Genome projects and their Contributions

This is a presentation about different Genome projects like Rice genome project, Maize genome project, Wheat Genome project and Human genome project. It highlights how they were conducted and what the science community gained by conducting them. A side about the future challenges of such genome projects is also added.

1. GENOME PROJECTS AND
THEIR CONTRIBUTIONS

2. INTRODUCTION
•Genome projects are ultimately
scientific endeavours that aim to
determine the entire genome
sequence of an organism, be it an
animal, fungus, bacteria, plant, virus,
archaeon or protist.
•The protein coding genes and other
important genome coded features are
annotated.
•Genome sequence of an organism
includes the collective DNA sequence
of each chromosome in the

3. •For the Human species, a complete genome
sequence will involve 46 separate chromosome
sequences.
•For the Rice species-Oryza sativa, a complete
genome sequence will involve 24 separate
chromosome sequences.
•For the Maize species-Zea mays, a complete
genome sequence will involve 20 separate
chromosome sequences.
•For the Wheat species-Triticum aestivum, a
complete genome sequence will involve 42
separate chromosome sequences.

4. RICE GENOME PROJECT

5. RICE GENOME PROJECT
•Rice (Oryza sativa) is one of the most important crops in the
world.
•Rice is the principal food of half of the world's population.
•The rice genome is well mapped and characterized,
•It is smallest of the major cereal crop genomes at an estimated
400-430 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.

6. REASONS FOR RICE BEING A MODEL PLANT:
•The small size of its genome (430 Mb).
•Its relatively short generation time.
•Its relative genetic simplicity (it is diploid).
•Easy to transform genetically.
•Belongs to the grass family.
•It has greatest biodiversity among the cereal crops.

7. WHY WE SHOULD SEQUENCE RICE?
•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.

8. MILESTONES IN RICE GENOME PROJECT:
•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 indicaand japonica
rice genomes and development of new generation markers.
•Synteny between genomes of rice and other cereals.

9. DISCOVERIES IN RICE GENOME:
•Size of Rice Genome 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.

10. •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.

11. APPLICATIONS OF RICE GENOME PROJECT:
•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.

12. MAIZE GENOME PROJECT

13. MAIZE GENOME PROJECT
•Maize (Zea mays) plays many varied and important roles.
•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.

14. 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)
•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).
•Wide adaptability, especially for stressed environments.

15. CHALLENGES FACED
•The Maize genome has 2,500 million base pairs, and 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.
•Organization of maize genome 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.

16. 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.

17. •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.

18. METHOD OF MAIZE GENOME SEQUENCING
•Genetic and physical maps-The project led by Joachim Messing
delivered a high-resolution, sequence-ready map of the maize
genome.
•Using 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.
•Using BAC sequences.
•Using EST sequences.
•Methyl-filtered and High C0t genome sequences enriched for
genes.

19. APPLICATIONS OF MAIZE GENOME PROJECT
•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

20. WHEAT GENOME PROJECT

21. WHEAT GENOME PROJECT
•Wheat was the first domesticated crop.
•It is the youngest polyploid species among the agricultural
crops.
•Along with the crops of Rice and Maize, wheat provides about
60% of the calories and proteins that are required for our daily
life.
•Wheat is best adapted to temperate regions, unlike rice and
maize, which prefer tropical environments.
•To meet requirements of humans by the year 2050, grain
production must increase at an annual rate of 2% on an area of
land that will not increase much beyond the present level.
•In addition to food security, wheat genome sequencing will lead

22. INTRODUCTION OF WHEAT GENOME
PROJECT
•Sequencing the wheat genome had long been considered an
impossible challenge, due to the high complexity of the wheat
genome.
•But improving the average wheat yields had 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.

23. CHALLENGES FOR WHEAT GENOME PROJECT
•Wheat is one of the most important crop in the world, yet it has
one of the most challenging genomes to sequence.
•Bread wheat is a hexaploid (6 ploidy), 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.

24. •Wheat genome has:
•17 Gb draft sequence –Individual chromosome arms
•123 201 gene loci –Evenly distributed
•Comparative analysis of diploid relatives shows that there is
high conservation and very limited gene loss.
•There is Gene gain and duplication after speciation.
•There is no sub genome dominance –Adopted very well

25. GOALS OF WHEAT GENOME PROJECT
•A major goal of the Wheat Genome project was to establish a
high quality reference sequence of wheat genome, anchored to
the genetic/phenotypic maps.
•This would 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).

26. MILESTONES
•Gene sequences to individual chromosomes were assigned
using the survey sequences of the 21 bread wheat
chromosomes.
•Physical maps were developed 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.

27. METHODS USED FOR WHEAT GENOME
PROJECT
•Genome sequencing projects can be generally divided into
whole genome shotgun (WGS) method or by BAC method.
•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 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.

