The document provides a history of genomics, beginning with Mendel's work in 1866 establishing the gene concept and laws of genetics. Key developments include the discovery of DNA in 1871, the chromosomal theory of inheritance in 1902, and the discovery of linkage in 1910. The structure of DNA was elucidated in the 1950s, leading to the development of recombinant DNA technology in the 1970s and DNA sequencing techniques in the 1970s-80s. The first whole genome of an organism was sequenced in 1995. More recent developments include next generation sequencing starting in 2005 and the advent of CRISPR/Cas9 genome editing in 2012. The document concludes with discussing the potential use of CRISPR to target genes in the diamondb

1. HISTORY OF GENOMICS
Course Title: Genomics in Crop Improvement (GP-603)
Presented by:
SONAL CHAVAN
Ph.D. First year
Dept. of Genetics and Plant Breeding
Professor Jayashankar Telangana State
Agricultural University
Hyderabad, Telangana

2. GENOMICS
GENOME means the single set of chromosomes.
It represents the total genetic information
present in an organism.
GENOMICS: Genomics is a discipline
in genetics that applies recombinant DNA, DNA
sequencing methods, and bioinformatics to
sequence, assemble, and analyze the function
and structure of genomes
The term genomics was coined by Thomas H.Roderick in 1987.

3. GENOMICS
Branches
of
Genomics
Structural Genomics: Structural genomics deals with the
determination of the complete sequence of genomes or
the complete set of proteins produced by an organism.
Functional Genomics: Functional genomics is defined as
determination of the function of a gene product.
Comparative genomics: The study of differences and
similarities in genome structure and organization of
different organisms is called comparative genomics
Epigenomics is the study of the complete set of epigenetic modifications on the
genetic material of a cell, known as the epigenome.
• Epigenetic modifications - DNA methylation and histone modification
• Epigenetic modifications are reversible modifications on a cell’s DNA or histones
that affect gene expression without altering the DNA sequence.

4. 1866 – Mendel postulates Gene concept
•G.J. Mendel
•Pea -7 traits
•Experiments in Plant
Hybridization
Two Basic Laws of
Genetics
Law of Segregation
Law of Independent Assortment

5. 1871 – Nucleic acids discovered
In 1871, Meischer
discovered
Nucleic acids and called
it as Nuclein.

6. 1902 – Chromosomal theory of inheritance
 The hypothesis that genes are located in chromosomes was
designated as Sutton-Boveri hypothesis, more commonly called as
Chromosomal theory of Inheritance
Evidences for the theory:
1. Parallels in the behaviour of Genes and
Chromosomes
2. Sex linkage
3. Non-disjunction of X Chromosome
4. Attached X Chromosome
5. Linkage and chromosome maps
6. The Bar eye locus of Drosophila
7. Numerical changes in chromosomes
8. Y-Linked Inheritance
9. Genetic material
10. In Situ Hybridization
11. Transgenic Organisms

7. 1910 – Linkage concept
The Concept of Linkage originated
when Morgan demonstrated in
1910 that the white eye (w) gene
of Drosophila is located in the X
chromosome (Sex linkage).
•The tendency of two or more genes
to stay together during inheritance is
known as LINKAGE.
• Linked genes do not show independent
Segregation.
• Coupling Phase
• Repulsion Phase
• Complete Linkage
• Incomplete Linkage
1913 – First Linkage map – Drosophila melanogaster

8. 1927 – X-rays can induce mutations
• A mutation is a change in phenotype,
which is sudden, heritable and is not
produced due to segregation or
recombination.
• H.J.Muller discovered the mutagenic
action of X-rays in 1927 in Drosophila.
X-rays:
 Non-particulate ionizing radiations
Produced by X-ray tubes
Highly penetrating and sparsely ionizing

9. 1934 – X-ray crystallography

10. 1941- Genes direct synthesis of enzymes
One- gene- one- enzyme
• Beadle and Tatum
• Neurospora crassa
• Mutants by using X-
rays and UV-rays (on
conidia)
• Mutants unable to
synthesize pyridoxin
(pdx), thaizole half of
thiamine (thi) or p-
aminobenzoic acid (pab)
• Inability was governed
by a single gene.

