, University of Auckland, Auckland, New Zealand 3 Dipartimento di Scienze Agroalimentari, Ambientali e Animali, University of Udine, Via delle Scienze 206 - 33100 Udine – Italy 4The New Zealand Institute for Plant & Food Research Ltd, (Plant & Food Research), Hawke’s Bay Research Centre, Private Bag 1401, Havelock North, New Zealand [email protected]

Dynamic changes in global gene expression during the apple response to Venturia inaequalis Apple scab caused by the ascomycete fungus Venturia inaequalis is one of the most serious diseases affecting the apple industry. However, the molecular mechanisms of the apple response to V. inaequalis are not well understood. Here, changes in global gene expression patterns was studied, of apple leaves from the susceptible accession ‘Royal Gala’ and resistant accession A248R04T010 carrying the scab resistance gene Rvi5. The numbers of differentially expressed genes between inoculated leaves and non-inoculated controls (water control) were 2995 and 5427 at 24h and 48h post inoculation, respectively, in A248R04T010, but only 31 and 419 in ‘Royal Gala’. The results also showed that the responses of transcription factor (TF) WRKYs to V. inaequalis mainly started at 48h post inoculation, while the responses of MYB TFs to V. inaequalis could start as early as 24h post inoculation in A248R04T010. Furthermore, among the differentially expressed genes in A248R04T010, almost all the WRKYs were upregulated, while there were similar numbers of up-regulated and down-regulated MYBs. Pathogenesis-related genes, biosynthetic genes involved in secondary metabolic pathways, and cell wall genes were differentially expressed in A248R04T010, while very few of these genes were differentially expressed in ‘Royal Gala’ in response to V. inaequalis inoculation. Our studies demonstrate dynamic changes in global gene expression during the apple pathological response to V. inaequalis and provide valuable data for future studies on the molecular mechanisms of apple responses to this fungus.


Akiko Kozaki

Organisation

Shizuoka university

Email Address

[email protected]

Poster Title

Functional analysis of INDETERMINATE DOMAIN family genes mainly expressed in seeds.

Abstract

Seeds accumulate large amounts of storage compounds such as carbohydrates, proteins and oils. Therefore, seeds represent the major source of nutrients for animals and humans. There is also tremendous interest in using seeds as a sustainable alternative to fossil reserves. The main metabolic pathways necessary for oil, starch or protein accumulation are well characterized. However, the overall regulation of partitioning between the various pathways remains unclear. Understanding the mechanism of regulation of seed development and germination could provide new molecular tools for improving the qualities of crop seeds Seed development consists of different developmental phases, i.e., maturation, dormancy, and germination. Studies have shown that many components, including plant hormones, such as gibberellins (GA) and abscisic acid (ABA), light, and temperature are involved in seed development. However, the mechanism which controls the transition between different developmental stages is still unclear. The purpose of the research is to clarify the molecular mechanisms which control the transition between these different developmental phases. We found that five INDETERMINATE DOMAIN (IDD) family transcription factors in Arabidopsis mainly expressed in seeds are involved in the regulation of seed development. The IDD family transcription factor was first identified as a regulator of maize flowering and recent studies show that some IDD transcription factors play important roles in GA signaling pathway, root patterning and gravitropism. We analyzed T-DNA tag lines of these genes and found that these T-DNA lines showed different GA and ABA during germination and hypocotyl elongation. The expression of genes involved in GA or ABA signaling in T-DNA tag lines during seed development was also analyzed and several genes showed different expression from wild type plants. In this presentation, we are going to discuss the function of these genes in seed development and germination.


Senthil Kumar Thamilarasan, Jeong Suk Hyeon Han, Sathishkumar Natarajan, Jong-In Park and Ill Sup Nou

Organisation

Sunchon National University

Email Address

[email protected]