28. CONCLUSIONS OF WHEAT GENOME
PROJECT
•Constructed 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.
•Explored 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 homologous
chromosome groups.
•Identifying genomic sequence tags using gene-enrichment
procedures such as hi-C₀ᵗor methyl filtration, ESTs, and full-length
cDNAs of 2x, 4x, and 6x wheat for an accurate estimation of the
wheat unigene set.
•

29. HUMAN GENOME PROJECT

30. HUMAN GENOME
•The human genome is the complete set of genetic information
for humans (Homo sapiens).
•The human genome is by far the most complex and largest
genome.
•Its size spans a length of about 6 feet of DNA, containing more
than 30,000 genes.
•The DNA material is organized into a haploid chromosomal set
of 22 (autosome) and one sex chromosome (X or Y).
Male human
chromosomes
Female Human
chromosomes

31. The Human Genome Project
Human Genome Sequencing

32. SALIENTFEATURE OF HUMAN GENOME
•Human genome consists the information of 24 chromosomes (22
autosome + X chromosome + one Y chromosome); in Homo
sapiens 2n = 2x = 46
•The human genome contains over 3 billion nucleotide pairs.
•Human genome is estimated to have about 30,000 genes .
•Average gene consists of 3000 bases. But sizes of genes vary
greatly, with the largest known human gene encoding dystrophin
containing 2.5 million base pairs.
•Only about 3 %of the genome encodes amino acid sequences of
polypeptides and rest of it junk (repetitive DNA).
•The functions are unknown for over 50% of the discovered genes.

33. •The repetitive sequences makeup very large portion of human genome.
Repetitive sequences have no direct coding function but they shed light
on the chromosome structure, dynamics and evolution.
•Chromosome 1 has most genes (2968) and Y chromosome has the
lowest (231).
•Almost all nucleotide bases are exactly the same in all people. Genome
sequences of different individuals differ for less than 0.2% of base
pairs.
•Most of these differences occur in the form of single base differences in
the sequence. These single base differences are called single nucleotide
polymorphisms (SNPs).
•One SNP occurs at every ~ 1,000 bp of human genome.
•About 85% of all differences in human DNAs are due to SNPs.

34. Human Chromosome 1
Human Chromosome Y

35. WHAT WAS HUMAN GENOME PROJECT?
•The Human Genome Project was an international research effort
to determine the sequence of the human genome and identify
the genes that it contains.
•The US Human genome Project is a 13 year effort, which is
coordinated by the Department of Energy and National
Institutes of Health (NIH).

36. GOALS OF HUMAN GENOME PROJECT
•To identify all the genes in human DNA.
•To develop a genetic linkage map of human genome.
•To obtain a physical map of human genome.
•To develop technology for the management of human genome
information.
•To know the function of genes.
•Determine the sequences of the 3 billion chemical base pairs that make
up human DNA.
•Store this information in public databases.
•Develop tools for data analysis.
•Transfer related technologies to the private sectors.

37. MILESTONES OF HUMAN GENOME PROJECT
•1986-The birth of the Human Genome Project.
•1990-Project initiated as joint effort of US Department of Energy and
the National Institute of Health.
•1994-Genetic Privacy Act: to regulate collection, analysis, storage
and use of DNA samples and genetic information isproposed.
•1996-Welcome Trust joins the project.

38. •1998-Celera Genomics (a private company founded by Craig
Venter) formed to sequence much of the human genome in 3
years.
•1999-Completion of the sequence of Chromosome 22-the
first human chromosome to be sequenced.
•2000-Completion of the working draft of the entire human
genome.
•2001-Analysis of the working draft are published.
•2003-HGP sequencing is completed and Project is declared
finished two years ahead of schedule.

39. ISSUES OF CONCERN:
Ethical, Legal and Social issues of the Human Genome Project
•Fairness in the use of genetic information.
•Privacy and confidentiality of genetic information.
•Psychological impact, stigmatization, and discrimination.
•Reproductive issues.
•Clinical issues.
•Uncertainties associated with gene tests for susceptibilities and
complex conditions.

40. •Fairness in access to advanced genomic technologies.
•Conceptual and philosophical implications.
•Health and environmental issues.
•Commercialization of products.
•Education, Standards, and Quality control.
•Patent issues.

41. FUTURE CHALLENGES
•Gene number, exact locations, and functions
•Gene regulation.
•Chromosomal structure and organization
•Non-coding DNA types, amount, distribution, information
content, and functions
•Coordination of gene expression, protein synthesis, Proteomes
and post-translational events

42. •Predicted vs experimentally determined gene function
•Evolutionary conservation among organisms
•Disease-susceptibility prediction based on gene sequence
variation
•Genes involved in complex traits and multigene diseases
•Developmental genetics, genomics

43. REFERENCES
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http://pubmed.ncbi.nlm.nih.gov/12481042/. [Accessed: 18-Apr-2021]
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