Biotechnology and Biosafety Capacity

of Sri Lanka

Prof. Athula Perera

Senior Professor; Director PGIA

University of Peradeniya

Sources of information

CARP, NSF

Presentations – 2009, 2010

Who, What, When, Where?………. A Glimpse!

Local funding agencies

CARP Recurrent budget distribution by discipline 2003

Source: INFORM-National database 2003

Estimated number of researchers/science and technology personnel in the Biotech Sector

Within the definition of biotechnology in Sri Lanka,

264 personnel are engaged in teaching and research in biotechnology

Source: Database of Ministry of Environment and Natural Resources, 2005

CARP: FAO Report: 2007Dept. Agric. Biology, Faculty of Agriculture, University of PeradeniyaMolecular Characterization/ Genetic Diversity Assessment -Rice, Aspergillus; Gene isolation - Rice

salt tolerant genes; Molecular pathology - Banana, Tomato, Rice; Marker Aided Selection/Use of Molecular Markers for crop improvement; Biological control

Dept. Crop Science, Faculty of Agriculture, University of PeradeniyaMicropropagation of woody & floral species; Secondary metabolite production

Agric. Biotechnology Centre, Faculty of Agriculture, University of PeradeniyaMolecular characterization of Nelli, Garcenia; Molecular breeding of tomato, chilli

Dept. of Botany, Faculty of Science, University of PeradeniyaMarker assisted breeding for abiotic stress tolerance

Dept. of Botany, Faculty of Science, University of RuhunaGenetic differentiation of fishes, mangroves; Genetic characterization of Munronia; Biological control of

soil-borne pathogens; Molecular characterization of cinnamum; Molecular characterization of genes of Pythium and Pseudomonas interaction.

Dept. of Zoology, Faculty of Science, University of RuhunaPhylogeny of freshwater fish; Phylogeny of crustaceans

A Summary….

Institute Technology Organism/GeneFoAg, UoPeradeniya

Molecular characterization

Rice, Aspergillus, Nelli, Garcenia

Gene isolation Rice/Salt tolerance.

Molecular breeding, Molecular pathology

Tomato, Chilli,Banana, Tomato, Rice

Micropropagation,Secondary metabolites

Woody, Floral sp.

FoSci. UoRuhuna Mol. Characterization Fish, Mangroves, Cinnamum, Munronia

Biological controlPhylogeny

Soil-borne pathogensFreshwater fish, Crust.

FoSci. UoPeradeniya

Marker Assisted Selection

Abiotic stress tolerance

NSF Journal Publications : 2007 - 2009Callusing and regeneration of three genotypes of Oryza sativa ssp. indica by 2,4 dichlorophenoxy acetic acid (2,4-D). 2007. Detection of sequence characterized amplified region (SCAR) markers linked to sex expression in Carica papaya L. 2007. Potential of RAPD markers for identification of fruit types of Artocarpus heterophyllus Lam. (Jackfruit). 2007.Genetic diversity in a population of Dendrocalamus giganteus Wall. ex Munro (giant bamboo) in the Royal Botanic Gardens in Peradeniya. 2007.Isolation of raw starch hydrolysing fungi and purification of alpha-amylase from Geotrichum candidum. 2009Analysis of coconut (Cocos nucifera L.) diversity using microsatellite markers with emphasis on management and utilisation of genetic resources. 2009.Assessment of genetic diversity of tea (Camellia sinensis L.O. Kuntze) as revealed by RAPD - PCR markers. 2009In-vitro dialysability of iron in green leafy vegetables and seasonal variation of total iron content. 2007.In vitro thrombolytic activity of Sri Lankan black tea Camellia sinensis (L.) O. Kuntze. 2008. Somatic embryogenesis in papaya (Carica papaya L. cv. Rathna).2008Setting up a polymerase chain reaction assay for the detection of toxic cyanobacteria. 2008.The effect of DNasel enzyme on food pathogens subjected to different food processing treatments.2007.In vitro mass propagation and greenhouse establishment of Munronia pinnata (Wall) Theob. (Binkohomba).2007.Production of embryogenic callus from leaf explants of Camellia sinensis (L.).2007Systemic resistance induced by Trichoderma harzianum RU01 against Uromyces appendiculatus on Phaseolus vulgaris. 2009.In vitro mass propagation and greenhouse establishment of Withania somnifera (L.) Dunal (Solanaceae) and comparison of growth and chemical compounds of tissue cultured and seed raised plants. 2009.

