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D E P A R T M E N T O F P L A N T B R E E D I N G A N D G E N E T I C S
J A W A H A R L A L N E H R U K R I S H I V I S H W A V I D Y A L A Y A
2 2 / 0 7 / 2 0 2 0
J A B A L P U R
A SPECIFIC SEQUENCE OF NUCLEOTIDE IN DNA OR
RNA THAT IS LOCATED ON CHROMOSOME AND IS A
FUNCTIONAL UNIT OF INHERITANCE CONTROLLING
THE EXPRESSION OF TRAIT
HAPLOID SET OF CHROMOSOME INCLUDE BOTH
CODING AND NON CODING DNA AS WELL AS
MITOCHONDRIAL DNA AND CHLOROPLAST
STUDY OF THE WHOLE GENOME OF ORGANISM AND
INCORPORATED ELEMENTS FROM GENETICS
1871
FRIEDRICH MIESCHER PUBLISHES HIS
PAPER IDENTIFYING THE PRESENCE
OF ‘NUCLEIN’AND ASSOCIATED
PROTEINS, IN THE CELL NUCLEUS.
1904
WALTER SUTTON AND THEODOR
BOVERI PROPOSE THE
CHROMOSOME THEORY OF
HEREDITY AFTER
1910
ALBRECHT KOSSEL IS AWARDED
THE FIRST NOBEL PRIZE IN
PHYSIOLOGY OR MEDICINE FOR
DISCOVERY OF THE FIVE
NUCLEOTIDE BASES.
1950
ERWIN CHARGAFF FINDS THAT
CONCENTRATIONS OF THYMINE AND
ADENINE, AND CYTOSINE AND GUANINE,
ARE ALWAYS FOUND IN EQUAL
AMOUNTS IN SAMPLES OF DNA.
1952
THE HERSHEY-CHASE
EXPERIMENTS ARE CARRIED OUT
TO DEMONSTRATE THAT DNA,
RATHER THAN PROTEIN, CARRIES
OUR GENETIC INFORMATION.
TIMELINE: HISTORY OF GENOMICS
1953
JAMES WATSON AND FRANCIS
CRICK, WITH CONTRIBUTIONS FROM
ROSALIND FRANKLIN
AND MAURICE WILKINS, DISCOVER
THE DOUBLE HELIX STRUCTURE OF
DNA.
1961
MARSHALL NIRENBERG, HAR GOBIND KHORANA
AND COLLEAGUES, CRACK THE ‘CODE FOR
LIFE’. THEY IDENTIFY HOW THE LETTERS IN DNA
ARE READ IN BLOCKS OF THREE CALLED A
“CODON”. EACH CODON SPECIFIES AN AMINO
ACID WHICH IS ADDED TO THE PROTEIN DURING
SYNTHESIS.
1968
MARSHALL NIRENBERG, HAR GOBIND
KHORANA AND ROBERT HOLLEY SHARE THE
1968 NOBEL PRIZE FOR PHYSIOLOGY AND
MEDICINE FORMER FOR CRACKING THE
GENETIC CODE, AND HOLLEY’S WORK
SEQUENCING THE FIRST tRNA MOLECULE.
1977
FREDERICK SANGER DEVELOPS A DNA
SEQUENCING TECHNIQUE WHICH HE
AND HIS TEAM USE TO SEQUENCE THE
FIRST FULL GENOME – THAT OF A VIRUS
CALLED PHIX174.
1980
FRED SANGER SHARES THE NOBEL
PRIZE FOR CHEMISTRY WITH WALLY
GILBERT AND PAUL BERG, FOR
PIONEERING DNA
SEQUENCING METHODS.
TIMELINE: HISTORY OF GENOMICS
1983
THE POLYMERASE CHAIN
REACTION (PCR) IS DEVELOPED – A
TECHNIQUE USED FOR AMPLIFYING
DNA – BY DR KARY MULLIS AT THE
CETUS CORPORATION IN
CALIFORNIA, USA.
1985
ALEC JEFFREYS DEVELOPS A METHOD FOR
DNA PROFILING. A DNA PROFILE IS
PRODUCED BY COUNTING THE NUMBER OF
SHORT REPEATING SEQUENCES OF DNA
SEQUENCE FOUND AT TEN SPECIFIC
REGIONS OF THE GENOME.
