1 / 30

Molecular Marker

Molecular Marker. Characterization of plant genotypes Morphological markers Physiological markers Biochemical markers Molecular markers etc. Widely-used markers. To distinguish varieties / genotypes by observation / measurement Characteristics:

sholcomb
Télécharger la présentation

Molecular Marker

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript


  1. Molecular Marker Characterization of plant genotypes Morphological markers Physiological markers Biochemical markers Molecular markers etc.

  2. Widely-used markers To distinguish varieties / genotypes by observation / measurement Characteristics: growth habit, fruit color, shape, etc. resp rate, PS content, hormone balance, etc. fruit size, plant height, sugar content, etc.

  3. Molecular Marker Useful when other methods not available / possible Very similar morphology / anatomy Growth and development stages Environmental factors Analysis of banding patterns Statistics for evaluation of polymorphism

  4. Molecular marker Study and management of genetic resources Identifying and distinguishing genotypes Marker assisted selection (MAS) Complementary tool for DUS studies of cultivars Distinctiveness / Uniformity / Stability

  5. Molecular markers Protein-based marker: Isozyme / Allozyme multiple molecular forms of an enzyme similar / identical catalytic activity enzyme assay on PAGE DNA-based marker

  6. Isozyme marker

  7. Isozyme marker Enzyme Isozyme locus # allozymes Shikimate dehydrogenase Sdh-1 1 Phosphoglucose isomerase Pgi-1 2 Pgi-2 2 Aminonentidase Amp-1 3 Amp-2 4 Amp-3 3 Amp-4 4 Alcohol dehydrogenase Adh-1 2 Phosphogluconate dehydrogenase Pgd-1 2 Pgd-2 1 Glu oxaloacetate transaminase Got-1 1 Got-3 1

  8. DNA-based markers Approach: Hybridization Polymerase Chain Reaction Types: RFLP Minisatellite RAPD SCAR SSR AFLP SNP etc

  9. DNA-based markers Patterns of small DNA sequences Constant landmarks in the genome May or May not have biological function Linked to conserved or variable regions

  10. RFLPs Restriction Fragment Length Polymorphisms Digestion with restriction enzymes Size fractionation on agarose gel Southern hybridization (genomic or cDNA probe) Analysis of hybridized restriction fragments

  11. RFLPs Polymorphism: homologous pieces of different lengths mutation on restriction sites mutation between restriction sites

  12. RFLPs Several bands per lane Highly polymorphic in a population at a locus – max 2 alleles in an individual Co-dominant marker Laborious / Time consuming Usually use isotope

  13. RFLPs

  14. PCR-RFLPs

  15. SSR or microsatellites Simple Sequence Repeat several bases per repeat tandem repeats flanked by unique sequences primer design based on flanking sequences polymorphism: number of repeating units

  16. SSR or microsatellites Easy to detect via PCR High polymorphism Co-dominant marker Library screening or Database search require for sequence identification

  17. SSR or microsatellites

  18. RAPDs Random Amplified Polymorphic DNAs PCR with 1 short primer (usu decamer) low annealing temperature primer annealing in inverted orientation at optimal distances amplified products analyzed on agarose gel

  19. RAPDs Polymorphisms: base changes at annealing sites insertion/deletion within amplified fragments Results: presence or absence of the bands Cannot distinguish homozygote / heterozygote

  20. RAPDs Simple, fast, relatively inexpensive assay Many loci to be identified in 1 rxn Can be automated Inconsistent results (short primer / low temp) Less informative for mapping with dominant nature different lengths not identifiable

  21. RAPDs

  22. AFLPs Amplified Fragment Length Polymorphisms digestion with 2 enzymes (rare/frequent cutters) eg EcoRI and MseI ligation of synthetic adapters to RFs pre-selective amplification primers corresponding to adapter sequences

  23. AFLPs Amplified Fragment Length Polymorphisms selective amplification 1-5 nt added to 3’ end of each primer 1 nt added to each primer 1/16 amplified banding patterns analyzed by PAGE

  24. AFLPs Many loci to be identified in 1 rxn High efficiency in detecting polymorphic DNA More consistent pattern than RAPDs Dominant marker Technically challenging / labor intensive

  25. AFLPs

  26. SNPs or SSCPs Single Nucleotide Polymorphisms Single-Stranded Conformation Polymorphisms SNP: major genetic source of phenotypic variability differentiate individuals within a species

  27. SNPs or SSCPs Mobility of ssDNA dependent of nt sequence looping or compaction Polymorphisms at a single locus base change by point mutation or small insertion / deletion

  28. SNPs or SSCPs Specific primers to amplify target region Asymmetric PCR (1 primer in excess) Regular PCR (denaturing ds DNA) ss PCR products analyzed by electrophoresis Base change revealed by labeled nucleotides in automated sequencer

  29. SNPs or SSCPs Many approaches for detection PCR-RFLP primer extension allele specific oligonucleotide ligation allele specific hybridization sequencing

  30. SNPs or SSCPs

More Related