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PLANT GENETIC MARKERS
Pla
nt
Bio
tech
nol
ogy
DrIr Sukendah MSc
bull A genetic marker is a gene or DNA sequence with a known location on a chromosome that can be used to identify cells individuals or speciesbull A Variation (which may arise due to
mutation or alteration in the genomic loci) that can be observedbull A genetic marker may be a short DNA
sequence such as a sequence surrounding a single base-pair change (single nucleotide polymorphism SNP) or a long one like minisatellites
What Genetic Marker -
Marker - types
Morphological marker
Protein - based marker
DNA - based marker
MARKERS- PENANDA
Perfect marker
Close linkage with the trait of interestand marker
- Reproducable- Easy to use and economical
Polymorphic Multiallelic Codominat Non epistatic
1 Morphological Marker
bull colour size shapehelliphellipbull Cheap and fast
- but influenced by environmentalconditions
Dalam coklat
Dalam hijau
Protein-based marker
Common protein marker Isozymes
Multiple forms of the same enzyme
- allozyme one enzyme and one locus- isozyme one enzyme more than one locus (gene duplication gene families)To be useful as markers isoforms
must be electrophoretically resolvable and detectable by in-gel assay methods
Limited to those enzymes that can detected insitu = thin coverage of the genome
Dimeric and multimeric enzymes addcomplexity
Pattern can be influenced by environment andtissue-type specific
DNA - based marker
bull Advantagesndash not influenced by environmentndash expressed in all tissues
RFLPs - restriction fragment lengthpolymorphismsPCR-based markersRAPDsSSRsAFLPs
RFLPs - restriction fragment length polymorphisms
Electrophoretic comparison of the size of definedrestriction fragments derived from genomic DNA Cutting (restricting) DNA with one or more endonucleases1048708 Separation of restriction fragments according to molecular weight1048708 Denature the DNA1048708 Transfer by capillarity to a membrane1048708 Hybridize to a given probe1048708 Types of DNA and implications (mt cp nDNA )
RFLPs - restriction fragment length polymorphisms
PCR-based markersRAPDs Random Amplified Polymorphic DNA markers
Basis Detection of differences in patterns ofDNA amplification from short primers of arbitrary sequence1048708 Method Compare PCR and RAPD1048708 Denaturation of DNA and annealing of primers1048708 Primer extension1048708 Repeat cycling for 20 x1048708 Electrophorese PCR products1048708 Stain and score Variability is then scored as thepresence or absence of a specific amplification product
RAPDs Random Amplified Polymorphic DNA markers
Advantages1048708 More polymorphic than RFLPs1048708 Simple and quick1048708 Selective neutrality1048708 Disadvantages1048708 RAPD markers is that they are dominant and do not permit the scoring of heterozygous individuals1048708 Reproducibility among labs may be a problem
bull A genetic marker is a gene or DNA sequence with a known location on a chromosome that can be used to identify cells individuals or speciesbull A Variation (which may arise due to
mutation or alteration in the genomic loci) that can be observedbull A genetic marker may be a short DNA
sequence such as a sequence surrounding a single base-pair change (single nucleotide polymorphism SNP) or a long one like minisatellites
What Genetic Marker -
Marker - types
Morphological marker
Protein - based marker
DNA - based marker
MARKERS- PENANDA
Perfect marker
Close linkage with the trait of interestand marker
- Reproducable- Easy to use and economical
Polymorphic Multiallelic Codominat Non epistatic
1 Morphological Marker
bull colour size shapehelliphellipbull Cheap and fast
- but influenced by environmentalconditions
Dalam coklat
Dalam hijau
Protein-based marker
Common protein marker Isozymes
Multiple forms of the same enzyme
- allozyme one enzyme and one locus- isozyme one enzyme more than one locus (gene duplication gene families)To be useful as markers isoforms
must be electrophoretically resolvable and detectable by in-gel assay methods
Limited to those enzymes that can detected insitu = thin coverage of the genome
Dimeric and multimeric enzymes addcomplexity
