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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 nontranscribed 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
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.
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
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)
Milestones in the rice genome sequencing
Dec 2002 – IRGSP finished highquality draft sequence (cloneby-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
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
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
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
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 genespecific 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 plantspecific 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.
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.
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.
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