NSF Journal Publications: 2007-2009• Rice : Micropropagation• Papaya: Somatic embryogenesis; SCAR

markers• Jak fruit: RAPD markers• Giant bamboo: Genetic diversity• Coconut: Diversity using Microsatellites• Tea: Embryogenic callus formation;

Genetic diversity using RAPDs• Leafy vegetables: In-vitro studies• Medicinal plants: In-vitro propagation

• Other publications….• Medical:• A study of immunological profile, disease characteristics and socioeconomic

status of a population of rheumatoid arthritis patients in Sri Lanka. 2009. Dept.o Zoology, FoSci.+ National Hospital, Sri Lanka + I.B.M.B. UoC.

• Distribution of filarial elephantiasis and hydrocele in Matara district, Sri Lanka and an immunological survey in areas with relatively high clinical rates. FRTS Unit, FoM, UoR + FoSISci. Nihon Fukushi University,Japan

• Novel sequence variants and a high frequency of recurrent polymorphisms in BRCA1 gene in Sri Lankan breast cancer patients and at risk individuals. IBMB. UoC. + UoU, Sweden. + NCI, maharagama + FoM, UoC.

• Natural Human Antibody Responses to Plasmodium vivax Apical Membrane Antigen 1 under Low Transmission and Unstable Malaria Conditions in Sri Lanka. 2006. DoZ, FoSci. UoC + MRI, FoM, UoC., BPRC, The Netherlands

• Agriculture• Comparative analysis of starch properties of different root and tuber crops

of Sri Lanka 2009. DoAg.Bio. FoAg. UoP + NARC, Japan.• AFLP Analysis of Genetic Relationships and Diversity of Sri Lankan Oryza

sativa Cultivars.2010. IBMB, UoC. + AgBC, UoP. + PGRC• Ex situ conservation of medicinal plants in Valikamam area of the Jaffna

Peninsula. 2009. UoJ

A Summary…

Institute + Coll. Technology Organism/geneFoSci. UoC + IBMB Immunology, Dis.

chara.Rheumatoid, arthritis patients

IBMB UoC + UoU Sweden + Ncl Maharagama + FoM UoC

Sequence variation in BRCA1 gene

Breast cancer patients

FoSci. UoC + MRI + FoM UoC + BPRC, Netherlands

Natural human antibody response to malaria

Malaria

FoAg. UoP + NARC Japan

Starch properties Tuber crops

IBMB UoC + AgBC UoP + PGRC

AFLP analysis Rice

UoJ’pura Ex-situ conservation Medicinal plants

Presentations: 2009/2010 : Medicine• Identification of bacterial strain producing alpha-amylase –

University of Jaffna• Induction of CD80 gene expression in B-lymphocytes –

Sabaragamuwa University + ICGEB, India• Molecular diagnostics for confirmation of infectious diseases in Sri

Lanka : University of Kelaniya• Use of VectoBac for control of Culex mosquitoes : UoK• Genetic diversity in Plasmodium vivax surface protein: University of

Colombo• Isolation of fungus from Ophiorhiza producing anti-cancer agent:

University of Sri J’pura• Effect of ovarian aspartic proteinases in modulating IGFBP-3:

University of Peradeniya + University of Hokkaido, Japan.• Characterization of antibodies against venom of Sri Lankan cobra: UoP• Molecular diagnosis of Tuberculosis in Kandy & Matale: UoP• Comparison of multiplex RT-PCR with clinical data in diagnosis of

dengue fever: UoP

A Summary….

Institution Technology Organism/GeneUoJaffna Microbiology Bacterial strains

Uo Sabaragamuwa + ICGEB, India

Gene expression CD 80 gene

Uo Kelaniya Molecular diagnosisVectoBac

Infectious diseasesControl of Culex

UoColombo Genetic diversity P. vivax

UoJ’pura Isolation of fungus Anti-cancer agent

UoP + UoH JapanUoPUoPUoP

ProteinasesMol. Charact.Mol. DiagnosisRT-PCR

IGFBR-3Antibody venom- CobraTuberculosisDengue

Agriculture (Plants/Crops)• Transformation protocol for Sri Lankan rice – FoSci. University of

Colombo• Locally isolated fungus to control Tea Spider mites – FoAg, University

of Peradeniya + Tea Research Institute• Diversity of Sri Lankan egg plants based on SSR characterization –

FoAg, UoP, HORDI, Polytechnical University, Spain• Molecular screening of rice germplasm for fragrance- RRDI, FoAg. Wayamba

University• Detection of virus & viroids in citrus by RT-PCR – Plant Virus Indexing

Centre, FoSci. University of Sri Jayawardenapura • Effects of biofilmed biofertilizers on soil-plant-microbes interactions in tea –

Sabaragamuwa University +IFS• Micropropagation of citrus – FoSci. Sab. Un. + HORDI• In-vitro propagation of carnation – FoSci. Sab. Un. + ITI • Proteomic analysis of Arabidopsis mutant of CSN to investigate gene-specific

functions: Faculty of Sci. University of Colombo• RAPD-PCR studies on six Sri Lankan traditional rice varieties: FoSci.