11. 1943- Study of Bacterial genetics
Griffith- 1928
Transformation
Zinder and Lederberg- 1952
Transduction
Lederberg and Tatum- 1946
Conjugation

12. 1944 – DNA as transforming principle
Griffith -1928
Transformation
Diplococcus pneumoniae
Avery, MacLeod and McCarty-
1944
In-vitro
DNA as transforming principle
Hershey and Chase- 1952
T2 phage of E.coli
Universal acceptance of DNA as
the genetic material

13. 1950 – Chargaff’s rules
Chargaff had proposed the
following four rules concerning
duplex DNA:
1. The first parity rule
2. The second parity rule
3. The cluster rule
4. The GC rule

14. 1951 – First protein sequenced
• Insulin
• Chain A and chain B

15. 1953 – Double helix model of DNA
The data of Wilkins, Franklin and
others on X-ray crystallography of
purified DNA revealed :
•Multistranded nature of DNA
•Diameter of approx 22 Amstrong
•Groups spaced 3.4 A along its
length
•Repeating unit occurring at every
34 A
Features of Double helix model of
Watson and Crick:
•Two polydeoxynucleotide strands
•Antiparallel
•Complementary strands
•Errors in base pairing leads to
occurance of mutations

16. 1956 – Crystallization of DNA polymerase
• DNA polymerase is the chief enzyme of DNA replication.
• DNA polymerase activity was discovered by KORNBERG in 1956; this
activity was due to DNA polymerase I.

17. 1961 – Elucidation of Genetic code
• The number and sequence of bases in
mRNA specifying an amino acid is known as
Codon.
• The set of all the codons that specify the
20 amino acids is termed as the Genetic
code.
• In 1954, Gammow suggested that a codon
had 3 bases.
• In 1961, Crick and coworkers concluded
from genetic studies in T4 phage of E.coli
that a codon had most likely three bases
and that the code was nonoverlapping,
degenerate and commaless.
• Poly U= Phenylalanine by Nirenberg and
Matthei

18. 1961- Lac operon
An Operon consists of a
group of structural genes
whose transcription is
regulated by the same set
of genes viz., regulator
gene, promoter and
operator sequences.
• Jacob and Monod
• Lac operon
• Negative inducible
control

19. 1965 – Sequenced yeast tRNA
• Existence of tRNA was demonstratd
by Hoagland and coworkers in 1957.
• Holley and coworkers – Sequenced
yeast tRNA (alanine-tRNA) in 1964.
• Transfer RNA (tRNA)
• Size – 3S
• Has 76-95 nucleotides
• Have 15-20% unusual bases
• Clover leaf model – secondary
structure
• L-shaped tertiary structure

20. 1970
• Temin and Baltimore independently discovered Reverse transcriptase
• Hamilton O. Smith discovers first site-specific restriction enzyme

21. 1973 – Recombinant DNA technology
A recombinant DNA molecule
is produced by joining together
two or more DNA segments
usually originating from
different organisms.
• A DNA segment that is
inserted into a vector for
cloning is called DNA insert.
•The vector containing a DNA
insert are generally called
recombinant DNA.

22. 1977 – Advent of DNA Sequencing
• Determination of nucleotide or base sequence of a DNA molecule or
fragment is known as DNA Sequencing.

23. 1980 – DNA markers (RFLP)
1990 – RAPD
1995 – AFLP
2001 – SRAP
2003 – TRAP

24. 1985 – Developed PCR
The polymerase chain reaction (PCR) technique was developed by Kary Mullis in 1985.
It generates microgram quantities of DNA copies (upto billion copies) of the desired DNA
(or RNA) segment, present even as a single copy in the initial preparation in a matter of
few hours.

25. 1986 – DNA sequencing automated
1991 – Use of ESTs
1995 – Sequence of first whole genome

26. Timeline of genome sequencing of different
organisms

27. 1996 - Sequence of Saccharomyces cerevisiae
• Automation in DNA sequencing was developed by Applied
Biosystems
1998 - Sequence of Caenorhabditis elegans
• Sequence of first human chromosome
2000 - Sequence of Arabidopsis thaliana
• Rough draft of human genome sequence
2001 - First draft of human genome published
2002 - Genome sequence of 2 rice subspecies
• Mouse genome sequenced
• HapMap project started

28. 2003 – Human genome project
completed
2004 - Rat genome sequenced

29. 2005 – Release of 454 GS-20, first NGS
• First NGS machine released by Roche
Next Generation Sequencing:
• High throughput DNA sequencing
Technique
• Employs Micro and Nanotechnologies
 Reduce sample size
 Low reagent cost
 Less time
• Massive parallel sequencing
• Sequence thousands of sequences at once
• Produce enormous amount of data

30. 2006 – Illumina/ Solexa
2008 – 1000 genomes project started
The 1000 genomes project ran between 2008 and 2015, creating the largest
public catalogue of human variation and genotype data. The International
Genome Sample Resource (IGSR) was set up to do this with the following aims:
1. Ensure the future access to and usability of the 1000 genomes reference
data
2. Incorporate additional published genomic data on the 1000 genomes
samples
3. Expand the data collection to include new populations not represented in
the 1000 genomes project

32. CRISPR
• CLUSTERED REGULARLY
INTERSPACED PALINDROMIC
REPEATS (CRISPR/Cas9)
The discovery of CRISPR/Cas9 gene editing system has revolutionized research in animal
and plant biology with its utility in genome editing being first demonstrated in 2012 in
mammalian cells (Jinek et al., 2012).

