Genomics refers to the study of the entire genome of an organism. It deals with mapping genes on chromosomes and sequencing entire genomes. While work on genomics began with prokaryotes like bacteria, research has now been conducted on crop plants like rice and Arabidopsis thaliana. Genomics is an interdisciplinary field that uses tools from molecular biology, robotics, and computing to study genomes. It provides information on genome size, gene number, gene function, and evolution. Genomics has applications in crop improvement through gene mapping, marker-assisted selection, and transgenic breeding. However, genomic research also faces limitations due to high costs, technical challenges, and complexity of traits.

1. WELCOME
HARSHVARDHAN D. GAIKWAD
PLANT PATHOLOGY

2. Genomics

3. What is the definition of genomics?
Study of genomes

4. What is the genome?
Entire genetic compliment of an organism

5. Genomics
The complete set of DNA found in each cell is
known as the genome
Most crop plant genomes have billions of
nucleotide bases
Arabidopsis thaliana has 120 million bases that
encode approximately 25,000 genes
The entire Arabidopsis genome was sequenced in
2000

6. Origin of terminology
The term genome was used by German
botanist Hans Winker in 1920
Collection of genes in haploid set of
chromosomes
Now it encompasses all DNA in a cell
In 1986 mouse geneticist Thomas Roderick
used Genomics for “mapping, sequencing
and characterizing genomes”
New terms: Functional genomics,
transcriptomics, proteomics, metabolomics,
phenomics (Omics)

7. Origin of Genomics
Human Genome Project
– Goal: sequence 3 billion base pairs
– High-quality sequence (<1 error per 10 K bases) ACGT
Immensity of task required new technologies
– Automated sequencing
Decision to sequence other genomes: yeast and
bacteria
– Beginnings of comparative genomics

8. What is genomics?
A marriage of molecular biology, robotics,
and computing
Tools and techniques of recombinant DNA
technology
– e.g., DNA sequencing, making libraries and PCRs
High-throughput technology
– e.g., robotics for sequencing
Computers are essential for processing and
analyzing the large quantities of data generated

9. •The term genomics
was first used by
Thomas Roderick in
1986.
•It refers to the study
of structure and
function of entire
genome of a living
organism.
Genomics
Structure of Chromosome
Function of all the genes
Genomics

10. DNA sequence
1 gtcgacccac gcgtccgtct tgaaagaata tgaagttgta aagagctggt aaagtggtaa
61 taagcaagat gatggaatct ggggctccta tatgccatac ctgtggtgaa caggtggggc
121 atgatgcaaa tggggagcta tttgtggctt gccatgagtg tagctatccc atgtgcaagt
181 cttgtttcga gtttgaaatc aatgagggcc ggaaagtttg cttgcggtgt ggctcgccat
241 atgatgagaa cttgctggat gatgtagaaa agaaggggtc tggcaatcaa tccacaatgg
301 catctcacct caacgattct caggatgtcg gaatccatgc tagacatatc agtagtgtgt
361 ccactgtgga tagtgaaatg aatgatgaat atgggaatcc aatttggaag aatcgggtga
421 agagctgtaa ggataaagag aacaagaaga aaaagagaag tcctaaggct gaaactgaac
Protein coding regions of Genes begin with ATG and end with either TAG,
TGA or TAA
atg atg gaa tct ggg gct cct… use genetic code..
M M E S G A P ..*
Study function of proteins and expression of genes in different organs and tissues
DNA to RNA to Proteins
transcription translation

11. Main points related to genomics are given below:
•It is a computer aided study of structure and function of entire
genome of an organism.
•It deals with mapping of genes on the chromosomes.
•It deals with sequencing of genes in an organism.
•It is a rapid and accurate method of gene mapping. It is more
accurate than recombination mapping and deletion mapping
techniques.
•The genomic techniques are highly powerful, efficient and
effective in solving complex genetic problems.
•Now the use of genomic techniques has become
indispensable in plant breeding and genetics.