University of Colombo + CARP• Callus initiation and plant regeneration from Philodendron: FoSci. UoC +

Mike Biotech Asia (Pvt) Ltd.

Agriculture…….cnt.• In-vitro grafting of sweet orange species: FoSci. University of Ruhuna +

PGRC, Gannoruwa • SRAP markers for identification of cinnamomum species: FoSci. UoR +

Cinnamon R.S., Matara• cpDNA sequence variation in cinnamon sp. of Sri Lanka: FoSci. UoR + CRS,

Matara• In vitro shoot multiplication of cashew: University of Wayamba• Detection of YHV infecting Peneus by RT-nPCR: UoW• Bioremediation of rubber latex: UoW• Genetic purity of pineapples by morphological and molecular traits: UoW• Genetic diversity of cashew using RAPDs: UoW• Transformation of tomato by Agrobacterium method: UoW• Variation of ref Gene in natural rubber producing plants: UoW• Detection of anthurium blight by ELISA: UoW• Evaluation of Microsatellite markers for salt tolerance in rice: FoSci.

UoPeradeniya + RRDI

Agriculture, crops…….• New varieties of tomatoes using molecular and classical

breeding. PGIA, UoP. 2010• In-votro mass production of a medicinal plant. 2009• Screening rice breeding lines for Xa21 gene using the

marker pTA248. 2009• Genetic linkage map of tea using SSRs. 2008• Detection of SCAR markers linked to sex expression in

papaya. 2008• Mitochondrial DNA-based analysis of variation among

Sri Lankan chicken and jungle fowl. 2009

A Summary…..Institute Technology Organism/GeneFoSci. UoColomboFoSci UoCUoC + CARPUoC + Mike Biot. Asia

Transgenic productionProteomicsRAPD-PCRMicropropagation

RiceArabidopsisTraditional RicePhilodendron

FoAg. UoP + TRIFoAg. UoP + HORDI + Polyt. U. Spain

BiocontrolMol (SSR) diversity

Tea mitesEgg plant

RRDI + UoWayamba Molecular screening Rice

PVIC DoA + UoJ’pura RT-PCR for virus det. CitrusUoSab. + IFSUoS + HORDIUoS + ITI

BiofertilizerMicropropagationIn-vitro propagation

TeaCitrusCarnation

UoR + PGRCUoR + CRSUoR + CRS

In-vitroSRAP markerscpDNA sequence

Sweet orangeCinnamomumCinnamomum

UoP + RRDI Mol. (SSR) markers Salt tol. Genes of rice

Summary Contd…Institute Technology Organism/GeneUoWayambaUoWUoWUoWUoWUoWUoWUoW]

In-vitro propagationDis.diag. RT-nPCRBioremediationMol. Charact.Mol. DiversityTransgenicsMol. VariationDisease diag.

CashewPeneusRubber latexPineappleCashewTomatoRef gene in rubberAnthurium blight

FoAg. UoPFoAg. UoP + AgBCFoAg. UoP + Nat.Bot.Gd

Mol. RelatednessMol. DiversityMol. characterization

Rhizobium sp.Mangrove sp.Exacum sp.

RRDI Biotech. applications Rice breeding

PGIA, UoP Molecular breeding Tomato

Agriculture….cnt.• Genetic relatedness of Rhizobium species nodulating legume crops:

FoAg. UoP• Genetic diversity of mangrove species using RAPDs: FoAg.UoP +

AgBC• Chracterization of Exacum species by RAPDs: FoAg. UoP + Nat. Bot.

Gardens• Biotechnology applications in rice breeding in Sri Lanka – RRDI, Rice

Congress 2010

• Animals, Aquaculture• Genetic diversity at TLR7 gene of Sri Lankan chicken and jungle

fowl – FoAg. University of Peradeniya + Chinese Acad. of Agric. Sciences

• Effect of thyroid hormone on zebra fish – Sab. Uni. + Katholieke University, Belgium

• Identification of pathogen in shrimp using PCR - Sab. Uni. + Nat. Aq. Res. Dev. Agency

Animals….cnt

• Use of florescence metabolites in Nile tilapia as a biomarker : FoSci. UoK

• Antibacterial properties of some Sri Lankan marine algae: FoSci. UoC• Electrophoretic analysis of Beta-Casein protein in milk: FoAg.

