CROP genome

projects
 RICE GENOME PROJECT
• Rice (Oryza sativa) is one of the most important crops in the
world.
• rice itself is the principal food of half of the world's
population
• The rice genome is well mapped and well characterized, and
it is the smallest of the major cereal crop genomes at an
estimated 400 to 430 Mb.
• 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.
WHY RICE IS A MODEL PLANT?
• The small size of its genome (430 Mb)
• Its relatively short generation time
• Its relative genetic simplicity (it is diploid, or has two copies
of each chromosome).
• Easy to transform genetically.
• Belongs to the grass family
• Its greatest biodiversity among the cereal crops
IMPORTANCE OF RICE
SEQUENCING
• It can address many different aspects of rice
research ,including genetic diversity and
productivity improvement.
• To design efficient ways to tap into wealth of rice
genome sequence information to address production
constraints in an environmentally sustainable
manner.
PROGRESS IN RICE GENOMICS
• Development of the first saturated (RFLP) map.
• The application of PCR based markers such as SSR markers.
• Identification of QTLs for many agronomically important
traits and marker assisted breeding.
• Development of efficient techniques for genetic
transformation which makes rice the easiest cereal to
transform.
• Complete sequencing and annotation of indica and japonica
rice genomes and development of new generation markers.
• Synteny between genomes of rice and other cereals.
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
 APPLICATIONS
• 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
 REFERENCES
• Scott A. Jackson,” Rice: The First Crop Genome”,
Rice (N Y). 2016; 9:
14.doi: 10.1186/s12284-016-0087-4(https://www.n
cbi.nlm.nih.gov/pmc/articles/PMC4803718/)
• http://rice.plantbiology.msu.edu/
• https://gigascience.biomedcentral.com/articles/10.1
186/2047-217X-3-7
• https://www.sciencedirect.com/science/article/pii/S1
369526699000473
 MAIZE GENOME PROJECT
• Maize (Zea mays or corn) plays many varied and important
roles in society
• It is not only an important experimental model plant, but also
a major livestock feed crop and a significant source of
industrial products such as sweeteners and ethanol. In this
study we report the systematic analysis of contiguous
sequences of the maize genome.
• The four-year, US$31-million project to sequence maize(Zea
mays) was led by a US-based consortium of researchers who
decoded the genome of an inbred line of maize called B73,
an important commercial crop variety.
 MAIZE AS A MODEL CROP
• An intermediate genome size compared to rice and wheat
• Typical outbreeding system with flexibility for inbreeding
• Multiple breeding products (inbreds, hybrids, synthetic
varieties, open pollinated varieties and improved landraces)
• Wide adaptability, especially for stressed environments
• Multiple-purpose crop: 5Fs food (grain), feed (grain and
stalk), fuel (grain and stalk), forage (young grain and stalk)
fruit (sweetcorn, baby corn, fresh corn)
• Maize is adapted to diverse environments
 CHALLENGES
• At 2,500 million bp, the maize genome is about 20 times
larger than that of Arabidopsis, about six times larger than
that of rice, and about the same size as the human genome.
• Its organization is more complex than the other genomes
sequenced to date.
• The genes of maize compose only about 20% of the genome
and are organized into islands of variable size that are
scattered throughout a sea of highly conserved, high-copy
retrotransposons and other repetitive sequences
• The cost of identifying most of the maize genes and placing
them on the integrated physical and genetic map was
estimated at approximately $52 million.
 GOLD STANDARD OF MAIZE GENOME
SEQUENCE
• The maize genome-sequencing project must provide the
complete sequence and structures of all maize genes and their
locations (in linear order) on both the genetic and physical
maps of maize.
• The gene space of B73 maize (gene sequences and adjacent
regulatory regions) should be of finished quality according to
currently acceptable standards (as per Bermuda/Ft. Lauderdale
agreements).
• If applicable, the sizes of gaps between the genes should be
estimated and draft sequences of repetitive DNA between genes
presented where possible.
• The sequence must be fully integrated with the genetic and
physical maps.
• Annotation should include gene models, predicted exon/intron
structure, incorporation of EST and full-length cDNA data,
gene ontology, and relationship with homologs in other
organisms, including but not limited to, the other sequenced
plant genomes.
• Annotation should be coordinated with existing maize
community and comparative databases with the eventual goal
of generating complete curation of the genomic sequences to a
standard set by established model organism databases.
 METHOD
• Genetic and physical maps-The project led by Joachim
Messing will deliver a high-resolution, sequence-ready map
of the maize genome.
• BAC-end sequences-This map will integrate 450,000
fluorescent-based BAC clone fingerprint reads, 450,000 end
sequences from 225,000 BACs, and 10× shotgun sequence
of about 140 BACs seeded from about 10 points throughout
the genome
• BAC sequences
• EST sequences
• Methyl-filtered and High C0t genome sequences enriched for
genes
• Whole genome shotgun sequences
 APPLICATIONS
• Maize gene sequencing and functional analysis will help
elucidate the molecular basis of agronomically important traits
and thereby facilitate improvements in maize and other crop
species.
• These agronomic improvements will have enormous impacts on
mankind through improving human health, increasing energy
production, and protecting our environment.
• The production of novel compounds in plants, including
industrial feed stocks, biofuels, and medicinal compounds will
increase the demand for corn and thereby directly benefit the
agricultural community.
• The production of nutritionally enhanced foods that are safer
and less allergenic than the foods we eat today will directly
benefit consumers.
