RICE GENOMICS: Progress and prospects

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RICE GENOMICS Progress and prospects
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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

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What is the rice genome?

• The worlds 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

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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.

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Model experimental crop Why rice?

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

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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.

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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

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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
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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)
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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
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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
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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
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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

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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 Hoods et al.)
Map-based sequencing
Syngenta-Myriad (funded Torrey Mesa Research
Institute)
Shot-gun sequencing
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Chromosome assignment of the participating
countries in the IGRSP
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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

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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

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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

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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

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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

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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.

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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.

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New directions of post-rice genome sequencing

• Functional analysis of predicted genes
• Analysis of coordinated expression of genes
  (genetic and biochemical networks)
• Proteomics
• Metabolomics

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The rice genome holds fundamental information in
its biological "power", including physiology,
development, genetics, and molecular evolution.
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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.
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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.
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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) 12 (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, 16911704,
August 2002, www.plantcell.org