Pattern can be influenced by environment andtissue-type specific
DNA - based marker
bull Advantagesndash not influenced by environmentndash expressed in all tissues
RFLPs - restriction fragment lengthpolymorphismsPCR-based markersRAPDsSSRsAFLPs
RFLPs - restriction fragment length polymorphisms
Electrophoretic comparison of the size of definedrestriction fragments derived from genomic DNA Cutting (restricting) DNA with one or more endonucleases1048708 Separation of restriction fragments according to molecular weight1048708 Denature the DNA1048708 Transfer by capillarity to a membrane1048708 Hybridize to a given probe1048708 Types of DNA and implications (mt cp nDNA )
RFLPs - restriction fragment length polymorphisms
PCR-based markersRAPDs Random Amplified Polymorphic DNA markers
Basis Detection of differences in patterns ofDNA amplification from short primers of arbitrary sequence1048708 Method Compare PCR and RAPD1048708 Denaturation of DNA and annealing of primers1048708 Primer extension1048708 Repeat cycling for 20 x1048708 Electrophorese PCR products1048708 Stain and score Variability is then scored as thepresence or absence of a specific amplification product
RAPDs Random Amplified Polymorphic DNA markers
Advantages1048708 More polymorphic than RFLPs1048708 Simple and quick1048708 Selective neutrality1048708 Disadvantages1048708 RAPD markers is that they are dominant and do not permit the scoring of heterozygous individuals1048708 Reproducibility among labs may be a problem
Marker - types
Morphological marker
Protein - based marker
DNA - based marker
MARKERS- PENANDA
Perfect marker
Close linkage with the trait of interestand marker
- Reproducable- Easy to use and economical
Polymorphic Multiallelic Codominat Non epistatic
1 Morphological Marker
bull colour size shapehelliphellipbull Cheap and fast
- but influenced by environmentalconditions
Dalam coklat
Dalam hijau
Protein-based marker
Common protein marker Isozymes
Multiple forms of the same enzyme
- allozyme one enzyme and one locus- isozyme one enzyme more than one locus (gene duplication gene families)To be useful as markers isoforms
must be electrophoretically resolvable and detectable by in-gel assay methods
Limited to those enzymes that can detected insitu = thin coverage of the genome
Dimeric and multimeric enzymes addcomplexity
Pattern can be influenced by environment andtissue-type specific
DNA - based marker
bull Advantagesndash not influenced by environmentndash expressed in all tissues
RFLPs - restriction fragment lengthpolymorphismsPCR-based markersRAPDsSSRsAFLPs
RFLPs - restriction fragment length polymorphisms
Electrophoretic comparison of the size of definedrestriction fragments derived from genomic DNA Cutting (restricting) DNA with one or more endonucleases1048708 Separation of restriction fragments according to molecular weight1048708 Denature the DNA1048708 Transfer by capillarity to a membrane1048708 Hybridize to a given probe1048708 Types of DNA and implications (mt cp nDNA )
RFLPs - restriction fragment length polymorphisms
PCR-based markersRAPDs Random Amplified Polymorphic DNA markers
Basis Detection of differences in patterns ofDNA amplification from short primers of arbitrary sequence1048708 Method Compare PCR and RAPD1048708 Denaturation of DNA and annealing of primers1048708 Primer extension1048708 Repeat cycling for 20 x1048708 Electrophorese PCR products1048708 Stain and score Variability is then scored as thepresence or absence of a specific amplification product
RAPDs Random Amplified Polymorphic DNA markers
Advantages1048708 More polymorphic than RFLPs1048708 Simple and quick1048708 Selective neutrality1048708 Disadvantages1048708 RAPD markers is that they are dominant and do not permit the scoring of heterozygous individuals1048708 Reproducibility among labs may be a problem
Perfect marker
Close linkage with the trait of interestand marker
- Reproducable- Easy to use and economical
Polymorphic Multiallelic Codominat Non epistatic
1 Morphological Marker
bull colour size shapehelliphellipbull Cheap and fast
- but influenced by environmentalconditions
Dalam coklat
Dalam hijau
