Sequencing the genomes of a number of native Vietnamese rice lines

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

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

5. Part 2: Analyzing genetic diversity, Selecting of elite native varieties Part 2.ppt Part 1: Collecting and building rice germplasm collections Part 1.ppt Part 3: Evaluating phenotype and developing phenotype database Part 3.ppt OBJECTIVES- CONTENTS - RESULTS 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. 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

6. For example: Determining blight bacterial resistant genes Blight bacterial resistant genes.doc Tep Thai Binh: Xa1, xa13, Xa21, Xa 26, Xa 27 andxa5 Toc lun: Xa1, Xa10, Xa12, xa13, Xa14, Xa15 Xa17,Xa21, Xa 26, Xa 27, Xa28, Xa29, Xa30, Xa31, Xa 32, X4_88 andxa5 Scientists have just found out and used 1-2 blight bacterial resistance genes in the native Vietnamese rice lines, previously 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

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