De novo Assembly and Transcriptome Analysis of Bulb Onion (Allium cepa L.) during Cold Acclimation using Contrasting Genotypes Bulb onion (Allium cepa) is one of the second most widely cultivated and consumed vegetable crops in the world. During winter where the temperature can be as low, plant could get cold injury and limit the production of bulb onion. However, the genomic resources available for bulb onion are still very limited. To date, no studies about heritably durable cold and freezing tolerance were carried out in bulb onion genotypes using high-throughput sequencing technology was applied. We sequenced cold (2°C) freezing (-5 and -15°C) treated and control (25°C) samples of cold freezing tolerant (CFT) and cold freezing susceptible (CFS) genotypes of A. cepa lines. Obtained a total of 4,52,194,370 high quality reads, after de novo assembled into 54,047 genes and generated with an average length of 1,331 bp. Based on similarity search with known public nonredundant (NR) database, including KEGG and COG. Differentially expressed genes (DEGs) were investigated using log10 value of FPKM method. Over 5,167 genes, 491 genes were common DEGs during freezing temperature in CFT and CFS libraries of 25vs-5°C respectively. Additionally, increase our understanding of the DEGs, we performed GO and KEGG pathway enrichment analyses of all genes and iPath interactive analysis found that 31 pathways several metabolism of carbohydrate, nucleotide, energy, cofactors and vitamins, other amino acids and xenobiotics biodegradation. Further confirmed the results with qRT-PCR were differently regulated and known to be associated with cold and freezing stresses. Additionally, we identified putative molecular markers of 4,437 SSRs and 6,076 SNPs also SNP substitution through in silico prediction. Our study is the first to provide the transcriptome sequence resource of Allium spp., for cold and freezing stress. These data provides a valuable resource of genetic and genomic studies of Allium sp.


Agnieszka Mudge, Carmel Pilotti and Ian Godwin

Organisation

University of Queensland (AM & IG) and PNG-OPRA (CP)

Email Address

[email protected]


Genomic Approaches To Understanding Diversity And Ganoderma Resistance In Oil Palm (ELAEIS GUINEENSIS JACQ.). Oil palm (Elaeis guineensis Jacq.) is a long term perennial crop of great economic importance to many countries in tropical Asia/Oceania, providing export revenue and much needed income to both large plantations and smallholders. Oil palm is the most efficient oil producing plant, with an annual production per hectare more than five times that of any other vegetable crop. Unfortunately basal stem rot (BSR) caused by the white rot fungus Ganoderma boninense poses a major threat to the oil palm industry, and hence to farmers’ livelihoods. The only long-term control for this disease is through implementation of improved cultural practices and the use of more resistant planting material. In this ACIAR-funded project we have a field trial of more than 2000 oil palm progenies from 81 partially nested families bred in Dami, PNG. The purpose of this trial is to identify germplasm that may be susceptible and/or resistant to BSR and identify molecular markers linked to these traits. We used simple sequence repeat (SSR) markers (Billotte et al., 2005) to ascertain the level of genetic diversity present in our trial palm populations and their parents. A total of 133 alleles were generated from 18 loci. Cluster analysis revealed associations among progenies which were in agreement with the pedigree data. We are now using GBS markers (DArTseq; Diversity Arrays, Canberra) to gain full genome coverage to undertake association with yield, yield components and BSR resistance.


Nalisha Ithnin, Intan Safinar Ismail, Leona Daniela Jeffery Daim, Tony Ooi Eng Keong, Hirzun Mohd Yusof, David Ross Appleton

Organisation


Email Address

[email protected]

Poster Title

Investigation of Phenolic Profiles in Ganoderma Infected Palms

Abstract

The detection of oil palm basal stem rot (BSR) disease instigated by Ganoderma boninense is a challenging task for researchers due to the indistinctness of its symptoms during the early stage of infection. In this study, the changes in oil palm biochemical composition were measured using phenolic compounds as biochemical indicators for BSR disease. A rapid and sensitive analysis protocol combining Ultra Performance Liquid Chromatography with Triple Quadrupole Mass Spectrometer (UPLC-TQMS) was used to detect and quantify each compound of interest. Ten phenolic compounds were found to be consistently present in oil palm leaves throughout 5 time points, with caffeic acid (91.75±0.20 ppb) in 6 month old seedlings being the most abundant in control followed by rutin in 5 month old seedlings (34.73±0.46 ppb). From differential analysis between control and infected samples, chlorogenic acid, syringic acid and rutin revealed important differences in concentration, suggesting their potentials as markers for BSR disease detection.