1990
HUMAN GENOME PROJECT IS
LAUNCHED. THE PROJECT AIMS TO
SEQUENCE ALL 3
BILLION LETTERS OF A HUMAN GENOME
IN 15 YEARS.
1995
THE FIRST BACTERIUM GENOME
SEQUENCE IS COMPLETED
(HAEMOPHILUS INFLUENZA).
1996
AN INTERNATIONAL TEAM
COMPLETE SEQUENCING THE
GENOME OF YEAST,
SACCHAROMYCES CEREVISIAE.
TIMELINE: HISTORY OF GENOMICS
1998
JOHN SULSTON AND BOB
WATERSTON PUBLISH THE GENOME
OF THE NEMATODE WORM, C.
ELEGANS.
1999
CHROMOSOME 22 IS THE FIRST HUMAN
CHROMOSOME TO BE SEQUENCED AS
PART OF THE HUMAN GENOME PROJECT.
ENSEMBL GENOME BROWSER
LAUNCHED.
2001
FIRST DRAFT OF THE HUMAN GENOME
SEQUENCE RELEASED.
2002
THE MOUSE IS THE FIRST MAMMAL TO HAVE ITS
FULL GENOME SEQUENCE COMPLETED.
THE MOUSE GENOME IS 14 PER CENT SMALLER
THAN THE HUMAN GENOME, BUT OVER 95 PER
CENT OF THE MOUSE GENOME IS SIMILAR TO
OURS.
2002
THE INTERNATIONAL HAPMAP PROJECT IS
LAUNCHED, WHICH AIMS TO PRODUCE A
‘CATALOGUE’ OF COMMON HUMAN
GENETIC VARIATIONS AND WHERE THEY
ARE FOUND IN THE GENOME.
TIMELINE: HISTORY OF GENOMICS
2003
HUMAN GENOME PROJECT IS
COMPLETED AND CONFIRMS HUMANS
HAVE APPROXIMATELY 20,000–25,000
GENES. THE HUMAN GENOME IS
SEQUENCED TO 99.99 PER CENT
ACCURACY.
2003
THE ENCODE PROJECT IS LAUNCHED BY
THE NATIONAL HUMAN GENOME
RESEARCH INSTITUTE AND AIMS TO
IDENTIFY AND
CHARACTERISE ALL THE GENES IN THE
HUMAN GENOME.
2008
NEXT-GENERATION SEQUENCING
PLATFORMS RESULT IN DRAMATIC DROP
IN SEQUENCING COSTS.
2013
THE U.S. SUPREME COURT RULES
THAT NATURALLY OCCURRING DNA
CANNOT BE PATENTED.
2014
CRISPR/CAS9 GENOME
EDITING IN PLANT
TIMELINE: HISTORY OF GENOMICS
WELCOMELETS EXPLORE GENOMICS
A NEW ERA OF GENETICS
about
Types
Branches
Application
Tools
Crop
Improvement
about
Types
Branches
Application
Tools
Crop
Improvement
GENOMICS
T. Roderick, 1986
•The study of structure and function of whole of the hereditary
material contains in a genome of a living organism.
•Genomics involves the study of all genes at the DNA mRNA
and proteome level as well as cellular or tissue level.
•The ultimate objective is to obtain DNA sequences of complete
genome and to understand the function of each of
those genes.
about
Types
Branches
Application
Tools
Crop
Improvement
FUNCTIONAL
GENOMICS
STRUCTURAL
GENOMICS
COMPARATIVE
GENOMICS
EPIGENOMICS
THE
CHARACTERIZA
TION OF
GENES AND
THEIR mRNA
AND PROTEIN
PRODUCTS.
THE DISSECTION
OF THE
ARCHITECTURAL
FEATURES OF
GENES AND
CHROMOSOME.
THE
EVOLUTIONARY
RELATIONSHIPS
BETWEEN THE
GENES AND
PROTEINS OF
DIFFERENT
SPECIES.
DNA
METHYLATION
PATTERNS,
IMPRINTING
AND DNA
PACKAGING.
about
Types
Branches
Application
Tools
Crop
Improvement
RNA SEQUENCING
TRANSCRIPTION REGULATION
G E N O M I C S
•DNA SEQUENCING
•GENETIC MAPPING
•GENETIC PROFILING
•DNA RECOMBINANT
TECHNOLOGY
TRANSCRIPTOMICS
.
