1.GENOME MAPPING
Ms.ruchiyadavlectureramity institute of biotechnologyamity universitylucknow(up)

2. GENOME MAPPING
GENETIC MAPPING
PHYSICAL MAPPING
3. GENOME MAPPING
Genetic mapping is based on the use of genetic techniques to construct maps showing the positions of genes and other sequence features on a genome.
Genetic techniques include cross-breeding experiments or,
Case of humans, the examination of family histories (pedigrees).
Physical mapping uses molecular biology techniques to examine DNA molecules directly in order to construct maps showing the positions of sequence features, including genes.
4. DNA MARKERS FOR GENETIC MAPPING
Mapped features that are not genes are called DNA markers. As with gene markers, a DNA marker must have at least two alleles to be useful. There are three types of DNA sequence feature that satisfy this requirement:
Restriction fragment length polymorphisms (RFLPs)
Simple sequence length polymorphisms (SSLPs), and
i) Minisatellites, also known as variable number of tandem repeats (VNTRs) in which the repeat unit is up to 25 bp in length;
ii) Microsatellites or simple tandem repeats (STRs), whose repeats are shorter, usually dinucleotide or tetranucleotide units.
single nucleotide polymorphisms (SNPs).
5. Restriction fragment length polymorphisms (RFLP)
6. RFLP DETECTION
7. Restriction fragment length polymorphisms (RFLPs)
8. 9. Pedigree based on RFLP analysis
10. 11. Linkage analysis shows that the disease gene D lies between markers c and d.
12. RFLP
Distance between RFLP markers is also defined in recombination units or cM.
13. Amplified Fragment Length Polymorphism (AFLP)
AFLPs are differences in restriction fragment lengths caused by SNPs or INDELs that create or abolish restriction endonuclease recognition sites.
The AFLP technique is based on the selective PCR amplification of restriction fragments from a total digest of genomic DNA
14. RAPD (Random Amplified Polymorphic DNA)
RAPD markers are DNA fragments from PCR amplification of random segments of genomic DNA with single primer of arbitrary nucleotide sequence.
RAPD does not require any specific knowledge of the DNA sequence of the target organism
The identical 10-mer primers will or will not amplify a segment of DNA, depending on positions that are complementary to the primers' sequence.
15. RAPD (Random Amplified Polymorphic DNA)
16. Simple sequence length polymorphisms (SSLPs),
Unlike RFLPs, SSLPs can be multi-allelic as each SSLP can have a number of different length variants.
17. VNTRs - Minisatellites
18. VNTRs - Minisatellites
19. Microsatellites: simple tandem repeats (STRs)
20. Simple tandem repeats (STRs)
21. STRs
Advantages
Easy to detect via PCR
Lots of polymorphism
Co-dominant in nature
Disadvantage
Initial identification,DNA sequence information necessary
22. MAPPING TECHNIQUES
Linkage analysis is the basis of genetic mapping.
The offspring usually co-inherit either A with B or a with b, and, in this case, the law of independent assortment is not valid.
Thus to test for linkage between the genes for two traits, certain types of matings are examined and observe whether or not the pattern of the combinations of traits exhibited by the offspring follows the law of independent assortment.
If not, the gene pairs for those traits must be linked, that is they must be on the same chromosome pair.
23. What types of matings can reveal that the genes for two traits are linked?
Only matings involving an individual who is
heterozygous for both traits (genotype AaBb) reveal
deviations from independent assortment and thus reveal
linkage.
Moreover, the most obvious deviations occur in the
test cross, a mating between a double heterozygote
and a doubly recessive homozygote (genotype aabb).
Individuals with the genotype AaBb manifest both
dominant phenotypes; those with the genotype aabb
manifest both recessive phenotypes.
24. 25. 26. How do we estimate, from the offspring of a single family, the likelihood that two gene pairs are linked?
Recombination fraction
LOD score
Haldane mapping function
27. Recombination Frequency
Recombination fraction is a measure of the distance between two loci.
Two loci that show 1% recombination are defined as being 1 centimorgan (cM) apart on a genetic map.
1 map unit = 1 cM (centimorgan)
Two genes that undergo independent assortment have recombination frequency of 50 percent and are located on nonhomologous chromosomes or far apart on the same chromosome = unlinked
Genes with recombination frequencies less than 50 percent are on the same chromosome = linked
28. Calculation of Recombination Frequency
The percentage of recombinant progeny produced in a cross is called the recombination frequency, which is calculated as follows:
29. Recombination Frequency
30. Recombination fraction
31. LOD SCORE

The LOD score is calculated as follows:

32. LOD = Z = Log10 probability of birth sequence with a given linkage probability of birth sequence with no linkage

By convention, a LOD score greater than 3.0 is considered evidence for linkage.

33. On the other hand, a LOD score less than -2.0 is considered evidence to exclude linkage.