used for student

1. GENOMICS
BHARAT LAL MEENA
GENETICS & PLANT BREEDING

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

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

4. 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

5. 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)

6. 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

7. 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

8. Genomics
Structure of Chromosome
Function of all the genes
•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

9. 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

10. 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.

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

12. 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.

13. 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

14. 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

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

16. 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?

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

18. • 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

19. Name of
crop
Botanical Name Genomic Size
(Mb)
Field Crops
Rice Oryza sativa 400
Sorghum Sorghum bicolour 1000
Maize Zea mays 2500
Barley HordeumVulgare 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 950
escueentum
Fruit Crops
Mango Mangifera indica 350
Citrus Citrus sp. 385
Banana Musa spientum 873

20. 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.

21. 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

22. .
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 6. Gene cloning
plants
7. Identification of 8. Marker Assisted
DNA markers selection
9. Transgenic 10. Construction of
breeding Linkage maps

23. 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.

24. 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.

25. 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.

26. 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

27. 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) genesequencing,
(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.

28. 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.

29. THANK YOU