12. How many types of genomes are there in
this world?
Prokaryotic genomes
Eukaryotic Genomes
Nuclear Genomes
Mitochondrial genomes
Chloroplast genomes

13. TYPES OF GENOMICS
Structural Genomics: It deals with the study of the
structure of entire genome of an organism. In other
words, it deals with the study of the genetic structure of
the each chromosome of the genome. It determines size
of the genome of a species in Megabases (Mb) and also
the number of genes present in the entire genome of a
species.

14. TYPES OF GENOMICS
Functional Genomics: It deals with the study of function of
all genes found in the entire genome of a living organism.
deals with transcriptome and proteome. The transcriptome
refers to complete set of RNAs transcribed from a genome
and proteome refers to complete set of proteins encoded by a
genome. genomics can be classified based on the
experimental material used and type of analysis carried out .
Functional genomics assigns functions to each and
every gene identified through structural genomics. Thus
function genomics is more complicated that structural
genomics

15. Why should we study genomes?
• Each and everyone is a unique creation!
• Life’s little book of instructions
• DNA blue print of life!
• Human body has 1013
cells and each cell has 6 billion
base pairs (A, C, G, T)
• A hidden language/code determines which proteins
should be made and when
• This language is common to all organisms

16. What can genome sequence tell us?
• Everything about the organism's life
• Its developmental program
• Disease resistance or susceptibility
• History
• Where you are going?

17. Now look at your neighbor and
say Hi!
• What do you see?
• Someone is different than you!
• Could be that your friend differs in
his/her sex, looks, nature, smartness,
or simply the way he/she dresses and
talks
• How much similarity you think you
share with your friend at the gene
level?
• 99.9% so we could fix genes if we
want

18. Now look at your own hands and legs
• Do they look similar? No!
• But they contain the same DNA in
each of their cells
• DNA makes RNA makes proteins
• Different genes are expressed
differently in different cells, tissues
and organs of an organism
• Having a gene does not mean it will
be expressed.

19. How will we change in this century because
of the Genomics?
• You will control the destiny of this
planet
• Big changes in our own life
• Biotechnology: more products
• GMOs: More food-More problems?
• Our society will not be the same!
• Individualized medicine
• Gene therapy
• Immortality? Disease free life?

20. Genome sequencing in some organisms
Species Year Genome size
(Mb)
No. of genes
identifies
Prokaryotes
Haemophillus
Mycoplasma
Methanococcus jannaschi
E.Coli
M.Tuberculosis
Eukaryotes
Yeast (S. cerevisiae)
Nemotode (C. elegans)
Fruitfly (D. melanogaster)
Arabidopsis thaliana
Human (Homo spiens)
Rice (Oryza sativa)
1995
1995
1996
1997
1998
1996
1998
2000
2000
2001
2002
1.83
0.58
1.66
4.64
4.41
12.00
97.00
180.00
125.00
3200.00
430.00
1740
500
1750
4400
4000
5800
19000
13600
25500
40000
56000
D. melanogaster Nemotode (C. elegans)

21. •The genomic research has so far been
carried out mainly on prokaryotes and a very
little work has been done on crop plants.
•In crop plants, the genome mapping has
been completed in two species, viz.
Arabidopsis thaliana (a weedy relative of
mustard) and rice (Oriza sativa).
•Now the work on genome mapping has
been initiated in several field crops and fruit
crops by the Indian Council of Agricultural
Research, New Delhi.
•The estimated genome size of some crop
plants is presented on next slide.
GENOMIOCS IN CROP PLANTS

22. Name of crop Botanical Name Genomic Size
(Mb)
Field Crops
Rice Oryza sativa 400
Sorghum Sorghum bicolour 1000
Maize Zea mays 2500
Barley Hordeum Vulgare 8000
Bread Wheat Triticum aestivum 16000
Chick pea Cicer arietinum 1000
Pigeonpea Cajanus cajan 1500
Field Pea Pisum sativum 4800
Soybean Glycine max 2000
Tomato Lycopersicon
escueentum
950
Fruit Crops
Mango Mangifera indica 350
Citrus Citrus sp. 385
Banana Musa spientum 873