33. CRISPR Timeline
YEAR EVENT
1987 The CRISPR mechanism first published
2000 More clustered repeats of DNA identified in other bacteria and
archaea, termed Short Regularly Spaced Repeats (SRSR)
2002 Term CRISPR-Cas9 published for first time
2005 Jennifer Doudna and Jillian Banfield started investigating CRISPR
2005 French scientists suggested CRISPR spacer sequences can provide cell
immunity against phage infection and degrade DNA
2005 American researchers identified new familes of Cas genes which
appeared to help in protecting bacteria against invading viruses
2007 Experiments demonstrate for the first time the role of CRISPR
together with Cas9 genes in protecting bacteria against viruses
2008 DNA, not RNA, demonstrated to be the molecular target of most
CRISPR-Cas systems

34. 2008 Scientists coin the term 'protospacer' to denote viral sequence
that corresponds to a 'spacer' in the CRISPR-Cas9 system
2008 Scientists characterised the RNA processing pathway in CRISPR
system
2008 Scientists published the RNA gene silencing pathway involved in
the CRISPR-Cas mechanism
2011 Classification of the CRISPR-Cas system is proposed
2011 Emmanuelle Charpentier and Jennifer Doudna joined forces to
investigate Cas9 enzyme
2012 First commercialisation of CRISPR-Cas 9 technology
2012 First patent application submitted for CRISPR-Cas 9 technology
2012 Publication of radically new gene editing method that harnesses
the CRISPR-Cas9 system
2012 Scientists at the Vilnius University published paper elucidating
the potential of CRSIPR/Cas9 to edit DNA
2012 Fast track application for CRISPR-Cas 9 technology submitted to
US patent office
2013 CRISPR-Cas is used in human genome editing

35. 2013 CRISPR-Cas is used to edit the genome of a zebrafish
2013 CRISPR-Cas shown to programme repression and activation of
gene transcription
2013 CRISPR-Cas is used in genome editing of Saccharomyces
cerevisiae, a yeast species used in wine making, baking and
brewing
2013 CRISPR-Cas mediated gene regulation shown to help regulation
of endogenous bacterial genes
2013 CRISPR-Cas used to engineer a rat's genome
2013 CRISPR-Cas used to engineer plant genomes including rice,
wheat, Arabidopsis, tobacco and Sorghum
2013 Improvements made to the specificity of CRISPR-Cas system
2015 Scientists suggest CRISPR/Cas9 used with stem cells could
provide human organs from transgenic pigs
2015 US scientists call for a voluntary worldwide moratorium on the
use of genome editing tools to modify human reproductive
cells

36. 2015 National Institutes of Health declared it will not fund any use of
genome editing technologies in human embryos
2015 UK Nuffield Council on Bioethics launched a new working group
to look into institutional, national and international policies and
provisions relevant to genome editing
2015 First report of genes edited in human embryos ignited global
ethical debate about gene editing technology
2015 Leading UK research councils, including the MRC, declared
support for using CRISPR-Cas9 and other genome editing
techniques in preclinical research
2015 Hinxton Group issues a statement indicating that most of the
ethical and moral questions raised about CRISPR and gene
editing have been debated before
2015 UK scientists sought license to genetically modify human
embryos to study the role played by genes in the first few days
of human fertilisation
2015 New protein, Cpf1, found, offering means to simplify gene
editing

37. 2015 CRISPR/Cas9 modified 60 genes in pig embryos in first step
to create organs suitable for human transplants
2015 UNESCO’s International Bioethic Committee called for ban on
genetic editing of human germline
2015 US scientists published a technique for overwriting changes
made by CRISPR/Cas 9
2015 US scientists genetically modified mosquitos using
CRISPR/Cas9 to prevent them carrying malaria parasite
2015 International Summit on Human Gene Editing met to
discuss the scientific, medical, ethical, and governance
issues associated with recent advances in human gene-
editing research
2015 Gene editiing tool, CRISPR, successfully used to improve
muscle function in mouse model of Duchenne muscular
dystrophy
2016 US scientists published improved version of CRISPR/Cas 9
with less risk of off-target DNA breaks
2016 UK scientists authorised to genetically modify human
embryos using CRISPR-Cas 9

