Safe transfer of rice germplasm

Contributors to this page: IRRI, Seed Health Unit, Los Baños, Philippines (Patria Gonzales, Evangeline Gonzales, Carlos Huelma, Myra Almodiel, Joel Dumlao).

Rice germplasm is under the mandate of IRRI. The Africa Rice Center works on this crop in Africa.
The following pages are grouped in the following sections:

•  Import and export requirements.
•  Technical guidelines for the safe movement of germplasm and detection of relevant pathogens and pests.
•   Best practices in place at IRRI.

At IRRI, The Seed Health Unit (SHU) has been designated as the Single Gateway for all incoming and outgoing rice seeds, rice grains (dehulled, polished, milled, powdered), non seed biological materials, and soil samples to and from the International Rice Research Institute.

As a Single Gateway, SHU ensures the following:

• that seed health status of rice seeds, rice grains for destructive analysis, non seed biological materials, and soil samples coming into IRRI (IMPORTED) meets Philippine plant quarantine regulations and standards before releasing to IRRI scientists (POST ENTRY CLEARANCE);
• that seed health status of rice seeds, rice grains for destructive analysis, non seed biological materials, and soil samples going out of IRRI (EXPORTED) meets plant quarantine regulations and standards of recipient countries (PHYTOSANITARY CERTIFICATION); and
• that the intellectual property rights protocols established by IRRI in line with its agreement with the International Treaty on Plant Genetic Resources for Food and Agriculture (ITPGRFA) are complied with in all incoming and outgoing materials (rice seeds, rice grains for destructive analysis, non seed biological.

SHU approach is to conduct seed health testing on all incoming and outgoing rice seeds.  In addition, the T.T. Chang Germplasm Genebank sends samples to SHU for seed health testing prior to storage.

Seed health testing activities: 

1.   Direct Visual Examination

Seedlots are examined for the presence of seed contaminants (i.e. storage insects, sclerotia, weed seeds, soil particles, seed of other crops, other plant parts) and seed conditions (i.e. insect-damaged seeds, discolored seeds, broken grains, smutted seeds, shriveled seeds, unfilled/partially filled seeds).  Any of these seed contaminants and /or seed conditions should not be present in the seedlots. If these are observed for outgoing seedlots, the applicants will be requested to do further cleaning or will be requested to replace seeds with seeds of better quality.  For incoming seedlots, SHU staff shall clean the seedlots.  Corresponding documentation are done (seed contaminants and seed conditions are qualified and quantified).

2.   Routine Seed Health Testing

• Blotter test - conducted for the detection of seedborne fungi.  The procedure is done in accordance to the International Seed Testing Association (ISTA) rules and standards. 
• Modified Baermann Funnel Method (Sedimentation Test) - conducted for the detection and extraction of seedborne nematodes.
• Macro test - conducted for the macroscopic detection of Tilletia barclayana, kernel smut fungi of rice.

Additional declarations (if stipulated in the Import Permit of Country of Destination.)
Seed Wash Assay test using semi selective media – conducted for the detection and isolation of seedborne bacteria.

3.   Other Activities

3.1    Seed Treatment

Recommended seed treatments

Seed treatments will be based on the results of seed health tests and on the requirements of the importing country. USA and India do not require chemical and physical seed treatments except fumigation. Standard treatments given to seeds are the following:

i. Hot water treatment. Presoak seed for 3 hours in tap water followed by dipping in hot water at 52-57^oC for 15 minutes and redrying to 14% MC. The hot water treatment may be followed by slurry or dusting of fungicide (Benlate) at 0.3% by seed weight as an ASEAN standardized seed treatment (1981 July 1-23, Kuala Lumpur Meeting).

ii.  Fungicidal treatment. Slurry treatment with Benlate 50 WP, Dithane M45, or a combination of both at 0.3% formulated product by seed weight (0.3 g/100 g seeds). Retest for efficacy of fungicidal treatments will be done on samples that have abnormally high infection. Samples that do not respond to treatments will be rejected or applicants will be asked for replacements.

iii.  Insecticidal treatment. The seeds may be treated with Diazinon at 0.5 g/100 g seeds when fumigation or hot water treatment could not be done.

Fumigation.  All seeds are fumigated with Phosphine gas at 2 g/cubic meter enclosed space at 28 ^oC for 72 hours.