Vivian A. Panes1, Ai Kitazumi2, Myles Butler2, Reshan D. Baoas1 and Benildo G. de los Reyes2 1Department

Organisation

of Biology, School of Science and Engineering, Ateneo de Manila University, Loyola Heights, Katipunan Avenue, 1108, Quezon City, Philippines 2Plant Molecular Genetics and Functional Genomics Laboratory, 5735 Hitchner Hall, University of Maine, Orono, Maine 04469, USA

Email Address

[email protected]


Unlocking the Transcriptome of the Mature Embryo of Moringa oleifera Lam.: An Oil Rich Plant Moringa oleifera seeds are capable of producing 40% edible oils that are gaining significance due to its nutritional advantages. Several studies have examined M. oleifera seed oil, nevertheless, these studies focused on the extraction of oil and methods of biodiesel production. There is a paucity of information on transcriptome level studies to determine the unigenes involved in oil biosynthesis metabolic pathways. The main objective of this study is to explore the transcriptome of the mature embryo of Moringa oleifera Lam. particularly the key genes related to oil biosynthesis. The transcriptome reflects the set of genes that are actively expressed at any given time produced in one or a population of cells in a given organism. Total RNA was extracted from thirty mature seed embryos obtained from 10 trees in Nueva Ecija, Philippines. RNA were pooled for cDNA library construction. Then, RNA-sequencing was done followed by de novo sequence assembly to provide a cost-effective and comprehensive means of transcriptome level information for M. oleifera. A total of 182,588 transcripts were generated in this study. Out of these transcripts, 3,210 unigenes are involved in oil biosynthesis. The most numerous group of unigenes are those involved in fatty acid metabolism with 874 unigenes, fatty acid biosynthesis with 872 unigenes and triacylglycerol metabolism with 552 unigenes. There are 25 unigenes encoding for transcription factors involved in regulating oil biosynthesis gene expression. This is the first transcriptome resource ever reported for M. oleifera mature seed embryo. These unigenes are unmatched in protein databases for M. oleifera. Hence, the transcriptome resource for the M. oleifera Lam. mature seed embryo generated in this study will be useful for the mapping of oil biosynthesis related genes and the understanding of metabolic pathways which could possibly be used to improve seed yield and oil content of M. oleifera.


Moloya Gohain*, Fei-Man Hsu, Kshitij Tandon, Lin-Yun Kuang, Pao-Yang Chen

Organisation

Institute of Plant and Microbial Biology, Academia Sinica, Taiwan

Email Address

[email protected]

Poster Title

Dynamics of transcriptome and methylome of rice during regeneration

Abstract

Background Tissue culture is used to establish desired phenotypes in plants. Callus culture and regeneration are critical steps in this process. Calli of Oryza sativa japonica (cv. TNG67) and Oryza sativa indica (cv. IR64) have varying regeneration efficiencies. Genetic diversity could partly account for such differences but the epigenetic response to different cell culture environment could also play a role. We aimed to study the role of DNA methylation during the tissue culture process in determining its outcome. Method We studied the transcriptomes (RNA-seq) and methylomes (BS-seq) of TNG67 and IR64 rice in comparisons between the embryonic stage (T0) versus 1. callus induced (T1) 2. callus sub-cultured (T2) 3. failed (TF) and 4. successfully (TS) regenerated calli. Findings Gene expression and DNA methylation in rice changes in the course of tissue culture. Stage-wise resolution of the methylome revealed a decline in the percentage of hyper methylated genes from 50% in the embryo to 25% in the regenerated calli. In contrast the percentage of upregulated genes increased from 50.8% to 54.2% in indica and from 46.83% to 51.55% in japonica as the embryo progressed towards regeneration. Differentially expressed genes (DEGs) and DMR associated DEGs between the embryonic stages and the later stages were related to carbohydrate metabolism, stress tolerance or cellular activities essential for growth, development and differentiation of the callus. Integrating the comprehensive transcriptome and methylome profiles with GO enrichment analysis we found an early emergence of processes responsible for imparting better stress-tolerance in TNG67 during the tissue culture process making it more resilient to external stressors than IR64. Conclusion The high resolution data from the embryo, the induced, sub-cultured and regenerated calli of both rice lines will serve as references for future molecular studies of rice epigenetics. Epimutations in stress related loci can be potential biomarkers for the pre-selection of calli for the improvement of regeneration protocols.

