Rice Genome Project a complete saga .(1).pptx

This slide includes all the data about Rice Genome Project which is a International consortium for sequencing whole rice genome .All the salient findings . The timelines , the countries involved including list of all laboratories and their role , with the objective and role of India in the project , India's work and institutions involved , timelines as a graphical representations , and the genome size no of genes , information about transposons , gene families and also it includes methodologies like shot gun approach they have used for sequencing , and how fidelity is maintained , how much gap they found , how many genomics libraries used , BAC ,PAC fosmids that are used, and all the bioinformatics tools that are used for contig assembly and gene annotation , it includes all maps and a simple description of the findings , based on the paper published bu IRGSP on 2004 , the total referencing is based on that paper .

1. RICE GENOME PROJECT

2. RICE Rice – Oryza sativa Chromosome number 2n= 24 Importance of Rice feeds about one half of the world’s population, mainly in Asia, Africa, and South America. Crucial for food security and nutrition. Major agricultural product with significant economic value. To feed ever growing population we need 30%more productivity in next 25 years

3. IRGSP The international Rice Genome Sequencing Project (IRGSP) was initiated in 1998 under the leadership of Japan It was a consortium of ten countries namely Brazil ,China, India Japan Korea Taiwan, Thailand , UK , U.S.A Involving 250 scientists with a fund allocation of US $ 200 million They sequenced japonica rice variety NIPPONBARE A highly accurate sequence was put in public domain in august 2005

4. Indian contribution India joined the project in 2000 and was given a task of of sequencing chromosome number 11 Task completed in oct 2004 28 members joint initiative of NRC Biotechnology , IARI, university of Delhi south campus and department of plant molecular biology , NRCPB DPMB UDSC IARI

5. MILESTONES 1997 – SEQUENCING OF RICE GENOME WAS INITIATED Feb 1998 IRGSP was launched under the coordination of RGP April 2000 MONSANTO produced a draft of the rice genome 95% FEB 2001 SYNGENTA produced a draft with 99% identified genome Dec 2002 IRGSP finished draft sequence of 366 Mb Dec 2004 IRGSP produced eitire rice genome with 99.99% accuracy

6. SALIENT FINDINGS OR FEATURES Genome size of rice is found to be 389Mb , ~260 M b larger than Arabidopsis 56,298 genes have been identified 37,544 are protein coding genes ~ 28000, 29,000 in case of Arabidopsis , gene density found to be one gene per 9.9 Kb . A total 2859 genes are unique to cereal and rice Between 0.38% and 0.43% of the nuclear genome contains organellar DNA fragments The transposon sites comprises of 35% of the genome , 11,487 Tos 17 retro transposition sites found , 3243 within gene SNP frequency 0.53- 0.7%, 80,127 polymorphic site A total of 18,828 Class 1 di, tri and tetra-nucleotide SSRs, representing 47 distinctive motif families, were identified One surprising outcome of the Arabidopsis genome analysis was the large percentage (17%) of genes arranged in tandem repeats32. When performing a similar analysis wi th rice, the percentage was comparable (14%)

7. METHODOLOGY Physical map and sequencing. Nine genomic libraries from Oryza sativa ssp. japonica cultivar Nipponbare were used to establish the physical map of rice chromosomes by polymerase chain reaction (PCR) screening, fingerprinting and end-sequencing. The PAC, BAC and fosmid clones on the physical map were subjected to random shearing and shotgun sequencing to tenfold redundancy, using both universal primers and the dye-terminator or dye-primer . The sequences were assembled using PHRED and Phrap ,using the TIGR Assembler Sanger sequencing used for initial stages. Next-generation sequencing (NGS) for further refinement.

8. ANNOTATION AND BIOINFORMATICS Gene models were predicted using FGENESH The predicted rice proteome was searched using BLASTP. Gene models with rice full-length cDNA, EST or cereal EST matches but without identifiable homologues in the Arabidopsis genome were searched for conserved domains/motifs using InterproScan , and for homologues in theSwiss-Prot database (http://us.expasy.org/sprot/) using BLASTP. Non-coding RNAs. Transfer-RNA genes were detected by the program tRNAscan SE (http://www.genetics.wustl.edu/eddy/tRNAscan-SE/). The miRNA registry in the Rfam database (http://www.sanger.ac.uk/Software/Rfam/) was used as a reference database for miRNAs. Transposable elements. The TIGR Oryza Repeat Database, together with other published and unpublished rice transposable element sequences, was used to create RTEdb (a rice transposable element databas

9. BIOINFORMATICS USED SNP discovery. BAC clones from an O. sativa ssp. indica var. Kasalath BAC library were end-sequenced. . sequences were subjected to BLASTN analysis against the pseudomolecules. SSR loci. The Simple Sequence Repeat Identification Tool (http://www.gramene.org/) was used to identify simple sequence repeat motifs, and the physical position of all Class 1 SSRs was recorded. The copy number of SSR markers was estimated using electronic (e)-PCR to determine the number of independent hits of primer pairs on the pseudomolecule

10. APPLICATION AND FUTURE PROSPECTOUS Applications Agricultural Improvements: Development of high-yield, disease-resistant, and stress-tolerant rice varieties. Biotechnology: Genetic engineering to enhance desirable traits. Conservation: Preservation of genetic diversity in rice. Challenges and Future Directions Current Challenges: Ensuring equitable access to genetic information. Addressing ethical and biosafety concerns. Future Research: Functional genomics to understand gene functions. Genome editing technologies like CRISPR for targeted improvements.

11. REFERENCES Sasaki, T. & Burr, B. International Rice Genome Sequencing Project: the effort to completely sequence the rice genome. Curr. Opin . Plant Biol. 3, 138–-141 (2000). IRGSPR physical map based sequence of rice genome (2004)