PROTEOMICS
.
PHENOMICS
.
INOMICS
METABOLOMICS
.
PROTEIN IDENTIFICATION ,QUANTIFICATION
POST TRANSLATION MODIFICATION
METABOLITE PROFILES, INTERMEDIATE,
HORMONES AND SIGNALING MOLECULE
ELEMENT PROFILING, BIOCHEMICAL
REGULATION, ELEMENT INTERACTION
HORMONES AND SIGNALING MOLECULE
EVALUATION OF TRAITS
LINK BETWEEN GENETIC, EPIGENETIC AND
ENVIRONMENTAL FACTORS
about
Types
Branches
Application
Tools
Crop
Improvement
GENE
SEQUENCING
AND
MAPPING
MARKERS
IDENTIFICATION
GENE
EDITING
TRANSGENIC
BREEDING
GENE
CLONNING
EVOLUTION
AND RISC
ASSESMENT
about
Types
Branches
Application
Tools
Crop
Improvement
MICROARRAY
A microscopic DNA chip attached
to solid surface used to measure
the expression of 1000 sub-gene
simultaneously.
MASS SPECTROMETRY
Analysis of oligonucleotides
PCR
In-vitro Amplification of specific
DNA or RNA sequence
SEQUENCER
Sequence and analyze whole
genomes.
ELECTROPHORESIS SYSTEM
Isolate DNA templates
ONLINE SOFTWARE'S
Data storage and analysis
Ex-
BLAST
FASTA
MUMmer
DIALIGN
about
history
timeline
teamsTools
Crop
Improvement
HERBICIDE TOLERANCE
Glyphosate tolerance in
tomato, tobacco, soybean,
cotton etc.
PATHOGEN RESISTANCE PEST RESISTANCE
CHILLING RESISTANCEFERTILITY RESTORATIONQUALITY IMPROVEMENT
Coat protein gene from TMV
has been transferred to
tobacco.
Insecticidal BT gene has been
isolated from Bacillus
thuringiensis bacteria and
transferred to plant like cotton,
tomato, tobacco
Delayed ripening through
decreasing ethylene
production
Hybrid seed production of
Brassica napus
Gene Glycerol-1-phosphateacyl-
tranceferace enzyme from
arabidopsis into tobacco
2000
ARABIDOPSIS
RICE
MAIZE
SORGHUM
CUCUMBER
2010
SOYBEAN
APPLE
PEACH
ORANGE
CHICKPEA
2009 2011
2002
TIMELINE: GENOME SEQUENCING IN PLANTS
2013
2012
BARLEY
TOMATO
WATERMELON
MUSKMELON
BANANA
CABBAGE
COCOA
POTATO
RESEARCH WORK
IN DIFFERENT CROPS
AN EMERGING SCIENCE
PADDY
CHILI
WHEAT
BARLEY
CHICKPEA
MAIZE
PADDY
CHILI
WHEAT
BARLEY
CHICKPEA
MAIZE
FEBRUARY
1998
APRIL
2000
FEBRUARY
2001
SEPTEMBER
1997
RICE
GENOME
SEQUENCE
INITIATED
IRGSP
LAUNCHED
MONSANTO
CO.