- 22 Contributing Author(s) Organisation Email Address


Sanimah Simoh, Chandradevan Machap, Mohd Waznul Adly Mohd Zaidan, Lina Rozano, Fazri Ab Rahim, Muhammad Aizuddin Ahmad, Alizah Zainal, Indu Bala Jaganath Biotechnology & Nanotechnology Research Centre, MARDI, Persiaran MARDI-UPM, 43400, Serdang, Selangor, MALAYSIA [email protected]

Metabolomics and gene expression studies to evaluate the anti-cancer activity of Phyllanthus and Curcuma spp extract mixture History showed that plants have been traditionally used for the treatment of various diseases since years ago. Last few decades had shown an explosion of research related to the role of bioactive compounds from plants to treat or reduce the risk of different type of cancers. The present study aims to evaluate the effectiveness of the formulated extracts of from two different herbs in reducing the proliferation of colon cancer cells using metabolomics and gene expression studies. Extract mixture of Phyllanthus and Curcuma spp was formulated and optimized based on the availability of the phytochemical contents and marker compounds present in both plants. Metabolomic analysis of the formulated extract showed a few significant bioactive compounds that could be the chemical markers of the formulated extracts. An investigation of the bioactivity of the formulated herbs primarily involved the application of in-vitro evaluation using colon cancer cell lines. The treatment of the extract formulation on human colon cancer cell lines showed that the formulation could inhibit the proliferation of colon cancer cells at a significant dose comparable to the anti-cancer drug. Gene expression study coupled with bioinformatics study showed that the formulated extract positively regulated 25 genes involve especially on the pathway of apoptosis, proliferation and antioxidants. This study suggests that the bioactive compounds in the formulated extract may exert the anticancer activity which can be evaluated further.


Nurshazwani Amalina Sudirman*, Arutchelvam Balakrishnan, Khairun Hafizah Mohd Zain, Hafiza Abidin, Airin Niza Za’ba, Fong Po Yee, Fairuz Farhana Mohd Rodzik, Mohd Nor Azizi Shabudin, Teh Chee Keng, Sukganah Apparow, David R. Appleton

Organisation


Email Address

[email protected]

Poster Title

Sime Darby’s High-throughput Marker Deployment In Oil Palm

Abstract

With the need to increase the performance of commercial Oil Palm planting materials, and based on robust in-house GWAS findings; Sime Darby has embarked into implementation of marker assisted selection in our breeding programs. We have developed and optimized a deployment pipeline tailored especially for oil palm using the available high throughput technology in the market. Sampling and DNA extraction capacity that stands up to 5000 samples per week and genotyping platform that can process 250,000 data points per day are the key components that drives our first 6 months experience of large-scale marker assisted breeding. To facilitate handling very large amounts of data, we have built information tools and protocols that are able to efficiently process and present information for selection of elite oil palms. Despite challenges, high throughput marker deployment in oil palm is possible and will provide an unprecedented opportunity for oil palm breeding programs.


Hyeon Jin Park, Won-Young Han, Won Tae Jeon, Jong Soo Ryu, Jin Woo Bae, Su Min Jo, Jong-Min Ko, In-Jung Lee and Hang Won Kang

Organisation


Email Address

[email protected]

Poster Title

Soybean Growth and Yield Response in Paddy Field Cultivation with P.E. mulching

Abstract

Soybean cultivation in paddy field has been maintained at high levels in Southern region of Korea. Overproduction of rice and following its price decline forced farmers to switch from rice to upland crop cultivation in paddy field. Recently, P.E. mulching is widely adopted in these regions, for saving its merits in reduction of manpower in weed control and conservation of soil moisture during drought season. Despite the importance of P.E. mulching, very few studies have examined the effects of P.E. mulching on soybean growth. Field experiment was conducted at Department of Southern Area, National Institute of Crop Science, RDA located in Miryang, Gyeongsangnam-Do in upland and paddy field with mid-late maturity cultivar Daewon. Soybean was planted in June 20 with interrow spacing of 55 cm × 20 cm (Non-mulching and P.E. covering). Soil moisture and temperature was recorded during soybean growth by using data logger (Spectrum Technologies Incorporated, 2010). Data on soybean growth parameters such as height, number of branches and nodes and length of each node were recorded from July 24 to August 13. The effect of P.E. mulching on soybean growth and lodging was recorded in a week interval. Also soybean yield components and yield were measured after seeds were air-dried until seed moisture reaches 14%. Experimental data were analysed by using PROC DMRT for mean comparison. Soil moisture content was higher in P.E. mulching than non-mulching plot in both paddy and upland field. Soil moisture content and soil temperature were less varied in paddy field because of the high water retention capacity. P.E. mulching in paddy field had a significant impact on plant height, and node number compared to non-mulching plot. Plants in non-mulching plot showed longer internode length from the beginning (i.e., first), which is located between the cotyledonary node (V0) and unifoliolar node (V1) to fifth internode (V4), whereas in P.E. mulching plot recorded longer internode length only from sixth internode (V5). Tenth internode showed the longest length in P.E. mulching (7.6 cm) than the plants in non-mulching plot, which is responsible for lodging. Higher possibility of yield potential of P.E. mulching plot in paddy field due to more nodes availability to serve as sites for flowering and pod development, but the possibility of stem lodging also increases due to acceleration of plant growth. The interaction of site and treatments had no significant effect on grain weight and yield in both paddy and upland cultivation. In paddy field, grain weight and yield were increased by 8.2%, and 9.9%, respectively in P.E. mulching than non-mulching plot. However about 2 days maturation delay was observed in P.E. mulching plot (paddy). Higher moisture content beneath cover material (especially in paddy field) promotes soybean growth, resulting in higher yield.

