Genomics Tools for Crop Improvement - Presentation

Genomics Tools for Crop Improvement - Presentation

1. Genomics tools for crop
Improvement

2. Need of Novel tools in Breeding
What is Genomics
Types of Genomics
Genomics tools
Genomics tools for Crop Improvement

3. History
Agriculturewasahumanintervention
byhuman10,000yearsago.
Startedtocultivatecropsforfoodandfeed
purpose.
Startedtoselectcropsbasedonneed.
Domesticationofwildcropsweredone.
Altered traits: seed retention on
the plant, easier harvesting,
greater size of the harvested
seeds or fruits, changes in plant
form, reduction or loss of bitter
and toxic substances

4. Crop Improvement
Improvement of Yield
Best agronomic and soil
management Practices
Infrastructure Development
Require High Cost, and time
consuming
Development of
superior cultivars
using Breeding
Simple and
Sustainable

5. Methods in crop improvement
Methods
Wide
Hybridization
HeterosisMutation
Hybridization between a crop
plant and a related wild
species
Iftwodistinctinbredplantswere
crossedtogether,theresulting
progenyexceededbothparentsin
vigorandyield.
Genetic variation can be induced by
mutationsor changes in the DNA
sequences of the plants.

6. Theplantbreedingmethodsdescribedabove
enabledustomakeremarkableimprovementsin
theyieldandquality
By2025,therewillbeadditional2billionmouthsto
feedwhichrequiredoublingofcropproduction
Increaseinyieldwithnoadditionallandsavailable
forcultivationdependsondevelopmentofhigh
yieldingvarietiessuitableformarginalcultivation
Needforadditionaltoolstoincreaseefficiencyof
breedingmethodsforgeneticenhancementand
propagation
Biotechnology

7. Biotechnological Tools in
Crop Improvement

8. Tools available with Biotechnology
G
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o
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T
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s
g
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n
i
c
Tissue
culture

9. Breedingtechnologypipelinefrompasttopresentto
future.
Genomics
Based
Approaches
Reduces time
period to
develop Elite
cultivar
Considerably

10. Genome - Transcriptome - Proteome
(Graves and Haystead, 2002)
Omicsisageneraltermforabroaddisciplineofscienceandengineeringfor
analyzingtheinteractionsofbiologicalinformationobjectsinvariousomes.
genome,
proteome,
metabolome,
interactome.
What is ‘Omics’ ?
Central Dogma of Life

11. What is Genomics, Disciplines in
Genomics
disciplineingeneticsconcerningthestudyofthegenomesof
organisms.
howgenes&geneticinformationareorganizedwithinthegenome
&theirfunction
Structuralgenomicsfocusesonthecontent
andorganizationofgenomicinformation.
Functionalgenomics attemptsto
understandthefunctionofinformationin
genomes.
Structural
Genomics
Functional
Genomics
Comparative
Genomics
ComparativeGenomics

12. GTGCAGGACGCCCCGCTCATCGTTCTGGACGAGCCGACGA
GCGCCCTGGATGTGGCGAATCAGGCGAAGGTTCTCGCAAG
ATTCGGCAGTTGCGCGATGCCGGGTACGGGGTCATTTTCAC
GACCCAAACCCGGATCACGCCCTCATGCTGGATGCGACCGT
TGCCCTGCTTGGCTCGCACGATAGGTATCTGCAGATGCGCC
AGCTCAGCTTTGACGGGTCGCGCCTCGGAATGCCCGACAC
CGTGCCGATACCGTGCCAAACACAGCGCCTCAGGTATCTGC
AGATGCGCCAGCTCAGCTTTGACGGGTCGCGCCTCGGAGG
TGCTCACGAGCGAGGTTCTTTCGTGCACCTTCAATACCGTG
CCCTATGCTTGTGAGGGGCGTATCCCTAGCACGCCTGCCCC
ACCCAGGCCGCCGCCGGGTTATCAACTATCCGTTGTACACC
ACAGAAAGACACATCATGAAGATTACGAAGTTCCACACCGG
CGTTGCCCTGCCACTTCCCTGCTGCTGGCTGCGCTGACCG
GTTGCGGCGCCGCAAACACCGCCTTCTCTCCCGCCTCGGA
ATGCCCGACACCGTGCCGATACCGTGCCAAACACAGCGCCT
CAGGTATCTGCAGATGCGCCAGCTCAGCTTTGACGGGTCGC
GCCTCGGAGGTGCTCACGAGCGAGGTTCTTTCGTGCACCT
CATGCTGGATGCGACCGTTGCCCTGCTTGGCTCGCACGAT
Structura
l
Genomic
s
Functional
Genomics
CCCTGGATGTGGCGAATCAGGCGAAGGTTCTCGCAAG
ATTCGGCAGTTGCGCGATGCCGGGTACGGGGTCATTT
TCACGACCCAAA CCCGGATCACGCCCTCATGCTGGAT
GCGACCGTTGCCCTGCTTGGCTCGCACGATAGGTATC
TGCAGATGCGCCAGCTCAGCTTTGACGGGTCGCGCCT
CGGAATGCCCGACACCGTGCCGATACCGTGC CAAACA
CAGCGCCTCAGGTATCTGCAGATGCGCCAGCTCAGCT
TTGACGGGTCGCGCCTCGGAGGTGCTCACGAGCGAG
GTTCTTTCGTGCACCTTCAATACCGTGCCCTATGCTTGT
GAGGGGCGTATCCCTAGCACGCCTGCCCCACCCAGGC
CGCCGCCGGGTTATCAACTATCCGTTGTACACCACAGA
AAGACACATCATGAAGATTACGAAGTTCCACACCGGCG
TTGCCCTGCCACTTCCCTGCTGCTGGCTGCGCT
Heat
Tolerance