PRODUCED
A DRAFT
SEQUENCE
(95%)
SYNGENTA
PRODUCED
DRAFT
SEQUENCE
(99%)
DECEMBER
2002
FINISHED
HIGH
QUALITY
DRAFT
SEQUENCE
EXCEPT
366 MB
DECEMBER
2004
IRGSP
FINISHED
RGP WITH
99.99%
ACCURAC
Y
PADDY
CHILI
WHEAT
BARLEY
CHICKPEA
MAIZE
PADDY
CHILI
WHEAT
BARLEY
CHICKPEA
MAIZE
PADDY
CHILI
PADDY
BARLEY
MAIZE
CHICKPEA
PADDY
CHILI
WHEAT
BARLEY
CHICKPEA
MAIZE
PADDY
CHILI
WHEAT
BARLEY
CHICKPEA
MAIZE
0 1
0 2
0 3
•HIGH TECHNICAL SKILL
•EXPANSIVE AND LABORIOUS TECHNIQUE
•LIMITED GENE AVAILABILITY
•LACK OF PROPER MARKERS
•SOME ANNOTATED OPEN READING FRAMES ARE
SUBSEQUENTLY FOUND NOT TO ENCODED PROTEIN
LIMITATIONS
•POST TRANSLATIONAL MODIFICATIONS THAT INFLUENCE
THE PROTEIN FUNCTION AND CELLULAR LOCALIZATION
OFTEN CANNOT BE PREDICTED FROM THE SEQUENCE
01
02
TISSUE CULTURE FREE
TRANSFORMATION
IMPROVED VARIETIES FOR WORLD
AGRICULTURE
TISSUE CULTURE FREE
TRANSFORMATION03
04
F U T U R E
A S P E C T
NON GMO GENOMICS BREEDING
3-D MODELLING OF PLANT USING
GENOTYPES
THANK YOU

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Genomics in Crop improvement

  • 1. D E P A R T M E N T O F P L A N T B R E E D I N G A N D G E N E T I C S J A W A H A R L A L N E H R U K R I S H I V I S H W A V I D Y A L A Y A 2 2 / 0 7 / 2 0 2 0 J A B A L P U R
  • 2. A SPECIFIC SEQUENCE OF NUCLEOTIDE IN DNA OR RNA THAT IS LOCATED ON CHROMOSOME AND IS A FUNCTIONAL UNIT OF INHERITANCE CONTROLLING THE EXPRESSION OF TRAIT HAPLOID SET OF CHROMOSOME INCLUDE BOTH CODING AND NON CODING DNA AS WELL AS MITOCHONDRIAL DNA AND CHLOROPLAST STUDY OF THE WHOLE GENOME OF ORGANISM AND INCORPORATED ELEMENTS FROM GENETICS
  • 3. 1871 FRIEDRICH MIESCHER PUBLISHES HIS PAPER IDENTIFYING THE PRESENCE OF ‘NUCLEIN’AND ASSOCIATED PROTEINS, IN THE CELL NUCLEUS. 1904 WALTER SUTTON AND THEODOR BOVERI PROPOSE THE CHROMOSOME THEORY OF HEREDITY AFTER 1910 ALBRECHT KOSSEL IS AWARDED THE FIRST NOBEL PRIZE IN PHYSIOLOGY OR MEDICINE FOR DISCOVERY OF THE FIVE NUCLEOTIDE BASES. 1950 ERWIN CHARGAFF FINDS THAT CONCENTRATIONS OF THYMINE AND ADENINE, AND CYTOSINE AND GUANINE, ARE ALWAYS FOUND IN EQUAL AMOUNTS IN SAMPLES OF DNA. 1952 THE HERSHEY-CHASE EXPERIMENTS ARE CARRIED OUT TO DEMONSTRATE THAT DNA, RATHER THAN PROTEIN, CARRIES OUR GENETIC INFORMATION. TIMELINE: HISTORY OF GENOMICS
  • 4. 1953 JAMES WATSON AND FRANCIS CRICK, WITH CONTRIBUTIONS FROM ROSALIND FRANKLIN AND MAURICE WILKINS, DISCOVER THE DOUBLE HELIX STRUCTURE OF DNA. 1961 MARSHALL NIRENBERG, HAR GOBIND KHORANA AND COLLEAGUES, CRACK THE ‘CODE FOR LIFE’. THEY IDENTIFY HOW THE LETTERS IN DNA ARE READ IN BLOCKS OF THREE CALLED A “CODON”. EACH CODON SPECIFIES AN AMINO ACID WHICH IS ADDED TO THE PROTEIN DURING SYNTHESIS. 1968 MARSHALL NIRENBERG, HAR GOBIND KHORANA AND ROBERT HOLLEY SHARE THE 1968 NOBEL PRIZE FOR PHYSIOLOGY AND MEDICINE FORMER FOR CRACKING THE GENETIC CODE, AND HOLLEY’S WORK SEQUENCING THE FIRST tRNA MOLECULE. 1977 FREDERICK SANGER DEVELOPS A DNA SEQUENCING TECHNIQUE WHICH HE AND HIS TEAM USE TO SEQUENCE THE FIRST FULL GENOME – THAT OF A VIRUS CALLED PHIX174. 1980 FRED SANGER SHARES THE NOBEL PRIZE FOR CHEMISTRY WITH WALLY GILBERT AND PAUL BERG, FOR PIONEERING DNA SEQUENCING METHODS. TIMELINE: HISTORY OF GENOMICS