Protein-based marker
Common protein marker Isozymes
Multiple forms of the same enzyme
- allozyme one enzyme and one locus- isozyme one enzyme more than one locus (gene duplication gene families)To be useful as markers isoforms
must be electrophoretically resolvable and detectable by in-gel assay methods
Limited to those enzymes that can detected insitu = thin coverage of the genome
Dimeric and multimeric enzymes addcomplexity
Pattern can be influenced by environment andtissue-type specific
DNA - based marker
bull Advantagesndash not influenced by environmentndash expressed in all tissues
RFLPs - restriction fragment lengthpolymorphismsPCR-based markersRAPDsSSRsAFLPs
RFLPs - restriction fragment length polymorphisms
Electrophoretic comparison of the size of definedrestriction fragments derived from genomic DNA Cutting (restricting) DNA with one or more endonucleases1048708 Separation of restriction fragments according to molecular weight1048708 Denature the DNA1048708 Transfer by capillarity to a membrane1048708 Hybridize to a given probe1048708 Types of DNA and implications (mt cp nDNA )
RFLPs - restriction fragment length polymorphisms
PCR-based markersRAPDs Random Amplified Polymorphic DNA markers
Basis Detection of differences in patterns ofDNA amplification from short primers of arbitrary sequence1048708 Method Compare PCR and RAPD1048708 Denaturation of DNA and annealing of primers1048708 Primer extension1048708 Repeat cycling for 20 x1048708 Electrophorese PCR products1048708 Stain and score Variability is then scored as thepresence or absence of a specific amplification product
RAPDs Random Amplified Polymorphic DNA markers
Advantages1048708 More polymorphic than RFLPs1048708 Simple and quick1048708 Selective neutrality1048708 Disadvantages1048708 RAPD markers is that they are dominant and do not permit the scoring of heterozygous individuals1048708 Reproducibility among labs may be a problem
1 Morphological Marker
bull colour size shapehelliphellipbull Cheap and fast
- but influenced by environmentalconditions
Dalam coklat
Dalam hijau
Protein-based marker
Common protein marker Isozymes
Multiple forms of the same enzyme
- allozyme one enzyme and one locus- isozyme one enzyme more than one locus (gene duplication gene families)To be useful as markers isoforms
must be electrophoretically resolvable and detectable by in-gel assay methods
Limited to those enzymes that can detected insitu = thin coverage of the genome
Dimeric and multimeric enzymes addcomplexity
Pattern can be influenced by environment andtissue-type specific
DNA - based marker
bull Advantagesndash not influenced by environmentndash expressed in all tissues
RFLPs - restriction fragment lengthpolymorphismsPCR-based markersRAPDsSSRsAFLPs
RFLPs - restriction fragment length polymorphisms
Electrophoretic comparison of the size of definedrestriction fragments derived from genomic DNA Cutting (restricting) DNA with one or more endonucleases1048708 Separation of restriction fragments according to molecular weight1048708 Denature the DNA1048708 Transfer by capillarity to a membrane1048708 Hybridize to a given probe1048708 Types of DNA and implications (mt cp nDNA )
RFLPs - restriction fragment length polymorphisms
PCR-based markersRAPDs Random Amplified Polymorphic DNA markers
Basis Detection of differences in patterns ofDNA amplification from short primers of arbitrary sequence1048708 Method Compare PCR and RAPD1048708 Denaturation of DNA and annealing of primers1048708 Primer extension1048708 Repeat cycling for 20 x1048708 Electrophorese PCR products1048708 Stain and score Variability is then scored as thepresence or absence of a specific amplification product
RAPDs Random Amplified Polymorphic DNA markers
Advantages1048708 More polymorphic than RFLPs1048708 Simple and quick1048708 Selective neutrality1048708 Disadvantages1048708 RAPD markers is that they are dominant and do not permit the scoring of heterozygous individuals1048708 Reproducibility among labs may be a problem
Protein-based marker
Common protein marker Isozymes
Multiple forms of the same enzyme