38. 2016 US scientists publish new base editing technique offering means
to alter genome without needing to cleave double-stranded
DNA or for a donor DNA template
2016 NIH gives green light for first clinical trial using gene editing
tool CRISPR/Cas 9 to treat patients
2017 US National Academies of Science and Medicine gave green
light to proceed with CRISPR in germ-line experiments
2017 CRISPR shown to be sensitive diagnostic tool for detecting single
target of DNA or RNA molecule
2017 Research published demonstrating how CRISPR-CAS9 can be
used to eliminate HIV in infected mice
2017 Research published demonstrating possibility of editing gene
defect in pre-implanted human embryos for preventing
inherited heart disease
2017 DNA of human embryos edited using CRISPR-Cas9 to study
cause of infertility
2017 Chinese researchers report correction of gene linked to beta
thalassaemia, inherited blood disorder, in human embryos
using base editing technique

39. 2017 New CRISPR technique published for editing RNA
2017 Base editing improvements announced for CRISPR technique,
providing means to change individual chemical letters of DNA
without need to cleave DNA
2018 Researchers identify pre-existing antibodies targeting CAS9
proteins raising possibility of immune responses undermining
utility of CRISPR-Cas9 for gene therapy
2018 First CRISPR-Cas9 clinical trial launched
2018 First gene-edited babies announced by Chinese scientist
2018 New gene modification technique (CRISPRa) makes it possible
to increase expression of its target gene
2018 CRISPR-Cas9 editing helped restore effectiveness of first-line
chemotherapies for lung cancer
2019 CRISPR-Cas9 used to control genetic inheritance in mice
2019 New DNA editing technique called 'prime editing' published

40. 2019 Chinese scientist convicted for using CRISPR-Cas9 in human
babies
2020 First patient received gene editing therapy with CRISPR
directly administered into the body
2020 Nobel Prize in Chemistry awarded to Emmanuelle
Charpentier and Jennifer Doudna 'for the development of a
method for genome editing'

41. • The diamondback moth, Plutella xylostella (L.), is a worldwide agricultural pest that
has developed resistance to multiple classes of insecticides.
• Genetics-based approaches show promise as alternative pest management
approaches but require functional studies to identify suitable gene targets.

43. • CRISPR/Cas9 system was used to target a gene, abdominal-A, which has an
important role in determining the identity and functionality of abdominal
segments.
• P. xylostella abdominal-A (Pxabd-A) has two structurally-similar splice isoforms (A
and B) that differ only in the length of exon II, with 15 additional nucleotides in
isoform A. Pxabd-A transcripts were detected in all developmental stages, and
particularly in pupae and adults.
• CRISPR/Cas9-based mutagenesis of Pxabd-A exon I produced 91% chimeric
mutants following injection of 448 eggs. Phenotypes with abnormal prolegs and
malformed segments were visible in hatched larvae and unhatched embryos, and
various defects were inherited by the next generation (G1).
• Genotyping of mutants demonstrated several mutations at the Pxabd-A genomic
locus. The results indicate that a series of insertions and deletions were induced in
the Pxabd-A locus, not only in G0 survivors but also in G1 individuals, and this
provides a foundation for genome editing.
• This study demonstrates the utility of the CRISPR/Cas9 system for targeting genes
in an agricultural pest and therefore provides a foundation the development of
novel pest management tools

44. In the adult stage, the external and internal genitalia of mutated males were abnormal.
This may explain the sterile females recovered in the study.

45. REFERENCES:
• Alice Maria Giani, Guido Roberto Gallo, Luca Gianfranceschi, Giulio Formenti.
2020. Long walk to genomics: History and current approaches to genome
sequencing and assembly. Computational and Structural Biotechnology Journal. 18
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• Sopan Ganpatrao Wagh and Manoj Baliram Pohare. 2020.. Current and Future
Prospects of Plant Breeding with CRISPR/Cas. Current Journal of Applied Science
and Technology. 38(3): 1-17.
• Pierre Baldi and G. Wesley Hatfield. 2002. A brief history of genomics. DNA
Microarrays and Gene Expression: From Experiments to Data Analysis and
Modeling. Cambridge University Press
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M. Gurr, Guang Yang, Xijian Lin, Yongping Huang, Minsheng You. 2016.
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46. • YuduanDing, HongLi, Ling-LingChen and KabinXie. 2016.
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47. THANK YOU