RICE GENOME SEQUENCING
• Rice is a model species for the monocotyledonous
plants and the cereals which are the greatest
source of food for the world's population.
• While rice genome sequence is available through
multiple sequencing projects, high quality, uniform
annotation is required in order for genome
sequence data to be fully utilized by researchers.
• The existence of a common gene set and uniform
annotation allows researchers within the rice
community to work from a common resource so
that their results can be more easily interpreted by
other scientists.
• The objective of this project has always
been to provide high quality annotation for
the rice genome.
• generated, refined and updated gene
models for the estimated 40,000-60,000
total rice genes, provided standardized
annotation for each model, linked each
model to functional annotation including
expression data, gene ontologies, and
tagged lines.
• The rice genome to other plant species by providing
comparative alignments to other plant species.
• We have provided training in bioinformatics to over
100 plant scientists, sharing our informatic
expertise with a broader range of scientists.
• We have developed agricultural genomics lecture
and teaching modules for educating high school
students and teachers on the significance of
agricultural genomics.
• This project is funded by the National Science
Foundation Plant Genome Research Program # DBI-
0321538 and DBI-0834043.
Rice-An Introduction
• Rice
• Scientific Name: Oryza sativa (Asian rice) or Oryza
glaberrima (African rice)
• Number of Chromosomes=12
• Genome Size=420 Mb(Megabase)
• Subspecies= Japonica or Sinica, Indica, Javanica
(now known as
tropical japonica)
• Pendulous inflorescence
• Edible part: Grain (caryopsis)
Rice-An Introduction
• As of 2009 world food consumption of rice was
531.6 million metric tons of paddy equivalent
(354,603 of milled equivalent), while the far largest
consumers were China consuming 156.3 million
metric tons of paddy equivalent (29.4% of the
world consumption) and India consuming 123.5
million metric tons of paddy equivalent (23.3% of
the world consumption).
Genome Sequencing
• A genome is all of a living thing's genetic material. It is the entire set of
hereditary instructions for building, running, and maintaining an
organism, and passing life on to the next generation. In most living
things, the genome is made of a chemical called DNA. The genome
contains genes, which are packaged in chromosomes and affect specific
characteristics of the organism.
• Genome sequencing is figuring out the order of DNA nucleotides, or
bases, in a genome—the order of As, Cs, Gs, and Ts that make up
an organism's DNA.
Rice Genome Sequencing
• The International Rice Genome Sequencing Project
(IRGSP) began in September 1997, at a workshop held
in conjunction with the International Symposium on
Plant Molecular Biology in Singapore. Scientists from
many nations attended the workshop and agreed to an
international collaboration to sequence the rice
genome. As a result, representatives from Japan, Korea,
China, the United Kingdom, and the United States met
six months later in Tsukuba to establish the guidelines.
The participants agreed to share materials and to the
timely release of physical maps and annotated DNA se-
quence to public databases. The IRGSP has evolved to
include 11 nations, and the IRGSP Working Group,
composed of a representative from each participating
nation, formulates IRGSP policies and finishing
standards.
Rice Sequencing Participants
and Chromosome
Site Assignments
Rice Genome Research Program (RGP; Japan)
Chromosome
1,6,7,8
Korea Rice Genome Research Program (Korea) 1
CCW (United States) 3,10
CUGI (Clemson University)
Cold Spring Harbor Laboratory
Washington University
Genome Sequencing Center
TIGR (United States) 3,10
PGIR (United States) 10
University of Wisconsin (United States) 11
National Center for Gene Research, Chinese Academy of Sciences (China) 4
Indian Rice Genome Program (University of Delhi) 11
Academia Sinica Plant Genome Center (Taiwan) 5
Genoscope (France) 12
Universidad Federal de Pelotas (Brazil) 12
Kasetsart University (Thailand) 9
McGill University (Canada) 9
John Innes Centre (United Kingdom) 2
Findings
• Genome size of Rice is 420 Mb
• A total of 37,544 non-transposable-element-related protein-coding
sequences were detected, compared with 28,000–29,000 in
Arabidopsis, with a lower gene density of one gene per 9.9 kb in
rice.
• A total of 2,859 genes seem to be unique to rice and the other
cereals, some of which might differentiate monocot and dicot
lineages.
• Between 0.38 and 0.43% of the nuclear genome contains organellar
DNA fragments, representing repeated and ongoing transfer of
organellar DNA to the nuclear genome.
• The transposon content of rice is at least 35% and is populated by
representatives from all known transposon superfamilies
Application
• Understanding-plant evolution & the differences between monocots
& dicots
• Improve-efficiency of rice breeding
• Improve-nutritional value of rice, enhance crop yield by
improving seed quality, resistance to pests and diseases & plant
hardiness
• Development of gene-specific markers for marker-assisted
breeding
of new and improved rice varieties
• How a plant responds to the environment and which genes
control various functions of plant
