1       MOLECULAR MARKERS:        RFLP,AFLP AND DATA ANALYSIS                           ASHW   IN                        ...
RFLP= Restriction fragment length polymorphism2        Different fragment lengths of base pairs that result from         ...
3       The DNA sample is broken into pieces (digested)        by restriction enzymes and the resulting restriction      ...
mechanism4    1.   DNA is cut into         fragments by the         restriction enzyme    2.   Fragments are         separ...
5       During RFLP typing restriction enzymes cut up        fragments into hundreds of fragments- some        containing...
6       DNA cut up from restriction enzymes is placed        on a plate coated with a gel medium (usually        agar or ...
Southern Blotting7       Once the electrophoresis process is        completed, the double stranded fragments of        DN...
Hybridization8   To visualize the separated RFLPs, the nylon sheet is treated with radioactively labeled    probes contai...
summary9   Portions of the DNA    molecule contain    sequences of bases that    are repeated numerous    times. These ta...
T-R X: software for the processing and    E analysis of T-RFLP data10
11AFLPAMPLIFIED FRAGMENT LENGTHPOLYMORPHISM
AFLP12     -A method based on PCR developed in 1995 by Zabeau,     Vos and co workers.     - Involves the use of RFLP and ...
AFLP13     The AFLP technique is based on the     principle of selectively amplifying a subset     of restriction fragment...
AFLP14        AFLP is a technique in which differences in restriction fragments         are revealed by PCR, and this not...
AFLP15     Procedures in AFLP:         - Digestion         - Adaptor Ligation         - Amplification         - Electropho...
Digestion     Two different restriction endonucleases are     used in digestion. One is 4-base cutter (MseI)     and the o...
Adaptor Ligation     - Two different adaptors (short double     stranded DNA sequences with sticky end) are     ligated to...
18
AFLP       19
AFLP20     Selected fragments are amplified (to have 50-150 bands on      the gel) and separated by polyacrylamide gel   ...
21
Electrophoresis     - polyacrylamide gel is used for separating     DNA bands.     - Normally, 30-100 DNA bands can be    ...
AFLP23       The main advantages of AFLP are       No need for known sequences in the genome       High reproducibility...
24
Polymorphism among     32 wheat samples     revealed by AFLP25
Selective Bases     - The number of DNA bands detected by     AFLP is high. It can be reduced by adding     selective base...
Characteristics of AFLP     - Dominant marker.     - DNA variation is detected by presence/                               ...
Advantages     - higher reproducibility compared to RAPD.     - highly polymorphic.28
Analysis of AFLP data29         Similarity (cluster analysis)         NJ (Neighbor Joining)         UPGMA (Unweighted P...
AFLP Clustering                 BioNumerics software package                                (Applied Maths, Kortrijk,Analy...
AFLP Data Map with UPGMA     dendogram from Urbanelli et al.     (2007): “Distinguishing taxa in the31   Pleurotus eryngii...
32     Thank you
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Ashwin aflp.ppt

  1. 1. 1  MOLECULAR MARKERS: RFLP,AFLP AND DATA ANALYSIS ASHW IN JAYALE ID no-
  2. 2. RFLP= Restriction fragment length polymorphism2  Different fragment lengths of base pairs that result from cutting a DNA molecule with restriction enzymes  Refers to variation in restriction sites between individuals in a population  These are extremely useful and valuable for geneticists.  On average two individuals (humans) vary at 1 in 1000 bp  The human genome is 3x109 bp  This means that they will differ in more than 3 million bp.  By chance these changes will create or destroy the recognition sites for Restriction enzymes
  3. 3. 3  The DNA sample is broken into pieces (digested) by restriction enzymes and the resulting restriction fragments are separated according to their lengths by gel electrophoresis  It refers to a difference between samples of homologous DNA molecules that come from differing locations of restriction enzyme sites.
  4. 4. mechanism4 1. DNA is cut into fragments by the restriction enzyme 2. Fragments are separated into bands by electrophoresis 3. DNA bands are transferred to a nylon membrane 4. A radioactive DNA probe is added to the membrane where it binds to specific fragments 5. X-ray film is placed on top of the nylon membrane to detect radioactive pattern
  5. 5. 5  During RFLP typing restriction enzymes cut up fragments into hundreds of fragments- some containing repeating sequences from the DNA molecule  It is necessary to follow this procedure with gel Electrophoresis  Electrophoresis  Once the DNA molecules have been cut up by restriction enzymes the fragments have to be sorted out.  This is accomplished through electrophoresis  Electrophoresis- a technique for separating molecules through their migration on a support medium under the influence of an electrical potential
  6. 6. 6  DNA cut up from restriction enzymes is placed on a plate coated with a gel medium (usually agar or starch)  When the gel is subjected to an electric potential the DNA fragments migrate across the plate  The smaller fragments move quickly across the plate, so the fragments are separated by size
  7. 7. Southern Blotting7  Once the electrophoresis process is completed, the double stranded fragments of DNA are chemically treated so the strands separate from each other.  The fragments are then transferred to a nylon membrane in the same manner as one would transfer an ink line onto a blotter.  Transfer process is called southern blotting after its developer Edward Southern.