UoP + FoVet. UoP• Application of PCR to detect KOI Herpes Virus in Carps: FoVet.

UoP• Effect of ovarian aspartic proteinases in modulating IGFBP-3:

FoM, UoP + Univ.of Hokkaido, Jpn.• Genetic characterization of Jaffna sheep: FoAg. UoP

A Summary….

Institution Technology Organism/GeneFoAg. UoP + Chinese Ac. Of Agric. Sci.

Genetic diversity TLR7 gene: Chicken, Jungle fowl

UoSab + Kath.o.Belgium Hormonal effects Zebra fish

UoS + Nat.Aq.Res.D.A Dis. Daig. by PCR Shrimp

UoKelaniya Biomarkers Nile tilapia

UoC Antibacterial action Marine algae

FoAg. UoP + FoVet.UoPFoAg. UoPFoVet. UoPFoM UoP + UoH. Japan

Electrophoretic anal.Molecular charac.Virus detection: PCRGene modulation

Milk proteinsJaffna sheepCarpIGFBP-3

Microbial; Industrial……• Identification of bacterial strain producing alpha-amylase – FoM,

University of Jaffna• Detection of virus & viroids in citrus by RT-PCR – Plant Virus Indexing

Centre + Faculty of Science, University of Sri Jayawardenapura • Production of polyclonal antiserum for identity of Xanthomonas in anthuriums

- PVIC + National Plant Quarantine Service• Effects of biofilmed biofertilizers on soil-plant-microbes interactions in tea –

Sabaragamuwa Universiity +IFS• Molecular diagnosis of Fusarium strains from Welsh onion – Sab. Uni. +

Yamaguchi Univ. Japan• Identification of pathogen in shrimp using PCR – Sab. Uni. + Nat. Aq.

Res. Res. Dev. Agency• Mol. Characterization of Bt isolates from Sri Lanka – Sab. Uni. + ITI,

IBMBB, U o Colombo• Induction of CD80 gene expression in B-lymphocytes – Sab. Uni. +

ICGEB, India• PCR-based detection assay for fungus in coconut fibre dust – Sab. Uni.

+ Genetech

Microbial, Industrial……..cnt.• Genetic diversity in Plasmodium vivax surface protein: FoSci. UoC• Proteomic analysis of Arabidopsis mutant of CSN to investigate gene-specific

functions: FoSci. UoC• Antimicrobial properties of bryophytes : FoSci. UoC + ITI• Antibacterial properties of some Sri Lankan marine algae: FoSci. UoC• Screening of spore-forming bacteria from sesame roots for growth &

protection properties: FoSci. UoR• Insecticidal activity of Hirsutella against cabbage aphids: FoSci. UoR + ITI • Biocontrol efficiency of Trichoderma isolates for postharvest anthracnose of

rambuttan: UoJ • Antibacterial activity of extracts of flowers of Vitex negundo: FoSci. UoJ• Begomovirus-DNA associated with YV disease of some weeds: FoSci. UoJ• Study of nutrients, antioxidant activity & sensory qualities of flower extracts

of Beli; FoM UoJ• Amplification of Alpha amylase gene of Geotrichum for cloning: UoW• Bioremediation of rubber latex: UoW

Microbial, Industrial….cnt• Screening for GM soyfood at selected supermarkets: FoAg. UoP

+ Genetech• 18S RDNA-based characterization of local Aspergillus: FoAg.

UoP• Electrophoretic analysis of Beta-Casein protein in milk:

FoAg.UoP + FoVet.• Application of PCR to detect KOI Herpes Virus in Carps: FoVet.

UoP• Effect of ovarian aspartic proteinases in modulating IGFBP-3:

FoM UoP + Univ.of Hokkaido, Jpn.• Characterization of antibodies against venom of Sri Lankan

cobra: FoM, UoP• Genetic relatedness of Rhizobium species nodulating legume

crops: FoAg. UoP

A Summary….