3.2    Crop Health Monitoring

Conducted during active growth of the crop namely: seedling stage (inspection is conducted at seedbed), maximum tillering/booting stage, flowering stage, and maturity stage, wet and dry season.

3.3    Dispatch

Seed Packages for dispatch are accompanied by required documents:  Import Permit, Phytosanitary Certificate (signed by duly authorized Plant Quarantine Officer), Standard Materials Transfer Agreement, and Plant Quarantine Seal.

All of these documents are pasted outside the package and photocopies of these documents are provided and placed inside the package in addition to the list of materials.

References and further reading

Mew TW, Misra JK. 1994. A manual of Rice Seed Health Testing. IRRI, Manila, The Philippines, 114,pp.

Mew TW, Gonzales P. 2002. A handbook of Rice Seedborne Fungi. Los Baños (Philippines): IRRI, and Enfield N.H.(USA) Science Publishers Inc. 83 pp.

Import/export of rice germplasm

Contributors to this page: IRRI, Seed Health Unit, Los Banos, Philippines(Patria Gonzales, Evangeline Gonzales, Carlos Huelma, Myra Almodiel, Joel Dumlao).

Rice is a crop under the mandate of IRRI. It is very important to remember that an International Phytosanitary Certificate is always required for any plant germplasm exchange.

The requirements of countries that request and receive seed from IRRI Headquarters located in Philippines have been collected from the permits granted to IRRI for exportation of rice experimental seed. It indicates specific requirements (July 2009) and the pathogens and pests that seed should be free of when it is imported to a given country. Additional information on documents required  by IRRI Seed Health Unit in compliance with the Philippine Plant Quarantine Service and IRRI’s Intellectual Property Rights for germplasm and Non-seed biological materials are provided.  The host country requirements for importing rice seed to the Philippines  are also provided. Non-seed biological materials for import are also regulated by the government of Philippines.

Please consider that:

• The information received from the same country may vary from one  permit to another; therefore the latest has been considered the valid one.
• It is always advisable before sending a shipment to contact the consignee in the recipient country to confirm the information reported in this table.

Flowcharts for import and export can be seen at the links below:

The Germplasm Import flowchart in place for import at the Seed Health Unit (SHU)

The Germplasm Export flowchart in place for export at the Seed Health Unit (SHU)

Guidelines for the safe transer of rice germplasm

Contributers to this page: IRRI, Seed Health Unit, Los Banos, Philippines(Patria Gonzales, Evangeline Gonzales, Carlos Huelma, Myra Almodiel, Joel Dumlao).

Technical Guidelines for the Safe Transfer of Germplasm and the Protection of CGIAR Germplasm Banks

Pathogens of quarantine significance of Rice (IRRI)

Bacteria - rice

Contributers to this page: IRRI, Seed Health Unit, Los Banos, Philippines(Patria Gonzales, Evangeline Gonzales, Carlos Huelma, Myra Almodiel, Joel Dumlao).

Bacterial blight

Scientific names

Xanthomonas oryzae pv. oryzae (ex Ishiyama) Swings et al.
Syn. X. campestris pv. oryzae (Ishiyama) Dye  

Significance

Yield losses (10-50%).

Symptoms

Blight (starts as water-soaked stripes a few centimeters below the leaf tip, or on the margin of the leaf blade; these stripes enlarge and turn yellow within a few days).

“Kresek” or wilting.

“Pale yellow leaf". 

Host range

Leersia sayanuka Ohwi; L. oryzoides (L.) Sw., L. japonica, Zizania latifolia (Griesb.)Turcz. ex Stapf., Leptochloa chinensis (L.) Nees, L. panacea (Retz.) Ohwi, L. filiformis , Cyperus rotundus L. and C. difformis.  

Geographic distribution

Asia, Australia, Africa, Latin America, the Carribean, and United States of America.

Biology and transmission

Survives primarily in rice stubbles and alternate weed hosts enters the host through stomata, wounds, and other injuries to leaves, hydathodes, cracks at the base of the leaf sheaths.

Irrigated and rainfed lowland ecosystems support the disease development.

Heavy rains with strong winds facilitate disease development by causing wounds in plants.

Dry weather helps bacterial exudates fall into irrigation water, spread the disease to neighboring fields.

Moderately high temperatures (25°C-30°C) increase the disease incidence.  