23. GENOME MAPPING IN INDIA
Lab Setup
The genome mapping is a very costly affair because it requires specialized
technical skill, sophisticated Laboratory, costly equipments, chemicals and
glass wares. Thus main or basic requirements of genome mapping are
listed below:
•High or specialized technical skill
•Sophisticated Laboratory facilities
•Costly equipments and Instruments
•Costly chemicals
•Costly glass wares
Such very expensive projects are taken up through International
Collaboration. Now intentional Consortia are available to take up such
research work.

24. Genome mapping Laboratories
Genome Institutes/Countries Involved
Human Genome (2001) USA, UK, China and Japan through Human Genome
Initiative project
Bacterial Genome (1995) several countries
Rice Genome (2002) IRRI, USA, China and Japan through International Rice
Genome Sequence Project.
Arabidopsis Genome
(2000)
USA, China and Japan
Wheat Genome Project International Genome Research on wheat by the
scientists from Mexico (CYMMIT), UK, USA and Japan
Brassica Genome China, Japan and USA under the Project Brassica
Genome Gateway
Cotton Genome USA, France and Australia and the International Cotton
Genome Initiative Project

25. Technical foundations of genomics
Molecular biology:
recombinant-DNA
technology
DNA sequencing
Library construction
PCR amplification
Hybridization
techniques
LogMW
Distance
. .
. .

26. Genomics relies on
high-throughput technologies
200 Automated
sequencers
Fluorescent dyes
Robotics
– Microarray spotters
– Colony pickers
High-throughput
genetics
ABI3700

27. Other Plant Genomes are
being sequenced
Large scale sequencing: rice, alfalfa
Grass ESTs: rice, maize, barley, wheat,
millet, sorghum, forage grasses
Dicot ESTs: alfalfa, bean, beet, cassava,
cotton, lettuce, potato, rapeseed, soybean,
sunflower, tomato, ice plant
Tree ESTs: apple, cherry, pine, poplar

28. Strawberry flavor development
Aharoni et al.
2000 Plant Cell
12:647-661

29. ..
ROLE OF GENOMICS IN CROP IMPROVEMENT
Genomics has various practical
applications in crop improvement. The
genome mapping is useful in the following
ways :
1.Genome size 2. Gene Number
3. Gene mapping 4. Gene sequencing
5. Evolution of crop
plants
6. Gene cloning
7. Identification of
DNA markers
8. Marker Assisted
selection
9. Transgenic
breeding
10. Construction of
Linkage maps

30. In the genomic research, both types of genes viz. major genes and minor genes can be
easily mapped. In other words, both oligogenic and polygenic traits can be
mapped. The mapping of Quantitative Trait Loci is possible by genome
mapping techniques which is not possible by conventional gene
mapping methods: viz. recombination and deletion techniques. Thus genomics
permits mapping of genes for all types of traits. Generally, the genome mapping is done
for following type of characters.
1. Morphological Characters: It includes highly heritable characters such as shape,
size, colour of leaf, flower, calyx., corolla etc. It also includes surface of leaf and stem
(hail)' or smooth).
2. Yield and yield contributing characters.
3. Genes controlling resistance to biotic and abiotic stresses. Biotic stresses
include insects, diseases and parasitic weeds. Abiotic stresses include, drought, soil
salinity, soil alkalinity, soil acidity, heat, frost, water logging, cold, etc.
4. Genes controlling quality characters. It includes keeping quality as well as
market quality.
5. Genes controlling toxic substances.
6. Genes controlling male sterility and self incompatibility in crop plants.
7. Genes controlling fertility restoration.
8. Apomictic genes especially in fruit crops.
9. Genes controlling adaptation to various agroclimatic conditions.
10. Gene controlling photo and thermo-insensitivity.
11. Genes controlling agronomic characters such as earliness, plant height, plant
type, elc.
12. Gene controlling non shattering habit in mung bean. Thus all type of characters can
be mapped through genomic studies.

