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GOVERNMENT POST GRADUATE COLLEGE FOR WOMEN SATELLITE TOWN

RAWALPINDI

ASSIGNMENT:
Genetics II
TOPIC:
RICE GENOME PROJECT
SUBMITTED TO:
Madam Sehrish
SUBMITTED BY :
Shagufta Gulzar(1431)
DEPARTMENT:
BS(Hons) Botany
VIII Semester



CONTENTS
INTRODUCTION..........................................................................
HABITAT.......................................................................................
MORPHOLOGY............................................................................
LIFE CYCLE..................................................................................
USE AS A MODEL ORGANISM...................................................
HISTORY.........................................................................................
METHODS......................................................................................
SIGNIFICANT FINDINGS............................................................
APPLICATIONS&IMPACTS........................................................
POST RICE GENOME SEQUENCING........................................
CONCLUSION................................................................................
REFERENCES...............................................................................










RICE GENOME PROJECT
INTRODUCTION:-
Oryza sativa, commonly known as Asian rice, is the plant species most commonly referred to
in English as rice. Oryza sativa is the cereal with the largest genome, consisting of 430Mb across
12 chromosomes. It is renowned for being easy to genetically modify, and is a model organism
for cereal biology is one of the most important crops worldwide, as it is the staple food for half
the world‘s population. More than 2 billion people in Asia obtain the majority of their calories
and protein from rice. As the world population continues to grow, as does the struggle to keep up
the food supply,improving rice production is a pressing matter in the early 21st century. This
makes rice the most economically and politically important crop.Rice is also the key plant to
understanding the genus Oryza, grass family (Gramineae) plants, and monocotyledons. Oryza is
estimated to have originated 50 M years ago and is represented by 23 species.Colinearity of
gene order (synteny) occurs across the grass family and many genes are mapped via this syntenic
relationship. Accurate rice sequence information would be useful not only for regarded as
isolation and breeding of the rice gene, but also for the molecular breeding of other important
crops such as maize, barley, sorghum, and wheat.
HABITAT:-
Oryza sativa, rice, is a genus of perennial grass in the Poaceae (grass family) that originated in
throughout tropical Asia India, Thailand, and southern China, was domesticated and diversified
in ancient times, and is now cultivated in wet tropical, semi-tropical, and warm temperate areas
around the world for the production of its cereal grain.
MORPHOLOGY:-
An annual grass with erect culm 0.6-2 m tall usually with four to five tillers.It has a tufted, erect,
hollow and slender or stout, smooth and hairless stem, 80—120—cm tall. Leaf blade flat with
parallel veins, 15—30—cm—long; ligule and auricle present; ligule usually 10—20—mm—
long.Inflorescence a loose terminal panicle of perfect flowers; each panicle branch bearing a
number of spikelets 7mm longflat,one flowered with or without awns., each with a single floret.
Each panicle holds 100-150 seeds.Each flower is surrounded by a lemma and palea at the base of
which are two small glumes. The lemmas may be awnless or variously awned. The rice grain
enclosed by the lemma and palea (hull) varies in size, texture and colour.