  8. 8. Hybridization8 To visualize the separated RFLPs, the nylon sheet is treated with radioactively labeled probes containing a base sequence complementary to the RFLPs being identified. Hybridization- the process of joining 2 complementary strands of DNA to form a double stranded molecule. Probes:- A molecular probe is a group of atoms or molecules attached to other molecules or cellular structures and used in studying the properties of these molecules and structures. Radioactive DNA or RNA sequences are used in molecular genetics to detect the presence of a complementary sequence by molecular hybridization. Types :a) genomic DNA probes. b) c DNA probes. c) RNA probes.
  9. 9. summary9 Portions of the DNA molecule contain sequences of bases that are repeated numerous times. These tandem repeats can distinguish one individual from another Materials are separated by electrophoresis where the DNA is separated by electric current A typical DNA fragment pattern shows 2 bands. RFLP are codominant marker.
  10. 10. T-R X: software for the processing and E analysis of T-RFLP data10
  11. 11. 11AFLPAMPLIFIED FRAGMENT LENGTHPOLYMORPHISM
  12. 12. AFLP12 -A method based on PCR developed in 1995 by Zabeau, Vos and co workers. - Involves the use of RFLP and PCR techniques. - Compared with the widely used RFLP, AFLP is faster, less labour intensive and provide more information. - An additional advantage over RAPD is their reproducibility. -Powerful approach to detect polymorphism.
  13. 13. AFLP13 The AFLP technique is based on the principle of selectively amplifying a subset of restriction fragments from a complex mixture of DNA fragments obtained after digestion of genomic DNA with restriction endonucleases.
  14. 14. AFLP14  AFLP is a technique in which differences in restriction fragments are revealed by PCR, and this not for one locus but for a larger number of loci in one reaction  In a first step the restriction fragments are generated by using two different enzymes (a frequent tetra-cutter and a more rare hexacutter)  Adapters are ligated to these fragments in order to have known sequences for primer design  Selected fragments are amplified (to have between 50-150 bands on the gel) and separated by polyacrylamide gel electrophoresis (detection by autoradiography or fluorescence)
  15. 15. AFLP15 Procedures in AFLP: - Digestion - Adaptor Ligation - Amplification - Electrophoresis
  16. 16. Digestion Two different restriction endonucleases are used in digestion. One is 4-base cutter (MseI) and the other one is 6-base cutter (EcoRI). MseI 5’TTAA3’ EcoRI 5’GAATTC3’16
  17. 17. Adaptor Ligation - Two different adaptors (short double stranded DNA sequences with sticky end) are ligated to the digested fragments. - One adaptor will complement to the M cut sel end, the other will complement to the EcoRI cut end.17
  18. 18. 18
  19. 19. AFLP 19
  20. 20. AFLP20  Selected fragments are amplified (to have 50-150 bands on the gel) and separated by polyacrylamide gel electrophoresis (silver staining, autoradiography or fluorescence)  This selection is made by using longer primers: every extra nucleotide decreases the number of fragments by 1/4, so 2 extra nucleotides on each primer will amplify 1/256  By repeating this second amplification with other primer pairs (other selective nucleotides) a different subset of the genome is amplified.
  21. 21. 21
  22. 22. Electrophoresis - polyacrylamide gel is used for separating DNA bands. - Normally, 30-100 DNA bands can be detected by AFLP on polycrylamide gel.22
  23. 23. AFLP23  The main advantages of AFLP are  No need for known sequences in the genome  High reproducibility  Many loci are simultaneously analysed  By changing the selective nucleotides a different part of the genome (and thus different loci) can be analysed  W hole genome analysis is (theoretically) possible  The main disadvantage: complex procedure.
  24. 24. 24
  25. 25. Polymorphism among 32 wheat samples revealed by AFLP25
  26. 26. Selective Bases - The number of DNA bands detected by AFLP is high. It can be reduced by adding selective bases (1-3 nucleotides) at the 3’-end of the PCR primers. - one additional selective base on the primer can reduced the number of DNA bands 16 folds. - three additional selective bases on the primer can reduce the number of DNA bands 4,000 folds.26
  27. 27. Characteristics of AFLP - Dominant marker. - DNA variation is detected by presence/ absence of DNA bands due to: a) presence/ absence of restriction sites b) additional bases (insertion) between two restriction sites are too large27
  28. 28. Advantages - higher reproducibility compared to RAPD. - highly polymorphic.28
  29. 29. Analysis of AFLP data29  Similarity (cluster analysis)  NJ (Neighbor Joining)  UPGMA (Unweighted Pair Group Method with Arithmetic mean)  AMOVA (Analysis of Molecular Variance)  Model-based  Maximum likelihood  Bayesian Example of a sequence distance matrix Image Source: http://media.wiley.com/CurrentProtocols/BI/bi0603/bi0603-fig-0002-1-full.gif
  30. 30. AFLP Clustering BioNumerics software package (Applied Maths, Kortrijk,Analysis Belgium).30 Clustering Dendrogram Fragment Visualization Source: Wikimedia Commons
  31. 31. AFLP Data Map with UPGMA dendogram from Urbanelli et al. (2007): “Distinguishing taxa in the31 Pleurotus eryngii (King Oyster Mushroom) complex using AFLPs” • 90 populations sampled • 94 AFLP loci scored Photos: (Top) The New York Times (Bottom L) Wikimedia Commons (Bottom R) http://steinpilz.up.seesaa.net
  32. 32. 32 Thank you
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