31. ACHIEVEMENTS
Limited progress has been made so far in the field of genomic research related to both
animals and crop plants. Important achievements of genomic research are briefly
presented below:
1. Bacteria
In bacterira, the genome mapping was first completed in influeza fever causing
bacterium, viz. Haemophillus injluenzae in 1995. This was the first case of genome
mapping in micro-organisms or prokaryotes. Since then genome mapping has been
completed in 165 species of bacteria.
2. Mycoplasma
In Mycoplasma, the genome mapping was first completed again in 1995 in
Mycoplasma genetalium. The genome size of this organism is 0.58 Mb and number of
genes are 500. In other words, 500 genes have been mapped in the genome of this
species.
3. Yeast
In yeast, the genome mapping was first completed in 1996. The genome size of yeast
is 12 Mb and 5,800 genes have been mapped so far.
4. Fruit Fly (Drosophila Melanogaster)
In fruit fly, the genome mapping was first completed in 2000. The genome size of fruit
fly is 180 Mb and 13,600 genes have been mapped so far.
5. Human (Homo sapiens)
The human genome was completed in 2001. The genome size of human is 3200 Mb
and 40,000 genes have been mapped so far.
6. Crop Plants
In crop plants, genome mapping has been completed in two species, viz. Arabidopsis
thaliana (a weedy relative of mustard) and rice.

32. The genome mapping of crop plants is gaining increasing importance
these days. It has several useful applications. However, there are some
limitations of genome mapping which are briefly presented below :
1. Very Expensive
The genomic research requires well equipped sophisticated laboratory.
The chemicals, equipments and glass wares used for such work are very
expensive. Thus lot of funds are required for carrying out genomic
research. Lack of adequate funds sometimes becomes limiting factor in the
progress of such project.
2. Technical Skill
The genome mapping work requires high technical skill. It requires
training of the scientists in the specialized field of genomics. It also
requires International collaboration with other leading genome research
laboratories which sometimes becomes limiting factor. The international
collaboration is possible if the crop on which genomic research work is to
be carried out is of global significance.
3. Laborious Work
The genome mapping requires detection of various DNA markers
(RFLP, AFLP, SSR, RAPD etc.) which is a laborious and time consuming
work. Huge populations related to F2, RILs, NILs and doubled haploids
need to be screened for such purpose. This limits the progress of work.

33. 4. Limited Genes Available
Firstly limited number of genes and promoters are available for
development of transgenics. Secondly such genes are protected
under IPR and therefore, can not be used for developing
transgenic plants.
5. Lack of Proper Markers
Most of the useful agronomic traits are governed by polygenes
and are complex in nature. Tightly linked DNA markers are yet to
be identified for such characters.
Bt Gene
•Cry gene series
•Antisense RNA technology for tomato
•Terminator gene
•Beta Carotene gene in rice
•Cry gene series
•Antisense RNA technology for tomato
•Terminator gene
•Beta Carotene gene in rice

34. Improved disease diagnostics from
genomics
Microarray analysis of
gene expression from
four different types of
tumors
Grouping of gene
expression patterns
shows very clear
differences among the
tumors
Used to tailor therapy to
individuals