LIFE CYCLE:-
Rice is an annual grass.It is sowed in springtime&it ripens according to the different
varieties,between september and october. The plant reaches a 80-150cm height and it takes 5
months,on average to ripens.In some hot and wet countries,it is possible to have more than one
harvest a year.
USE AS A MODEL ORGANISM:-
Rice (Oryza sativa) is used as the second-best model organism.Some desired features of future
improved rice varieties are superior grain quality, higher yield potential, enhanced resistance to
insect pests and diseases, and greater tolerance to stresses such as drought, cold, and nutrient
deficiencies.
 The world‘s first genome of a crop plant that was completely sequenced.
Rice like Arabidopsis is a model experimental plant. Perhaps the most significant factor
in selecting a model species is the small genome size of rice compared with other
members of the Gramineae family.
The genome size of rice is estimated to be 431 Mb.This is approximately one-half of the
DNA content of sorghum (760 Mb) and 17%, 8.8%, and 2.7% of the DNA content of
maize (2,504 Mb), barley (4,873 Mb), and wheat (15,966 Mb), respectively.
The reduced genome size in rice compared with these other grass species is attributable to
the diploid nature of rice, along with the reduced repetitive DNA content in rice relative
to other grass species.
A second criterion in selection of a model species is the availability of genetic and
molecular resources. There are currently over 2,200 mapped markers for rice that were
generated in a single mapping population of O. sativa spp. Japonica and O. sativa spp.
indica. The resulting density of approximately 1 marker per 190 kbp provides a deep
resource for current high throughput sequencing strategies.
Substantial conservation of gene order (synteny). It has enormous number of genes
controlling agronomically important traits.It has wide genetic diversity is present in the
genus Oryza.
HISTORY OF RICE GENOME SEQUENCING:-
In Sept 1997 -Sequencing of the rice genome was initiated as an international collaboration
among 10 countries.In Feb 1998 – IRGSP (International Rice Genome Sequencing Project)
was launched under the coordination of the Rice Genome Program (RGP) of Japan.In April
2000 – Monsanto Co. produced a draft sequence of BAC contigs covering 260 Mb of the rice
genome; 95% of rice genes were identified.In 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.In 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.In Dec 2004 – IRGSP produce the high-quality‘ sequence of the entire rice genome;
with 99.99% accuracy and without any sequence gap.
RICE GENOME PROJECT:-
The Rice Genome Research Program (RGP) was initiated in 1991.An international effort has
been established and is in the process of sequencing O. sativa spp. japonica var ―Nipponbare‖
using a bacterial artificial chromosome/P1 artificial chromosome shotgun sequencing strategy.
Annotation of the rice genome is performed using prediction-based and homology-based
searches to identify genes. Annotation tools such as optimized gene prediction programs are
being developed for rice to improve the quality of annotation. Resources are also being
developed to leverage the rice genome sequence to partial genome projects such as expressed
sequence tag projects, thereby maximizing the output from the rice genome project.
METHODS OF SEQUENCING:-
Map-based sequencing –Map based sequencing is done by International Rice Genome
Sequencing Project (IRGSP)& Monsanto Co (funded University of Washington –Leroy Hood‘s
et al.) In map-based sequencing each stretch of sequence is physically anchored to a
chromosome forming a contig of clones, which are individually sequenced.
Annotation pipeline system at RGP-Annotation pipeline system consists of automated
annotation, curation of auto predicted genes and storage of all data in a relational
database.Annotation means Adding pertinent information such as gene coded for, amino acid sequence,
or other commentary to the database entry of raw sequence of DNA bases.

SHOTGUN SEQUENCING:-
Shotgun sequencing is done by Beijing Genomics Institute (BGI)&Syngenta-Myriad (funded
Torrey Mesa Research Institue).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



SIGNIFICANT FINDING FROM 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. 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.71% putative
homology with Arabidosis, 90% Arabidopsis genes have putative homologue with rice.2,859
genes unique to rice and other cereals.
APPLICATIONS AND IMPACTS:-
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.
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.
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.
Functional analysis of predicted genes.
Analysis of coordinated expression of genes (genetic and biochemical networks)
Proteomics(The study of the full set of proteins encoded by a genome).
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).
CONCLUSION:-
The goal of this project was to create a database of mapped cereal genes and markers, and
provide a foundation for cereal functional genomics studies. The rice genome was chosen as the
appropriate model cereal genome and sequenced to greater than 99% coverage and accuracy.The
resulting genomic information enables development of RNA profiling, proteomics, and
accelerated crop breeding technologies. Gene predictions on the assembled sequence suggest that
the rice genome contains32,000 to 50,000 genes. The rice genome sequence provides a
foundation for the improvement of cereals, our most important crops.
REFERENCES:-
• International Rice Genome Sequencing Project. (2005). The map-based sequence of the
rice genome. Nature 436, 793-800. Author lists: Academia Sinica Plant Genome Center (
ASPGC) Teh-Yuan Chow, Hong-Hwa Chen, Mei-Chu Chung, Ching-San Chen, Jei-Fu
Shaw, Hong-Pang Wu, Kwang-Jen Hsiao, Ya-Ting Chao, Mu-kuei Chu, Chia-Hsiung
Cheng, Ai-Ling Hour, Pei-Fang Lee, Shu-Jen Lin, Yao-Cheng Lin, John-Yu Liou, Shu-
Mei Liu, Yue-Ie Hsing (Principal Investigator)
• Ueguchi-Tanaka, M., Ashikari, M., Nakajima M., Itoh H., Katoh E., Kobayashi M.,
Chow T., Hsing Y., Kitano H., Yamaguchi I And Matsuoka M. (2005) Nature 437, 693-
698.
• Gaut B (2002) Evolutionally dynamics of grass genomes. New Phytologist 154:15–28
• Ge S, Sang T, Lu BR, Hong DY (1999) Phylogeny of rice genomes with emphasis on
origins of
allotetraploid species. Proc Natl Acad Sci USA 96:14400–1440