13. Structural Genomics
concernedwithsequencingandunderstandingthecontentofgenomes
prepare
geneticand
physicalmapsofitschromosomes.
provideinformationabout
therelativelocationsofgenes,
molecularmarkers,and
chromosomesegments,
oftenessentialfor
positioningchromosomesegmentsand
aligningstretchesofsequencedDNAintoawhole-genomesequence.

14. Structural Genomics
Geneticmapsarebasedonratesofrecombinationandare
measuredinpercentrecombination,orcentimorgans.
MorphologicalData
MolecularMarkerData
Physicalmapsarebasedonthephysicaldistancesandare
measuredinbasepairs.
DNAsequencing
DideoxyMethodofDNAsequencing-BasedonterminationofDNA
synthesis
Maxam-Gilbertprocedure-ChemicaltreatmenttocleavetheDNA
Bothgeneticandphysicalmapsprovideinformationaboutthe
relativepositionsanddistancesbetweengenes,molecular
markers,andchromosomesegments.

15. Genomic sequencing timeline
The bacterium Haemophilas influenzae was the firstfree-living organism to be
sequenced.
Characteristics of Some Eukaryotic Genomes That Have
Been
Completely Sequenced

16. Functional Genomics
thesequencingandanalysisofgenesandnon-codingregionsofthe
genomeand
studyofexpressionprofilesofthesegenesin
differenttissues
atdifferentdevelopmentalstages
andunderdifferentbioticandabioticstresses

17. Functional Genomics
Identifythegeneinterest
GenomicDNAlibrary
cDNALibrary
Expressedsequencetags

18. Functional Genomics
Analysingtheexpressionofgenes
DifferentialDisplay
Subtractivehybridization
Microarrays
SerialAnalysisofGeneExpression
(SAGE)
Differential Display
Subtractive Hybridization
Microarray

19. Applications of genomics
Thefieldofgenomicsisatthecuttingedgeofmodernbiology;
Informationsformthisfieldhasmadesignificantcontributionsto
humanhealth,agriculture,andnumerousotherareas.
Ithasalsoprovidedgenesequencesnecessaryforproducing
medicallyimportantproteinsthroughrecombinantDNAtechnology.
Comparisonsofgenomesequencesfromdifferentorganismsare
leadingtoabetterunderstandingofevolutionandthehistoryoflife.

20. Application of Genomics : MAS

21. Conventional backcrossing
x P
2P
1
DonorElite cultivar
Desirable trait
e.g. disease resistance
•High yielding
•Susceptible for 1
trait
•Called recurrent
parent (RP)
P
1 x F
1
P
1x BC1
P
1x BC2
P
1x BC3
P
1x BC4
P
1x BC5
P
1x BC6
BC6F2
Visually select BC1 progeny that resemble RP
Discard ~50% BC1
Repeat process until BC6
Recurrent parent genome recovered
Additional backcrosses may be required due to linkage drag

22. Application of Genomics: MAS
Comparing conventional and marker-assisted
backcrossing
P
1 x F
1
P
1 x P
2
CONVENTIONAL
BACKCROSSING
BC1
VISUAL SELECTION OF BC1 PLANTS THAT
MOST CLOSELY RESEMBLE RECURRENT
PARENT
BC2
MARKER-ASSISTED
BACKCROSSING
P
1 x F
1
P
1 x P
2
BC1
USE ‘BACKGROUND’ MARKERS TO SELECT PLANTS
THAT HAVE MOST RP MARKERS AND SMALLEST %
OF DONOR GENOME
BC2

23. Marker-assistedselectionmaygreatlyincreasetheefficiencyand
effectivenessforbreedingcomparedtoconventionalbreeding.The
fundamentaladvantagesofMAScomparedtoconventional
phenotypicselectionare:
Simplercomparedtophenotypicscreening
Selectionmaybecarriedoutatseedlingstage
Singleplantsmaybeselectedwithhighreliability.
(1)greaterefficiencyor
(2)acceleratedlinedevelopmentinbreedingprograms.

24. Other Related areas
TranscriptomeisthemRNAcomplementofanentireorganism,
tissuetype,orcell;theassociatedfieldisTranscriptomics
Interactomeisthestudyofmolecularinteractionsinaholisticfashion
Glycomeisthetotallistofsugar(carbohydrate)moleculesinan
organism
TheLipidomeisthetotalityoflipids;theassociatedfieldis
Lipidomics

25. Genomics,
Proteomics,
Metabolomics
Transcriptomics