Molecular markers are useful tools for distinguishing plant varieties and genotypes. Some common types of molecular markers include isozyme markers, which analyze variations in enzyme activity, and DNA-based markers like RFLPs, SSRs, RAPDs, AFLPs, and SNPs. DNA-based markers detect polymorphisms by analyzing patterns in DNA sequences and can be used to study genetics, identify genotypes, and assist in plant breeding through marker-assisted selection.

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

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

3. Molecular Marker
Useful when other methods not av
Very similar morphology / ana
Growth and development stag
Environmental factors
Analysis of banding patterns
Statistics for evaluation of polymo

4. Molecular marker
Study and management of geneti
Identifying and distinguishing ge
Marker assisted selection (MAS)
Complementary tool for DUS stud
Distinctiveness / Uniformity /

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

6. Isozyme marker

7. Isozyme marker
Enzyme Isozyme locus # al
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 dehydrogenasePgd-1 2
Pgd-2 1
Glu oxaloacetate transaminase Got-1 1
Got-3 1

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

9. DNA-based marker
Patterns of small DNA sequence
Constant landmarks in the geno
May or May not have biological
Linked to conserved or variable

10. RFLPs
Restriction Fragment Length Polymo
Digestion with restriction enzym
Size fractionation on agarose ge
Southern hybridization (genomic
Analysis of hybridized restriction fra

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

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

13. RFLPs

14. PCR-RFLPs

15. SSR or microsatellite
Simple Sequence Repeat
several bases per repeat
tandem repeats flanked by uni
primer design based on flankin
polymorphism: number of rep

16. SSR or microsatellite
Easy to detect via PCR
High polymorphism
Co-dominant marker
Library screening or Database se
require for sequence identifi

17. SSR or microsatellite

18. RAPDs
Random Amplified Polymorphic D
PCR with 1 short primer (usu
low annealing temperature
primer annealing in inverted o
at optimal distances
amplified products analyzed o

19. RAPDs
Polymorphisms:
base changes at annealing site
insertion/deletion within ampl
Results: presence or absence of the
Cannot distinguish homozygote / h

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

21. RAPDs

22. AFLPs
Amplified Fragment Length Polymor
digestion with 2 enzymes (rare/f
eg EcoRI and MseI
ligation of synthetic adapters to
pre-selective amplification
primers corresponding to ad

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

24. AFLPs
Many loci to be identified in 1 rx
High efficiency in detecting polym
More consistent pattern than RA
Dominant marker
Technically challenging / labor in

25. AFLPs

26. SNPs or SSCPs
Single Nucleotide Polymorphisms
Single-Stranded Conformation Poly
SNP: major genetic source of phe
differentiate individuals within

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

28. SNPs or SSCPs
Specific primers to amplify targe
Asymmetric PCR (1 primer in
Regular PCR (denaturing ds
ss PCR products analyzed by ele
Base change revealed by labeled
in automated sequencer

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

30. SNPs or SSCPs