Institution Technology Organism/GeneFoM, UoJaffna Production of enzymes Bacterial strains

UoSab. + Yamag.Univ. JapanUoS + ITI + IBMBB UoCUoS + Genetech

Mol. diag. of Fusarium

Mol. CharacterizationPCR detection of fungus

Welsh onion

Bt isolatesCoconut fibre

UoC Genetic diversity P. vivaxFoSci. UoRFoSci. UoR + ITI

Screening of bacteriaBiocontrol: I’cidal activity

Sesame rootsCabbage aphids

UoJ’puraFoSci. UoJFoM, UoJ

BiocontrolAntibacterial activityAntioxidant activity

Rambuttan anthracnoseExtracts from flowersBeli flower extracts

UoWayamba Gene amplification Amylase geneFoAg. UoP + GenetechFoAg. UoP

Screening of GM Food18S RDNA analysis

Supermarket food itemsAspergillus

Other

• Research in Biotechnology: NSF Journal• Development of virtual Bioinformatics Workbench for sequence analysis:

FoSci. UoC• GM Testing facilities – AgBiotech Centre, FoAg., UoP; Genetech• International Links (NSF): • FABA (Federation of Asian Biotechnology Association), ICGEB,

SAARC, UNESCO, IUBMB (International Union of Biotechnology & Molecular Biology); University of Western Sydney

NSF Research Grants 2005-2010• Science: • Genetic diversity of green turtles – SIDA 2005• Isolation and characterization of proteolytic enzymes – SIDA 2005• Characterization of goat & sheep parasite and human filarial parasite – SIDA 2006• Isolation of rock phosphate solubilizing bacteria – RG 2010

• Medical• Molecular markers for P. falciparum infections – SIDA 2005• Association of thrombophilic polymorphisms with recurrent pregnancy loss – SIDA

2005• Early detection of Listeria monocytogenes in milk and milk products – RG 2006• Dengue virus serotypes and genetic variability in relation to disease severity – SIDA

2006• Bionomics of Anopheles culicifacies species complex – SIDA 2006• Determination of drug resistant gene mutations among M. tuberculosis – RG 2007• Recombinant proteins as diagnostic intermediates for chikangunya, dengue &

leptospirosis – RG 2009• Mutations and sequence variants in breast cancer susceptibility – RG 2010

• Agriculture & Livestock• Phylogenetic relationships of genus Cinnamomum – SIDA 2005• DNA typing, molecular characterization of Exacum – SIDA 2005• Genetic variation of rice blast fungus – SIDA 2006• Identification of drought resistant rice varieties using molecular methods – RG 2007• Control of tomato bacterial wilt – RG 2007• 18s rRNA/rDNA based molecular characterization of Aspergillus oryzae – RG 2007• Light regulated development in plants – translational research – RG 2007• Typing of nitrogen fixing bacteria associated with rice – RG 2008• Clonal propagation of Santanum album – RG 2009• Construction of exppression vector cassettes containing genes for wheat proteins –

RG 2010• Use of microsatellites for identification of exotic, domestic & wild swine meat – RG

2007• Genetic characterization of native goat types – RG 2007• Population genetic analysis of Penaeus monodon – RG 2010

Contribution of Private Sector• Genetech, Colombo, Sri Lanka• Biostores : DNA kits……> chemical reagents; DNA Fingerprinting: Parental;

Forensic; Genetech School of Gene Technology - Special courses, Post-A level; Undergrad; Postgrad

• Genetech Research Institute - Molecular life sciences• Human/Animal disease diagnostics; Molecular systematics – animal, plant,

microbial; Current: 3-year grant from NIH, USA to study dengue

• CIC Agri Biotech • Serendib Hort. Technologies (Pvt) Ltd.• Hayleys AgriBiotech• Others

Biosafety

Sri Lanka Ratified Cartagena Protocol Biosafety Framework National Biosafety Law Food Act Plant Protection Act

National biosafety framework contd…

Regulation

Food (Control of Import, Labelling and Sale of Genetically Modified Foods) Regulations 2006 and shall come into operation on 1st January 2007

Prohibitions

IMPORT, TRANSPORT, DISTRIBUTION AND SALE OF -

1.Genetically modified organism as food for human consumption

2.Food containing or consisting of genetically modified organism

3.Food produced from or containing ingredients produced from genetically modified organism

WITHOUT THE APPROVAL OF THE CFA

GMOs (including GM seeds) Plant Protection Act of 1999

Biosafety Law of Sri Lanka

Workshops/Training programs

NBFSL - > 40 workshops on Awareness, Risk Assessment & Management, GM Testing ICGEB Regional Training Programme

on GM Testing : FoAg, UoP Risk Assessment & Management –

National & Regional

If safe

Researchers/Scientists √Institutes √Collaborations – national, regional, international √Funds – individual, agencies √

National priorities ?National Policies: What the people need !

Mahinda ChintanayaNational Biotechnology Policy

National Biosafety PolicyNational Agriculture PolicyApex Body - Coordinate