RICE GENE DISCOVERY UNIT

Rice Gene Discovery (RGD) Unit was established in 2001 through the close collaboration between the National Center for Genetic Engineering and Biotechnology (BIOTEC) and Kasetsart University, Kamphaengsaen Campus. The RGD aims to develop important genomic tools for discovering genes underlying economic traits. On building up the research capacity in Thailand, RGD will make its in-house genomic tools for public access without charge and coordinate researchers from different expertise to work in networking.

Research Activities

1) Paving the road-map to breaking the yield barrier
Breeding superior rice varieties, breeders must think not only traits that contribute to high yield potential but also ability to avoid yield losses when facing diseases, insects and unfavorable environments. Sixteen economic traits were mapped using integrated linkage maps based on 12 genetic mapping populations. These mapping populations intentionally place the Thai Jasmine KDML105 at the central pivotal genome and well connected to desirable region where the target genes from donors are located. These strategies facilitate ‘gene pyramiding’, interchanging the chromosomal regions from the Thai Jasmine with those desirable donors. This is the most comprehensive and cumulative breeding efforts ever made in Thailand.

2) Structural Genomics
RGD participated in the International Rice Genome Sequencing Project (IRGSP) by taking the lead on chromosome 9 in 1999. The complete rice genome sequence is not only the means to uncover the life program of rice but also the means to discover new genes and innovate new rice strains for farmers that can double rice yield with superior quality for sustainable global food supplies in the next century. As a small, developing country, Thailand joining such an international sequencing efforts is not only a national pride but also the corner stone for Thailand to step into the genomics era.

3) Gene Discovery
Discovering genes underlying 16 target traits are on going project. In particular, two important QTL, submergence tolerance and grain aroma, were used as model for positional cloning. Two BAC libraries from KDML105 and FR13 A were developed for physical mapping and large-scale sequencing. These candidate genes have now been under functional investigation.

4) Bioinformatics
The complete rice genome sequence is freely accessible to the public. For rice breeders to benefit this most valuable information, RGD has developed a freely, accessible, curate genome browser. RiceGeneThresher is the most important informatics to discover new genes and function. The genome browser combined the whole genome sequences as BAC-by-BAC (japonica) or scaffolds (indica) with all existing genetic maps, molecular markers, EST, full-length cDNA. Integrated several gene prediction programs with protein and domain databases, hypothesis about the functions of unknown genes can be synthesized. RiceGeneThresher can be accessed via http://rice.kps.ku.ac.th.

5) Functional Genomics
Sixty percent of the predicted open reading frames in the rice genome is unknown. Two approaches have been implemented. One is to use transgenic approach and RNAi for over-expression or co-suppression of the candidate genes. The second approach we are now using is on the whole-genome mutagenesis called TILLING. More than 200,000 seeds from Jao Hom Nin were irradiated with fast neutron at 13 Gy. In the post-genomics era, screening of mutant lines can be targeted to specific candidate genes.

6) Molecular Breeding
The new way of breeding called ‘marker-assisted selection’ is the best example of how genomic technologies may contribute to improve rice yield and qualities. There are many success examples. One of it was the new breed of the Thai Jasmine rice varieties namely ‘Triluck’. This is the jasmine rice with combined new traits, submergence tolerance, bacterial leaf blight, and brown planthopper resistance, added into its genome by the using molecular markers in the backcross breeding.

Director
Assoc. Prof. Dr. Apichart Vanavichit

Key Researchers
Assoc. Prof. Dr. Apichart Vanavichit
Dr. Theerayut Toojinda