  • 5. 1983 THE POLYMERASE CHAIN REACTION (PCR) IS DEVELOPED – A TECHNIQUE USED FOR AMPLIFYING DNA – BY DR KARY MULLIS AT THE CETUS CORPORATION IN CALIFORNIA, USA. 1985 ALEC JEFFREYS DEVELOPS A METHOD FOR DNA PROFILING. A DNA PROFILE IS PRODUCED BY COUNTING THE NUMBER OF SHORT REPEATING SEQUENCES OF DNA SEQUENCE FOUND AT TEN SPECIFIC REGIONS OF THE GENOME. 1990 HUMAN GENOME PROJECT IS LAUNCHED. THE PROJECT AIMS TO SEQUENCE ALL 3 BILLION LETTERS OF A HUMAN GENOME IN 15 YEARS. 1995 THE FIRST BACTERIUM GENOME SEQUENCE IS COMPLETED (HAEMOPHILUS INFLUENZA). 1996 AN INTERNATIONAL TEAM COMPLETE SEQUENCING THE GENOME OF YEAST, SACCHAROMYCES CEREVISIAE. TIMELINE: HISTORY OF GENOMICS
  • 6. 1998 JOHN SULSTON AND BOB WATERSTON PUBLISH THE GENOME OF THE NEMATODE WORM, C. ELEGANS. 1999 CHROMOSOME 22 IS THE FIRST HUMAN CHROMOSOME TO BE SEQUENCED AS PART OF THE HUMAN GENOME PROJECT. ENSEMBL GENOME BROWSER LAUNCHED. 2001 FIRST DRAFT OF THE HUMAN GENOME SEQUENCE RELEASED. 2002 THE MOUSE IS THE FIRST MAMMAL TO HAVE ITS FULL GENOME SEQUENCE COMPLETED. THE MOUSE GENOME IS 14 PER CENT SMALLER THAN THE HUMAN GENOME, BUT OVER 95 PER CENT OF THE MOUSE GENOME IS SIMILAR TO OURS. 2002 THE INTERNATIONAL HAPMAP PROJECT IS LAUNCHED, WHICH AIMS TO PRODUCE A ‘CATALOGUE’ OF COMMON HUMAN GENETIC VARIATIONS AND WHERE THEY ARE FOUND IN THE GENOME. TIMELINE: HISTORY OF GENOMICS
  • 7. 2003 HUMAN GENOME PROJECT IS COMPLETED AND CONFIRMS HUMANS HAVE APPROXIMATELY 20,000–25,000 GENES. THE HUMAN GENOME IS SEQUENCED TO 99.99 PER CENT ACCURACY. 2003 THE ENCODE PROJECT IS LAUNCHED BY THE NATIONAL HUMAN GENOME RESEARCH INSTITUTE AND AIMS TO IDENTIFY AND CHARACTERISE ALL THE GENES IN THE HUMAN GENOME. 2008 NEXT-GENERATION SEQUENCING PLATFORMS RESULT IN DRAMATIC DROP IN SEQUENCING COSTS. 2013 THE U.S. SUPREME COURT RULES THAT NATURALLY OCCURRING DNA CANNOT BE PATENTED. 2014 CRISPR/CAS9 GENOME EDITING IN PLANT TIMELINE: HISTORY OF GENOMICS
  • 8. WELCOMELETS EXPLORE GENOMICS A NEW ERA OF GENETICS about Types Branches Application Tools Crop Improvement
  • 9. about Types Branches Application Tools Crop Improvement GENOMICS T. Roderick, 1986 •The study of structure and function of whole of the hereditary material contains in a genome of a living organism. •Genomics involves the study of all genes at the DNA mRNA and proteome level as well as cellular or tissue level. •The ultimate objective is to obtain DNA sequences of complete genome and to understand the function of each of those genes.