Excessive use of nitrogen especially organic N as late topdressing, phosphate, and K deficiency, excess silicate and Mg predispose plant to infection.

Detection/indexing method in place at the CGIAR Center

• At IRRI – Seed Wash Assay Test (using semi selective medium).
• Restriction Fragment Length Polymorphism (RFLP).
  • Requires database to reference.
• Amplified Fragment Length Polymorphism (AFLP).
• Labor intensive and not efficient for diagnostics.
• Oligonucleotide arrays.
• Macroarrays.
  • Hybridize sample DNA to anchored pathogen.
  • Specific oligos.
• Antibody-based = Enzyme-Linked ImmunoSorbent Assay (ELISA).
  • Requires increased processing time and expenses.

Treatment/control

• The disease can be effectively controlled with resistant cultivars.
• Cultural control includes avoiding excessive N fertilization, maintaining shallow water in nursery beds, providing good drainage during severe flooding, plowing under of rice sybbles and straw following harvest, and removing alternate hosts.
• Control of disease with copper compounds, antibiotics, and other chemicals has not proven effective.

Procedure followed at the centers in case of positive test

• Seeds found to be positive with the organism are deleted from shipments for export.
• Bacterial testing is not conducted on incoming rice seeds but shall be planted in post entry plant quarantine area only. Plants are closely monitored during its active growth. Plants showing disease symptoms are immediately destroyed and disposed according to the recommendation of the Philippine Plant Quarantine Service.

References and further reading

Ou SH. 1985. Rice Diseases 2nd ed. The Commonwealth Mycological Institute. UK

Mew TW, Misra JK. 1994. A Manual of Rice Seed Health Testing. IRRI.

Webster RK, Gunnel PS, editors. 1992. Compendium of Rice Diseases. The American Phytopathological Society. USA

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Bacterial Leaf Streak

Scientific names

Xanthomonas oryzae pv. oryzicola (Fang et al) Swings et al.
syn. X. campestris pv. oryzicola (Fang et al) Dye; X. translucens f.sp. oryzicola

Significance

Yield losses estimated at 1-17% depending on cultivar and climatic condition.

Symptoms

Translucent interveinal streaks (variable length on the leaf); old lesions become light brown.

Yellowish droplet of bacterial ooze on lesions under humid conditions; ooze look like beads under dry conditions.

Host range

All wild species of the genus Oryza can be infected and may serve as reservoirs of inoculum.

Geographic distribution

Widely distributed in Tropical Asia and in West Africa.

Biology and transmission

The bacterium survives largely on infected seed and straw; may also be able to survive in irrigation water.

The bacterium enters the host through stomates or wounds and multiplies in parechymatous tissue.

Bacterial exudates from leaf lesions are disseminated primarily by splashing and windblown rain, also by leaf contact and irrigation water.

Disease develops in both lowland and upland ecosystems.

Disease development is favored by rain, high humidity (more that 80%) and high temperature (more that 30°C).

Infected seeds and contaminated water can introduce the disease to new areas.

Detection/indexing method in place at the CGIAR Center

• At IRRI – Seed Wash Assay Test (using semi selective medium).   
• Restriction Fragment Length Polymorphism (RFLP).
  • Requires database to reference.
• Amplified Fragment Length Polymorphism (AFLP).
  • Labor intensive and not efficient for diagnostics.        
• Oligonucleotide arrays.
• Macroarrays.
  • Hybridize sample DNA to anchored pathogen.
  • Specific oligos.
• Antibody-based = Enzyme-Linked ImmunoSorbent Assay (ELISA).
  • Requires increased processing time and expenses.

Treatment/control

• The disease can be effectively controlled with resistant cultivars and the use of treated seeds.

Procedure followed at the centers in case of positive test

• Seeds found to be positive with the organism are deleted from shipments for export.
• Bacterial testing is not conducted on incoming rice seeds but shall be planted in post entry plant quarantine area only. Plants are closely monitored during its active growth. Plants showing disease symptoms are immediately destroyed and disposed according to the recommendation of the Philippine Plant Quarantine Service.

References and further reading

Ou SH. 1985. Rice Diseases 2nd ed. The Commonwealth Mycological Institute. UK

Mew TW, Misra JK. 1994. A Manual of Rice Seed Health Testing. IRRI.

Webster RK, Gunnel PS, editors. 1992. Compendium of Rice Diseases. The American Phytopathological Society. USA

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