35. In the past, the studies on genomics have been confined mostly to
proaryotes and a very little work has been Jone on crop plants. In future,
the genome research work needs to be directed towards the following
thrust areas.
Funding. Since genome mapping projects are very costly, there is
need of international collaboration for supporting such prestigious
projects.
Training. Some Laboratories are well equipped for genomic research.
Such organizations should impart training to scientist from various
countries to develop large number of skilled manpower in genome
mapping.
Material Sharing. The leading laboratories should develop and
distribute frame work DNA markers to various other research
laboratories for their use and further research.
Research Priorities. The research priorities should be defined. In
order to get International collaboration areas of common interest/global
significance should be identified for genomic research work.
Important Traits. In genome mapping, the major emphasis needs to
be given on characters of economic importance such as productivity,
quality and resistance to biotic and abiotic stresses.
Species. In the past genome mapping has been done mostly on micro-
organisms. In plants, such studies have been carried out with two
species, viz. Arbidopsis and rice In future genome mapping needs to be
carried out with almost all important field, vegetable and fruit crops.
The experienced gained in genome mapping of one species may be
helpful in the study of related species.

36. Genomics refers to the study of structure and
function of entire genome of a living organism
Gcnomics is of two types, viz. (i) structural genomics
and (ii) functional genomics. The former deals with
the study of the structure of entire genome, whereas
the latter deals with the study of the function of all
genes found in the entire genome of a living
organism.
Genomics has several practical applications in
crop improvement. Genomics is useful in
determining (i) genome size, (ii) gene number in the
genome, (tii) gene mapping, (iv) gene sequencing,
(v) tracing evolution of crops plants, (vi) gene
cloning, (vii) identification of DNA markers, (viii)
marker assisted selection, (ix) transgenic breeding,
(x) construction of linkage maps, and (xi) QTL
mapping.

37. The genome mapping work is carried out through
International collaboration. Now international consortia are
available for such expensive research work. The genome
mapping work is being done in USA, UK, China, Japan,
Australia. In India, genome mapping work is being done at NRC
PB, New Delhi, ICGEB, New Delhi, JNU, New Delhi and NBRI,
Lucknow. The genome mapping is possible for both qualitative
and quantitative characters.
The genome mapping work has been completed in a variety
of organisms such as bacteria, mycoplasma, yeasts,
nematodes, fruit fly, human and crop plants. In crop plants,
genome mapping has been completed in two species viz.
Arabidopsis thaliana and rice. Now genome mapping work has
been initiated in several crops such as wheat, barley, maize,
sorghum, chick pea, pigeon pea, field pea, soybean, Brassica,
Tomato, etc.
The genome mapping work has some limitations. It is very
expensive, requires high technical skill and is a laborius work.
Availability of limited number of genes and promoters and lack
of proper markers limit the scope of genome mapping work.
Adequate funding, proper training facilities and sharing of
material is essential for promoting genomic research. Future
thrust areas have been indicated.

38. ICGEB Lab, New Delhi

39. ICGEB Lab, New Delhi

40. Bioinformatics Centre
Dept. of Microbiology and Biotechnology Centre, M.S.University of Baroda,
Baroda, India 390002 Phone:91-0265-2794396 , Fax: 91-265-2792508

41. Centre for Cellular & Molecular Biology (CCMB)

42. National Research Centre for Plant Biotechnology
IARI New Delhi
The National Research Centre on Plant
Biotechnology was established in 1985 to
undertake research, teaching and training
personnel in the modern areas of
Molecular Biology and Biotechnology.
Since its inception, the Centre has grown
and has acquired high degree of scientific
competence and established excellent
research facilities. The Centre is working
towards achieving the national priorities
of increased agricultural productivity and
sustainability

43. Jawaharlal Nehru University
New Delhi
JNU Campus

44. National Botanical Research Institute, Lucknow.

45. Now functional genomic projects
are being initiated by the Department
of Biotechnology (DBT) and ICAR.
The DBT has initiated such work on
Rice and ICAR has taken up genome
sequencing work on several crops
such as Rice, Wheat, Maize,
Chickpea, banana, Tomato, Brassica,
etc. The ICAR has created genome
sequencing facilities for rice at
NRCPB, IARI, New Delhi. Facilities
for genome mapping of other crops
are also being created.
Department of Biotechnology (DBT)

46. Mexico's National Laboratory of Genomics

47. Marine Genomics Lab

48. THANK YOU