Keywords: P.E. mulching, shifting cultivation, moisture content, internode length, stem lodging


Jin Woo Bae, Su Min Jo, Hyeon Jin Park, Jong Soo Ryu, Won-Young Han, Won Tae Jeon, Jong-Min Ko and Hang Won Kang

Organisation


Email Address

[email protected]

Poster Title

Soybean Planting Date and Density for Harvesting with Combine

Abstract

Soybean is one of the most important leguminous crops in the world and it is being widely used in Korean food. Recently, Korean government is planning to expand soybean acreage in paddy because of over production and price descending of rice. There is also a challenge for solving the problem of aging population and rising wages. In this context, saving labor power cultivation will be helping hands to solve these problems. Using combine can save manpower up to 94% compared to customary practice. Objective of this study was to set planting skills for harvesting using machine, thus saving labor force and contribute to price stabilization. Soybean was planted during June 15 to July 5 with 15 days interval, and planting distance was 20, 30, 40 cm (2 column per high furrow to maintain constant cutting height). Soybean cultivar, Uram was used because of its high suitability for mechanization. Days to flowering was shorter in late planting compared with early planting because of shorter photoperiod and low temperature. Days to maturity was not varied in three of planting dates. Stem length was the highest in June 15 planting compared with other planting dates, but soybean planted in this date showed the smallest stem thickness, and this might contribute to high possibility of lodging. When lodging is seriously occurred, harvesting with combine can lead yield loss due to increased cutting height. Therefore, in early planting (June 15), cultivation method like pinching to prevent lodging is required. June 24 planting showed the similar soybean yield with June 15 planting, but significant lodging was occurred. Also, planting with spacing of 30 cm showed 4% yield increase with thicker stem diameter thus appropriate to combine harvesting.

Keywords: Soybean, density, combine harvesting, spacing, maturity


Su-Min Jo, Ki-Youl Jung, Won-Tae Jeon, Jong- Soo Ryu, Won-Young Han, Jin- Woo Bae, Hyeon Jin Park, Jong-Min Ko, Hang-Won Kang

Organisation Email Address


[email protected]

Antioxidant Compounds and Antioxidant Activity of Sorghum with Different Drainage Methods The main bioactive components of sorghum (Sorghum bicolor L. Moench) are known as tannins, phenolic acids, anthocyanins, phytosterols, policosanols, etc. Especially, tannins affect the antioxidant activity. Total polyphenol, flavonoid and tannin contents showed significant differences by drainage methods. This study investigated the changes of antioxidant contents and antioxidant activity of sorghum by drainage methods in poorly drained sloping paddy field. Soils with very poorly drained (VPDP) and imperfectly drained paddy soil (IDP) were used in this study. Two drainage methods such as under pipe drainage (UPD) and open ditch drainage (ODD) were installed within 1-m position at the lower edge of the upper paddy fields. The soil moisture contents of UPD and ODD were 18.52±4.58 and 19.01±4.25%, and 14.87±4.82 and 18.64±3.85%, cultivated in VPDP and in IDP respectively. Moisture, crude protein, crude fat and crude ash contents were 12.70∼14.50, 0.28∼7.02, 4.29∼5.04, and 1.31∼1.93 g/100 g, respectively. Similarly, P2O5, K, and Ca contents were 206.18∼822.84, 424.16∼579.36, and 27.78∼68.54 mg/100 g, respectively. The total polyphenol, flavonoid and tannin contents, and radical scavenging activity of the ethanolic extracts of sorghum were significantly varied between two drainage methods (UPD and ODD). The total polyphenol, flavonoid, and tannin contents by drainage methods (UPD and ODD) were 28.33∼50.26 mg GAE/g, 5.24∼17.10 mg CE/g, and 9.32∼25.75 mg TAE/g, respectively. The DPPH and ABTS radical scavenging activities were 20.00∼38.61 and 34.60∼74.73 mg TE/g(DPPH and ABTS), respectively. Therefore, antioxidant compounds and radical scavenging activity of the sorghum expected to be affected by different drainage methods. This study is expected to contribute as a reference of genomic research to develop new methods to increase antioxidants contained in sorghum.