  • 10. about Types Branches Application Tools Crop Improvement FUNCTIONAL GENOMICS STRUCTURAL GENOMICS COMPARATIVE GENOMICS EPIGENOMICS THE CHARACTERIZA TION OF GENES AND THEIR mRNA AND PROTEIN PRODUCTS. THE DISSECTION OF THE ARCHITECTURAL FEATURES OF GENES AND CHROMOSOME. THE EVOLUTIONARY RELATIONSHIPS BETWEEN THE GENES AND PROTEINS OF DIFFERENT SPECIES. DNA METHYLATION PATTERNS, IMPRINTING AND DNA PACKAGING.
  • 11. about Types Branches Application Tools Crop Improvement RNA SEQUENCING TRANSCRIPTION REGULATION G E N O M I C S •DNA SEQUENCING •GENETIC MAPPING •GENETIC PROFILING •DNA RECOMBINANT TECHNOLOGY TRANSCRIPTOMICS . PROTEOMICS . PHENOMICS . INOMICS METABOLOMICS . PROTEIN IDENTIFICATION ,QUANTIFICATION POST TRANSLATION MODIFICATION METABOLITE PROFILES, INTERMEDIATE, HORMONES AND SIGNALING MOLECULE ELEMENT PROFILING, BIOCHEMICAL REGULATION, ELEMENT INTERACTION HORMONES AND SIGNALING MOLECULE EVALUATION OF TRAITS LINK BETWEEN GENETIC, EPIGENETIC AND ENVIRONMENTAL FACTORS
  • 13. about Types Branches Application Tools Crop Improvement MICROARRAY A microscopic DNA chip attached to solid surface used to measure the expression of 1000 sub-gene simultaneously. MASS SPECTROMETRY Analysis of oligonucleotides PCR In-vitro Amplification of specific DNA or RNA sequence SEQUENCER Sequence and analyze whole genomes. ELECTROPHORESIS SYSTEM Isolate DNA templates ONLINE SOFTWARE'S Data storage and analysis Ex- BLAST FASTA MUMmer DIALIGN
  • 14. about history timeline teamsTools Crop Improvement HERBICIDE TOLERANCE Glyphosate tolerance in tomato, tobacco, soybean, cotton etc. PATHOGEN RESISTANCE PEST RESISTANCE CHILLING RESISTANCEFERTILITY RESTORATIONQUALITY IMPROVEMENT Coat protein gene from TMV has been transferred to tobacco. Insecticidal BT gene has been isolated from Bacillus thuringiensis bacteria and transferred to plant like cotton, tomato, tobacco Delayed ripening through decreasing ethylene production Hybrid seed production of Brassica napus Gene Glycerol-1-phosphateacyl- tranceferace enzyme from arabidopsis into tobacco
  • 15. 2000 ARABIDOPSIS RICE MAIZE SORGHUM CUCUMBER 2010 SOYBEAN APPLE PEACH ORANGE CHICKPEA 2009 2011 2002 TIMELINE: GENOME SEQUENCING IN PLANTS 2013 2012 BARLEY TOMATO WATERMELON MUSKMELON BANANA CABBAGE COCOA POTATO
  • 16. RESEARCH WORK IN DIFFERENT CROPS AN EMERGING SCIENCE PADDY CHILI WHEAT BARLEY CHICKPEA MAIZE
  • 23. 0 1 0 2 0 3 •HIGH TECHNICAL SKILL •EXPANSIVE AND LABORIOUS TECHNIQUE •LIMITED GENE AVAILABILITY •LACK OF PROPER MARKERS •SOME ANNOTATED OPEN READING FRAMES ARE SUBSEQUENTLY FOUND NOT TO ENCODED PROTEIN LIMITATIONS •POST TRANSLATIONAL MODIFICATIONS THAT INFLUENCE THE PROTEIN FUNCTION AND CELLULAR LOCALIZATION OFTEN CANNOT BE PREDICTED FROM THE SEQUENCE
  • 24. 01 02 TISSUE CULTURE FREE TRANSFORMATION IMPROVED VARIETIES FOR WORLD AGRICULTURE TISSUE CULTURE FREE TRANSFORMATION03 04 F U T U R E A S P E C T NON GMO GENOMICS BREEDING 3-D MODELLING OF PLANT USING GENOTYPES