- allozyme one enzyme and one locus- isozyme one enzyme more than one locus (gene duplication gene families)To be useful as markers isoforms
must be electrophoretically resolvable and detectable by in-gel assay methods
Limited to those enzymes that can detected insitu = thin coverage of the genome
Dimeric and multimeric enzymes addcomplexity
Pattern can be influenced by environment andtissue-type specific
DNA - based marker
bull Advantagesndash not influenced by environmentndash expressed in all tissues
RFLPs - restriction fragment lengthpolymorphismsPCR-based markersRAPDsSSRsAFLPs
RFLPs - restriction fragment length polymorphisms
Electrophoretic comparison of the size of definedrestriction fragments derived from genomic DNA Cutting (restricting) DNA with one or more endonucleases1048708 Separation of restriction fragments according to molecular weight1048708 Denature the DNA1048708 Transfer by capillarity to a membrane1048708 Hybridize to a given probe1048708 Types of DNA and implications (mt cp nDNA )
RFLPs - restriction fragment length polymorphisms
PCR-based markersRAPDs Random Amplified Polymorphic DNA markers
Basis Detection of differences in patterns ofDNA amplification from short primers of arbitrary sequence1048708 Method Compare PCR and RAPD1048708 Denaturation of DNA and annealing of primers1048708 Primer extension1048708 Repeat cycling for 20 x1048708 Electrophorese PCR products1048708 Stain and score Variability is then scored as thepresence or absence of a specific amplification product
RAPDs Random Amplified Polymorphic DNA markers
Advantages1048708 More polymorphic than RFLPs1048708 Simple and quick1048708 Selective neutrality1048708 Disadvantages1048708 RAPD markers is that they are dominant and do not permit the scoring of heterozygous individuals1048708 Reproducibility among labs may be a problem
Limited to those enzymes that can detected insitu = thin coverage of the genome
Dimeric and multimeric enzymes addcomplexity
Pattern can be influenced by environment andtissue-type specific
DNA - based marker
bull Advantagesndash not influenced by environmentndash expressed in all tissues
RFLPs - restriction fragment lengthpolymorphismsPCR-based markersRAPDsSSRsAFLPs
RFLPs - restriction fragment length polymorphisms
Electrophoretic comparison of the size of definedrestriction fragments derived from genomic DNA Cutting (restricting) DNA with one or more endonucleases1048708 Separation of restriction fragments according to molecular weight1048708 Denature the DNA1048708 Transfer by capillarity to a membrane1048708 Hybridize to a given probe1048708 Types of DNA and implications (mt cp nDNA )
RFLPs - restriction fragment length polymorphisms
PCR-based markersRAPDs Random Amplified Polymorphic DNA markers
Basis Detection of differences in patterns ofDNA amplification from short primers of arbitrary sequence1048708 Method Compare PCR and RAPD1048708 Denaturation of DNA and annealing of primers1048708 Primer extension1048708 Repeat cycling for 20 x1048708 Electrophorese PCR products1048708 Stain and score Variability is then scored as thepresence or absence of a specific amplification product
RAPDs Random Amplified Polymorphic DNA markers
Advantages1048708 More polymorphic than RFLPs1048708 Simple and quick1048708 Selective neutrality1048708 Disadvantages1048708 RAPD markers is that they are dominant and do not permit the scoring of heterozygous individuals1048708 Reproducibility among labs may be a problem
DNA - based marker
bull Advantagesndash not influenced by environmentndash expressed in all tissues
RFLPs - restriction fragment lengthpolymorphismsPCR-based markersRAPDsSSRsAFLPs
RFLPs - restriction fragment length polymorphisms
Electrophoretic comparison of the size of definedrestriction fragments derived from genomic DNA Cutting (restricting) DNA with one or more endonucleases1048708 Separation of restriction fragments according to molecular weight1048708 Denature the DNA1048708 Transfer by capillarity to a membrane1048708 Hybridize to a given probe1048708 Types of DNA and implications (mt cp nDNA )
RFLPs - restriction fragment length polymorphisms
PCR-based markersRAPDs Random Amplified Polymorphic DNA markers
