RICE GENOMICS: Progress and prospects

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

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

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.

Model experimental crop: Why rice?

Substantial conservation of gene order (synteny) Genome often allows prediction of gene position

across cereals

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.

Model experimental crop: Why rice?

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

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

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 adraft 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)

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

Milestones in the rice genome sequencing

Map-based sequencing - each stretch of sequence is physically anchored to a chromosome forming a contig of clones, which are individually sequenced

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

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

How rice was sequenced?

Who are the key players in sequencing projects?

International Rice Genome Sequencing Project (IRGSP)

Beijing Genomics Institute (BGI)

Monsanto Co. (funded University of Washington –Leroy Hood’s et al.)

Syngenta-Myriad (funded Torrey Mesa Research Institute)

Research Institution

Map-based sequencing

Shot-gun sequencing

Shot-gun sequencing

Map-based sequencing

Sequencing method

Chromosome assignment of the participating countries in the IGRSP

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

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

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

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

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

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.

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.

New directions of post-rice genome sequencing

Functional analysis of predicted genes

Analysis of coordinated expression of genes (genetic and biochemical networks)

Proteomics Metabolomics

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

DefinitionsAnnotation-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.

DefinitionsGenome- 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.

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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