RICE GENOMICS: Progress and prospects

1. RICE GENOMICS: Progress and prospects

2. What is genomics? • The genome of a plant, animal or microbe is the totality of its genetic information including all the genes and the non-transcribed sections of the DNA • Genomics is the study of this complete genetic content of an organism

3. What is the rice genome? • The world’s first genome of a crop plant that was completely sequenced • The genome with the fewest stuffer pieces, the rice genome, is the Rosetta Stone of all the bigger grass genomes. (Messing and Liaca, 1998) • Rice – like Arabidopsis – is a model experimental plant

4. Model experimental crop: Why rice? • Belongs to the grass family • Has a much smaller genome and the greatest biodiversity of cereal crops • Has a high degree of colinearity with the genomes of wheat, barley, and maize.

5. Model experimental crop: Why rice? • Substantial conservation of gene order (synteny) • Genome often allows prediction of gene position across cereals

6. Model experimental crop: Why rice? • Rice has a simple genetic system (diploid and disomic inheritance) • Has enormous number of genes controlling agronomically important traits; • Wide genetic diversity is present in the genus Oryza.

7. Why rice genome was sequenced? • It can address many different aspects of rice research, including genetic diversity and productivity improvement • To design efficient ways to tap into the wealth of rice genome sequence information to address production constraints in an environmentally sustainable manner

8. Milestones in the rice genome sequencing Sept 1997 – Sequencing of the rice genome was initiated as an international collaboration among 10 countries Feb 1998 – IRGSP (International Rice Genome Sequencing Project) was launched under the coordination of the Rice Genome Program (RGP) of Japan

9. Milestones in the rice genome sequencing April 2000 – Monsanto Co. produced a draft sequence of BAC contigs covering 260 Mb of the rice genome; 95% of rice genes were identified Feb 2001 – Syngenta produced a draft sequence and identified 32,000 to 50,000 genes, w/ 99.8% sequence accuracy and identified 99% of the rice genes An example of a genetic map of rice (chromosomes 1 and 2)

10. Milestones in the rice genome sequencing Dec 2002 – IRGSP finished high- quality draft sequence (clone- by-clone approach) with a sequence length, excluding overlaps, of 366 Mb corresponding to ~92% of the rice genome. Dec 2004 – IRGSP produce the high-quality’ sequence of the entire rice genome; with 99.99% accuracy and without any sequence gap

11. How rice was sequenced? Map-based sequencing - each stretch of sequence is physically anchored to a chromosome forming a contig of clones, which are individually sequenced

12. How rice was sequenced? Annotation pipeline system at RGP- consists of automated annotation, curation of auto predicted genes and storage of all data in a relational database

13. How rice was sequenced? • Shotgun sequencing involves generation of short DNA fragments that are then sequenced & linearly arranged • It enables full coverage of the genome in a fraction of the time required for the alternative BAC sequencing approach

14. Who are the key players in sequencing projects? Research Institution Sequencing method International Rice Genome Sequencing Project (IRGSP) Map-based sequencing Beijing Genomics Institute (BGI) Shot-gun sequencing Monsanto Co. (funded University of Washington –Leroy Hood’s et al.) Map-based sequencing Syngenta-Myriad (funded Torrey Mesa Research Institute) Shot-gun sequencing

15. Chromosome assignment of the participating countries in the IGRSP

16. Significant findings from the sequencing of rice genome • The rice genome is about 389 mb, 370.7 mb has been sequenced, 18.1 mb unsequenced. • Sequenced segment represents 99% of euchromatin and 95% of rice genome

17. Significant findings from the sequencing of rice genome • The rice genome has about 40,000 genes (37,344 coding genes) • One gene can be found every 9.9 kb, a lower density than that observed in Arabidopsis. • 29% in clustered gene families

18. Significant findings from the sequencing of rice genome • 71% putative homology with Arabidosis, 90% Arabidopsis genes have putative homologue with rice. • 2,859 genes unique to rice and other cereals

19. Applications and Impact • Development of gene- specific markers for marker-assisted • breeding of new and • improved rice varieties • Understand how a plant responds to the environment and which genes control various functions of the plant

20. Applications and Impact • Improve the nutritional value of rice, enhance crop yield by improving seed quality, resistance to pests and diseases, and plant hardiness • Useful in identifying plant-specific genes that can be potential herbicide targets

21. New directions of post-rice genome sequencing • Comparative genomics: • - Comparisons across species will be useful in • understanding the basis of major biological processes • Maize genomes and other cereals are on the way of sequencing only ‘gene-rich’ regions  using the high quality rice genome sequence as good standard for evaluating the gene coverage.

22. New directions of post-rice genome sequencing • Hasten the development of genetic markers in rice as well as in other grass genomes by focusing only in regions of the genome containing the gene of economic interest or importance.

23. New directions of post-rice genome sequencing • Functional analysis of predicted genes • Analysis of coordinated expression of genes (genetic and biochemical networks) • Proteomics • Metabolomics

24. The rice genome holds fundamental information in its biological "power", including physiology, development, genetics, and molecular evolution.

25. Definitions Annotation-Adding pertinent information such as gene coded for, amino acid sequence, or other commentary to the database entry of raw sequence of DNA bases. Bacterial Artificial Chromosome (BAC)- A vector used to clone DNA fragments of 100 to 300 kb insert size (average of 150 kb) in Escherichia coli cells. Based on the naturally occurring F-factor plasmid found in the bacterium Escherichia coli. Functional Genomic- The study of genes, their resulting proteins, and the role played by the proteins the body's biochemical processes. Gene family- A set of genes in one genome all descended from the same ancestral gene. A group of genes that has arisen by duplication of an ancestral gene. The genes in the family may or may not have diverged from each other.

26. Definitions Genome- The entire complement of genetic material in a chromosome set. The entire genetic complement of a prokaryote, virus, mitochondrion or chloroplast or the haploid nuclear genetic complement of a eukaryotic species. Metabolomics -the analysis of the thousands of small molecules such as sugars and fats that are the products of metabolism. If metabolomic information can be translated into diagnostic tests, it could provide earlier, faster, and more accurate diagnoses for many diseases. P1 Artificial Chromosome (PAC)- One type of vector used to clone DNA fragments (100- to 300-kb insert size; average, 150 kb) in Escherichia coli cells. Based on bacteriophage (a virus) P1 genome. Proteomics-The study of the full set of proteins encoded by a genome. Yeast Artificial Chromosome (YAC)-Originating from a bacterial plasmid; a YAC contains additionally a yeast centromeric region (CEN); a yeast origin of DNA replication (ARS); and two telomere regions (TEL). YACs are capable of cloning very large pieces of DNA up to 1 mb.

27. References Cantrell RP and Reeves TG. The cereal of the world s poor takes center stage. Science 2002, 296, 53. IRSG Sequencing Project. The map-based sequence of the rice genome. Nature Vol 436, pp. 793-800 Matsuoka M. New directions of post genome-rice sequencing. Plant Cell Physiol. 46(1): 1–2 (2005) Ronald P and Hei L. The most precious things are not jade and pearls… Science 2002, 296, 58 Serageldin I. World poverty and hunger - the challenge for science. Science 2002, 296, 54 The Plant Cell, Vol. 14, 1691–1704, August 2002, www.plantcell.org