Basis Detection of differences in patterns ofDNA amplification from short primers of arbitrary sequence1048708 Method Compare PCR and RAPD1048708 Denaturation of DNA and annealing of primers1048708 Primer extension1048708 Repeat cycling for 20 x1048708 Electrophorese PCR products1048708 Stain and score Variability is then scored as thepresence or absence of a specific amplification product
RAPDs Random Amplified Polymorphic DNA markers
Advantages1048708 More polymorphic than RFLPs1048708 Simple and quick1048708 Selective neutrality1048708 Disadvantages1048708 RAPD markers is that they are dominant and do not permit the scoring of heterozygous individuals1048708 Reproducibility among labs may be a problem
RFLPs - restriction fragment length polymorphisms
Electrophoretic comparison of the size of definedrestriction fragments derived from genomic DNA Cutting (restricting) DNA with one or more endonucleases1048708 Separation of restriction fragments according to molecular weight1048708 Denature the DNA1048708 Transfer by capillarity to a membrane1048708 Hybridize to a given probe1048708 Types of DNA and implications (mt cp nDNA )
RFLPs - restriction fragment length polymorphisms
PCR-based markersRAPDs Random Amplified Polymorphic DNA markers
Basis Detection of differences in patterns ofDNA amplification from short primers of arbitrary sequence1048708 Method Compare PCR and RAPD1048708 Denaturation of DNA and annealing of primers1048708 Primer extension1048708 Repeat cycling for 20 x1048708 Electrophorese PCR products1048708 Stain and score Variability is then scored as thepresence or absence of a specific amplification product
RAPDs Random Amplified Polymorphic DNA markers
Advantages1048708 More polymorphic than RFLPs1048708 Simple and quick1048708 Selective neutrality1048708 Disadvantages1048708 RAPD markers is that they are dominant and do not permit the scoring of heterozygous individuals1048708 Reproducibility among labs may be a problem
RFLPs - restriction fragment length polymorphisms
PCR-based markersRAPDs Random Amplified Polymorphic DNA markers
Basis Detection of differences in patterns ofDNA amplification from short primers of arbitrary sequence1048708 Method Compare PCR and RAPD1048708 Denaturation of DNA and annealing of primers1048708 Primer extension1048708 Repeat cycling for 20 x1048708 Electrophorese PCR products1048708 Stain and score Variability is then scored as thepresence or absence of a specific amplification product
RAPDs Random Amplified Polymorphic DNA markers
Advantages1048708 More polymorphic than RFLPs1048708 Simple and quick1048708 Selective neutrality1048708 Disadvantages1048708 RAPD markers is that they are dominant and do not permit the scoring of heterozygous individuals1048708 Reproducibility among labs may be a problem
PCR-based markersRAPDs Random Amplified Polymorphic DNA markers
Basis Detection of differences in patterns ofDNA amplification from short primers of arbitrary sequence1048708 Method Compare PCR and RAPD1048708 Denaturation of DNA and annealing of primers1048708 Primer extension1048708 Repeat cycling for 20 x1048708 Electrophorese PCR products1048708 Stain and score Variability is then scored as thepresence or absence of a specific amplification product
RAPDs Random Amplified Polymorphic DNA markers
Advantages1048708 More polymorphic than RFLPs1048708 Simple and quick1048708 Selective neutrality1048708 Disadvantages1048708 RAPD markers is that they are dominant and do not permit the scoring of heterozygous individuals1048708 Reproducibility among labs may be a problem
RAPDs Random Amplified Polymorphic DNA markers
Advantages1048708 More polymorphic than RFLPs1048708 Simple and quick1048708 Selective neutrality1048708 Disadvantages1048708 RAPD markers is that they are dominant and do not permit the scoring of heterozygous individuals1048708 Reproducibility among labs may be a problem
Advantages1048708 More polymorphic than RFLPs1048708 Simple and quick1048708 Selective neutrality1048708 Disadvantages1048708 RAPD markers is that they are dominant and do not permit the scoring of heterozygous individuals1048708 Reproducibility among labs may be a problem
