1. Sequencing the genomes of a number of native Vietnamese rice lines Drought tolerant rice Salt tolerant rice Blight bacterial Blast rice Brownplanthopper High quality rice Project title:

2. BACKGROUND Research project on: Sequencing the genomes of a number of native Vietnamese rice lines Under the program: Cooperation between Ministry of Science and Technology, Vietnam and Biotechnology and Biological Sciences Research Council, The United Kingdom A joint research project between : - Agricultural Genetics Institute (AGI) and Cuu Long Delta Rice Research Institute (CLRRI), Vietnam Academy of Agricultural Sciences (VAAS), Ministry of Agriculture and Rural Development (MARD), Vietnam. - John Innes Centre (JIC) and the Genome Analysis Centre (TGAC), Biotechnology and Biological Sciences Research Council (BBSRC), UK Budget of Vietnam side: 150 000USD Budget of UK side: 400 000 USD Duration: 30 months (from 01/2011 to 6/2013)

3. STATEMENT Genome sequencing of native Vietnam rice lines! - Vietnam is the center of genetic diversity of rice with valuable agronomic traits: drought/salinity tolerance, planthopper/blast/ blight bacterial resistance,… - The resources have not been exploited and used in rice breeding, effectively Sequencing the whole genome of rice will provide fully information at the molecular level for rice studying and breeding Sequencing the whole genome of crops still could not be carried out in Vietnam because of the shortage of facilities and technologies. - The cooperation with UK in order to sequence of whole genome of Vietnamese rice varieties is necessary. - The success of the project opens up a new approach in genomic research and applied exploitation for rice breeding.

4. ACADEMIC SIGNIFICANCE Sequencing the native Vietnamese rice varieties Sequencing the native Vietnamese rice varieties Approaching of advanced methods, modern equipments and cooperation with the world’s leading experts Developing comprehensive genome database for the native Vietnamese rice varieties Statement the ownership of Vietnam to the diverse genetic resource of native rice varieties Exploiting of the genome sequence information for rice study and breeding

5. OBJECTIVES- CONTENTS - RESULTS Part 1: Collecting and building rice germplasm collections Part 1.pptPart 1.ppt Part 2: Analyzing genetic diversity, Selecting of elite native varieties Part 2.ppt Part 3: Evaluating phenotype and developing phenotype database Part 3.pptPart 3.ppt Part 4: Genome sequencing and developing genotype database (co-work with UK partner) Part 4.ppt Part 5: SNPs mapping and CAPS marker designing Part 6: Establishing of the website for sharing phenotype and genotype database Part 7: Training and international cooperation Part 7.ppt Objectives: - Sequencing a number of native Vietnamese rice varieties with high yield, good quality as well as the ability of coping with the adverse biotic and abiotic conditions. - Training of Vietnamese scientists in the field of genome sequencing and using bioinformatics in management and exploitation of the rice genome data.

6. APPLIED ORIENTATIONS Screening genes responsible for high yield, good quality, brownplanthopper/ blast/ blight bacterial resistance, drought/ salinity tolerance in the native Vietnamese rice lines Designing functional markers for assisting precise selection of individuals harboring target gene Tep Thai Binh: Xa1, xa13, Xa21, Xa 26, Xa 27 and xa5 Toc lun: Xa1, Xa10, Xa12, xa13, Xa14, Xa15 Xa17, Xa21, Xa 26, Xa 27, Xa28, Xa29, Xa30, Xa31, Xa 32, X4_88 and xa5 Scientists have just found out and used 1- 2 blight bacterial resistance genes in the native Vietnamese rice lines, previously For example: Determining blight bacterial resistant genes Blight bacterial resistant genes.doc

7. APPLIED ORIENTATIONS SNPs mapping; screening of high quality SNPs →Apply for : - Studying of genetic diversity - Assessing and conservation of genetic resources Reference sequence (>gi|161376415|gb|EU155083.1|) Reference sequence (>gi|161376415|gb|EU155083.1|) Native rice varieties of Vietnam: `SNPs of fragrance genes.docSNPs of fragrance genes.doc Tam xoan Bac Ninh: 96 SNPs ; Tam xoan Hai Hau: 50 SNPs Te Nuong: 97 SNPs Nang thom cho Dao: 83 SNPs Thom lai: 116 SNPs Native rice varieties of Vietnam: `SNPs of fragrance genes.docSNPs of fragrance genes.doc Tam xoan Bac Ninh: 96 SNPs ; Tam xoan Hai Hau: 50 SNPs Te Nuong: 97 SNPs Nang thom cho Dao: 83 SNPs Thom lai: 116 SNPs For example: fragrance gene

8. APPLIED ORIENTATIONS Exploiting native rice genetic resources of Vietnam: - Searching for targets genes, gene families and QTLs that related to high yield, good quality, brownplanthopper/blast/blight bacterial resistance, drought/salinity tolerance ; - Searching for candidate genes that are responsible for high yield, good quality, brownplanthopper/blast/blight bacterial resistance, drought/salinity tolerance. Classifying of Indica and Japonica subspecies for studying on the genetic background effectively interacting to resistance genes - Detecting the functional genes sequence for designing the functional markers tightly linked to target genes. - Pyramiding target genes for rice breeding by mean of MAS and MABC, fast and accurately.

9. CONCLUSIONS AND RECOMMENDATIONS CONCLUSIONS - 36 native Vietnamese rice varieties have been sequenced; - We built the database for phenotype and genotype of 36 rice varieties belong to 6 groups; - The website of the project have been established to share information with other institutes and universities; - We have been identifying target genes, and designing functional markers for rice breeding. RECOMMENDATIONS - Establishing of bioinformatics lab with equipments and modern computer system with power enough for genome analysis and data storage; - Sending staff to intensive training program in bioinformatics. - Continuing phase II of the project: Exploiting of the available genome sequencing for breeding of rice varieties with high yield, good quality, and coping with adverse biotic and abiotic conditions.

10. ACKNOWLEDGEMENTS Giles Oldroyd and Christian Rogers Mario Caccamo, Sarah Ayling, Bernardo Clavijo and Melanie Febrer Ham L. H., Khoa N. T., Diep N.T. Ha D. T. T. and colleagues

11. THANK YOU!