Project Information

Reference Number 20170309
Project Title Validation study of potential candidate genes and promoters involved in high out-crossing trait in rice
Project Type Contained Use (Greenhouse)
Status Ongoing
Name of Institution International Rice Research Institute
Cooperating Institution N/A
Supervising IBC International Rice Research Institute (IRRI)
Project Leader(s)

Dr. Kshirod K. Jena
Dr. Inez H. Slamet-Loedin
Dr. Sung-Ryul Kim
Dr. Giriyappa Dasanna Prahalada

Experimental Facility/Site Genetic Transformation Laboratory (GTL), Genomics and Genetics Laboratory (GGL) and the CL4 glass bays at the International Rice Research Institute
Purpose / Objectives

To validate gene function of newly identified candidate genes and promoters involved in increasing out-crossing trait in rice which can be used in hybrid rice breeding.

Biosafety measures

Appropriate biosafety measures as implemented by IRRI, and as per the requirements of the DOST-BC will be strictly observed and followed. Transgenic and untransformed control plants will only be grown in CL4 glass bays, a well-contained facility.

Biosafety measures that will be taken:
• All vectors will be kept in the plasmid collection of Genetic Transformation Laboratory (GTL) after construction.

• The tested plants will be kept in isolation in the CL4 glass bays to prevent access of unauthorized personnel.

• Plant materials for disposal will be placed in sealed plastic bags and disposed of in dedicated disposal pit for transgenic materials.

• Plants grown in CL4 will be destroyed and the pots and soil will be autoclaved at high temperature and high pressure.

• All material movement and disposal will be done only under supervision of the IRRI-IBC and the Bureau of Plant Industry-Plant Quarantine Service (BPI-PQS)

• Access to GTL, GGL and CL4 facilities are for authorized staff only.

• A barcode entry system is applied in the facilities to record the entry of personnel; a log book is available for visitors not having IRRI access card system.

• Transgenic seeds harvested from CL4 will be destroyed and will not be kept after the completion of the experiment.

Conditions for Approval

a) Activities shall be conducted at the Genetic Transformation Laboratory (GTL), Genetics and Genomics Laboratory (GGL) and CL4 glass bay which are located at the KJ Lampe Building of the International Rice Research Institute in Los Baños, Laguna.

b) Prior to the initiation of the activities, the proponent/s shall discuss the monitoring schedule with the Department of Agriculture-Bureau of Plant Industry (DA-BPI) to identify the activities that will require their presence. The proponent/s through the IBC shall furnish the DOST-BC with a copy of the agreed monitoring schedule.

c) The proponent shall adhere as closely as possible to the schedule of activities reflected in the submitted Gantt chart.

d) Any modifications in the schedule of activities shall be made with the concurrence of the IRRI-IBC and the DOST-BC.

e) Signage should be in place indicating that the facility is restricted/limited access;

f) The proponent must provide a logbook to record access of personnel to the experimental facility.

g) The proponent must take measures to ensure that only the DOST-BC authorized personnel are allowed inside the experimental facilities.

h) The experimental facilities must be kept under lock when not in use.

i) In case of undue destruction of experimental materials resulting from unauthorized entry of personnel or breach of containment of experimental facilities, the proponent shall implement measures to prevent the inadvertent escape of any viable material within the facility.

j)The proponent and the supervising IBC shall be held accountable for the undue destruction of the experimental materials and the consequences that their inadvertent escape may cause to the surrounding environment.

k) The DOST-BC should be informed in advance of any visitations by unauthorized persons.

l) The DOST-BC shall be informed immediately of any intrusion by unauthorized persons. 

m) The proponent shall striclty observe proper disposal procedures for all the experimental materials. 

n) Movement of all materials will be done in accordance with all relevant biosafety and phytosanitary requirements of the Philippines.

o) Any additional requirement that the DOST-BC may impose, as necessary, for the duration of the experiment shall be complied with.

p) The proponent shall submit through the IBC a completion report within 90 days after completion of the experiment following the prescribed format.

q) The IBC shall submit to the DOST-BC a report on the completion of this project following the prescribed format.

Date of Approval (DD-MM-YYYY) 22-07-2017
Date of Completion (DD-MM-YYYY) N/A
Executive Summary

Rice (Oryza sativa L.) is the most important food crop in the world, feeding over half of the global population. Hybrid rice varieties have some strength, especially in high grain yield. However, high F1 seed cost is a major limiting factor of the adoption of hybrid rice cultivars to rice farmers in South and Southeast Asian countries. A practical way to improve hybrid seed production is to increase the out-crossing rate. For this, near isogenic lines (NILs) having long-exerted stigma (increased stigma length) in the popular cultivar IR64 and the cytoplasmic male sterile (CMS) backgrounds were developed using the wild rice relative, O. longistaminata which has naturally long-exerted stigma. Through QTL analysis, the major QTL conferring increased stigma length in rice was identified. Fine-mapping of this QTL as done and five genes and promoters were identified to be involved in high out-crossing rate. This project aims to validate the potential candidate genes for stigma elongation which influences pollen capturing capacity in rice.

1. To conduct over-expression study of the candidate genes from O. longistaminata in commercial variety, IR64 background.

2. To transfer the genomic sequences including native promoter, coding sequence, and transcription terminator of candidate genes from O. longistaminata into IR64 background for complementation test.

3. To knock-out candidate genes in NILs (IR64 background) having long exerted stigma through CRISPR/Cas9-induced knock-out approach

4. To study the expression of the listed candidate genes from O. longistaminata in IR64 (O. sativa) background.

Five rice genes related to high out-crossing trait will be studied. The studies will be conducted in DOST-BC approved facilities in IRRI which are the Genetic Transformation Laboratory, The Genetics and Genomics Laboratory and the CL4 glasshouses. The project is expected to run for two years. All plant materials that will be generated are solely for validation purposes only and will be destroyed upon completion of the experiments.