rice genomics: progress and prospects. what is genomics? the genome of a plant, animal or microbe...
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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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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