Key words: sorghum (Sorghum bicolor L. Moench), drainage method, polyphenol, radical scavenging activity


Anusha Nair, Ainul Masni Othman, Katharina Mebus, Koo Ka Loo, Wong Yick Ching, Hirzun Mohd Yusof, David Ross Appleton & Harikrishna Kulaveerasingam

Organisation

Sime Darby Technology Centre Sdn. Bhd., Sime Darby Plantation, Malaysia

Email Address

[email protected]

Poster Title

Lipases in Oil Palm Fruits

Abstract

Lipase enzyme (EC 3.1.1.3) plays a major role in breaking down triacylglycerols (TAGs) to free fatty acids (FFA) in Elaeis guineensis oil palm fruits upon harvesting and bruising. High levels of FFA deteriorates the oil and should be removed during the refining process. However, this increases the cost of processing. The aim of this research is to identify the key lipases that are highly involved in FFA accumulation after the harvesting process. Twenty five lipase genes were identified in oil palm mesocarp tissue through bioinformatics analysis. The lipases sub-domain consists of esterase or lysophospholipase, lipase 3, partial α/ß hydrolase, patatin-SDP like, serine esterase and SGNH plant lipase like. Among the lipase genes tested upon bruising of oil palm fruits, LIP_1 gene had the highest expression level upon bruising of the fruits, while LIP_26922 showed highest upon harvesting of the fruits. Seven other lipase genes showed high expression levels over time after bruising of the fruits. Tissue blot analysis on the localization of LIP_26922 was found to be concentrated in the exocarp layer of the oil palm fruits. Currently, indepth research are being done to investigate the methods to reduce the expression of these lipases in the fruits.


Saeid Kadkhodaei, Siti Nor Akmar Abdullah, Farzaneh Ahmadi and Siti Mariyam Ijab

Organisation

Institute of Tropical Agriculture, Universiti Putra Malaysia

Email Address

[email protected] [email protected]

Poster Title

In silico analysis of phosphate-starvation-inducible PHT1 gene from oil palm

Abstract

Specific combinations of motifs in the promoter regions of genes regulate functional processes in the cells. Analysis of such promoter regions in specific functional contexts can be used to decipher molecular mechanism regulating the gene expression in response to internal and external stimuli. Furthermore, in silico characterization of the encoded protein product might help in better understanding of the role of gene of interest in the identified cellular process. The aim of this study was to utilize both oil palm high-affinity phosphate transporter (EgPHT1) coding and promoter sequences in silico analysis to predict Pi-starvation-associated motifs as well as the functional domains embedded in the protein structure. Phosphate is an important macronutrient but its uptake is hampered in acidic tropical soils used in oil palm cultivation. In our initial study we identified a cDNA clone specifically expressed under phosphate-starvation condition in oil palm roots. The deduced amino acid sequence has the characteristic PHT1 structure with 12 transmembrane domains separated by a central hydrophilic region. The main domains predicted in EgPHT1 include binding-protein-dependent transport system inner membrane component, major facilitator superfamily, transmembrane receptor, ATP synthase A chain and NADHUbiquinone/plastoquinone. Phylogenetic analysis revealed Oryza sativa-OsPT6 as the most similar PHT gene to EgPHT1. Comparison of 77 promoter motifs identified within 1500 bp upstream of ATG of this gene with 10 promoters of high- and low-affinity phosphate transporter genes from both monocots and dicots showed that they contain a number of common motifs. Among them, a few occur at significantly (p