 REFERENCES
• https://www.ncbi.nlm.nih.gov/pmc/articles/PMC13
10546/
• https://www.nature.com/news/2009/091119/full/
news.2009.1098.html
• https://www.nsf.gov/pubs/2004/nsf04614/nsf0461
4.htm
• https://www.maizegdb.org/
 WHEAT GENOME PROJECT
• Wheat was the first domesticated crop and is the youngest
polyploid species among the agricultural crops
• Together with rice and maize, wheat provides >60% of the
calories and proteins for our daily life.
• Wheat is best adapted to temperate regions, unlike rice and
maize, which prefer tropical environments.
• To meet human needs by 2050, grain production must
increase at an annual rate of 2% on an area of landthat will
not increase much beyond the present level.
• In addition to food security, wheat genome sequencing will
lead to improved human health and nutrition.
 INTRODUCTION
• Sequencing the wheat genome has long been considered an
insurmountable challenge, due to the high complexity of the
wheat genome.
• But improving average wheat yields has become a major
objective with genome sequencing as its prerequisite
• The International Wheat Genome Sequencing Consortium
(IWGSC) was created in 2005 by a group of wheat growers,
plant scientists, and public and private breeders to change
this paradigm.
 CHALLENGES
• Wheat is probably the most important crop in the world, yet it
has one of the most challenging genomes.
• Bread wheat is a hexaploid, with three complete genomes
termed A, B and D in the nucleus of each cell.
• its genome is more than 15 billion DNA bases long, harbours 6
copies of each chromosome and contains many
hard-to-sequence repetitive stretches.
• About 90% of the wheat genome consists of repeated sequences
and 70% of known TEs
• 17 Gb draft sequence – Individual chromosome arms
• 123 201 gene loci – Evenly distributed
• Comparative analysis –diploid relatives – high conservation
and very limited gene loss
• Gene gain and duplication after speciation
• No sub genome dominance – Adopted very well
 GOALS
• To establish a high quality reference sequence of the wheat
genome anchored to the genetic/phenotypic maps. This will
provide high resolution links between wheat traits and
variations and the associated sequence features (i.e., genes,
regulatory motifs, intergenic regions etc) and polymorphisms
(Single Nucleotide Variants (SNPs), Structural Variations
(SV) and to establish a high quality reference sequence of
the wheat genome anchored to the genetic/phenotypic maps.
This will provide high resolution links between wheat traits
and variations and the associated sequence features (i.e.,
genes, regulatory motifs, intergenic regions etc) and
polymorphisms (Single Nucleotide Variants (SNPs),
Structural Variations (SV)).
 MILESTONES
• use of survey sequences of the 21 bread wheat
chromosomes to assign gene sequences to individual
chromosomes
• developed physical maps to provide resources for
sequencing
• delivered a reference sequence for each of the
chromosomes
• produced a gold standard genome sequence by
integrating chromosome based genomic resources with
the IWGSC whole genome assembly.
 METHODS
• Genome sequencing projects can be generally divided into
whole genome shotgun (WGS) methods or BAC by BAC
methods.
• WGS attempts to sequence the genome in one go, by
generating a large amount of sequence data and then
assembling this to produce a representation of the string of
letters which make up the genome.As wheat is polyploidy it
is not usually preferred.
• The alternative BAC by BAC approach requires breaking the
genome down to relatively small pieces (c. 120 kbp),
ordering these as a minimal tiling path, then sequencing each
of the BACs in the tiling path.But this method is very
expensive and time consuming.
 CONCLUSIONS
• Constructing an accurate, sequence-ready, global physical
(BAC-contig) map anchored to the high-resolution genetic and
deletion maps of the 21 chromosomes of the hexaploid wheat
genotype Chinese Spring.
• Exploring the use of flow-sorted chromosome- and arm-specific
libraries in the assembly of the global physical map and in
preparation for the sequencing of the gene-containing regions
of homeologous chromosome groups.
• Identifying genomic sequence tags using gene-enrichment
procedures such as hi-C0t or methyl filtration, ESTs, and
full-length cDNAs of 2x, 4x, and 6x wheat for an accurate
estimation of the wheat unigene set.
• Leveraging rice sequence and wheat-rice gene synteny,
comparative genetics, and wheat unigenes toward the
development of high-resolution genetic and deletion maps of
the 21 chromosomes of Chinese Spring wheat.
• Integrating bioinformatics at every step for project
management, data analysis, improved methods of sequence
annotation, and dissemination of data
• Engaging all wheat stakeholders and educational institutions
(K–12) globally, especially in developing countries, and locally
in all aspects of the research, technology transfer, workforce
training, and promotion of science.
• Maintaining all data, materials, and resources in the public
domain and free of intellectual property rights.
• Organizing an international steering committee to coordinate
and execute all aspects of the wheat genome sequencing
project.
 REFERENCES
• http://wheatgenome.info/details.php
• https://www.nature.com/articles/d41586-017-05312-1
• Bikram S. Gill et al.,” A Workshop Report on Wheat
Genome Sequencing”, Genetics. 2004 Oct; 168(2):
1087–1096.doi: 10.1534/genetics.104.034769(https://www.n
cbi.nlm.nih.gov/pmc/articles/PMC1448818/)
• https://cnrgv.toulouse.inrae.fr/Projects/Plant-genome-sequen
cing/IWGSC-The-International-Wheat-Genome-Sequencing-
Consortium
• http://www.wheatgenome.org/
Acknowledgement
• Bhoomika PP