Genome mapping

1. genetic map - allows relative positions of heterozygous linked alleles to be located (a) I I I I I I I I I I I I I I I I I I I I I I physical map - allows precise location of specific DNA sequence to be located. (b) clone map (c) Sequence -Allows sequence of nucleotides to be determined AGGTCGCGATGCTA Genome mapping

2. Techniques Used in the Human Genome Project Genetic Linkage Mapping 1.Linkage mapping can be used to locate genes on particular chromosomes and establish the order of these genes and the approximate distances between them. 2.This idea is based on the fact that the further apart linked genes are on chromosomes the more likely crossing over will take place resulting in more recombinants being formed. 3.The greater the number of recombinants, the further apart linked genes are on a chromosome. Working out the number of recombinants relative to the parental genotypes gives a percentage value which is called the recombinationfrequency.

4. Genetic Linkage Mapping relies on having genetic markers that are detectable – sometimes these are genes that cause disease, traced in families by pedigree analysis. The marker alleles must be heterozygous and be linked on the same chromosome so that recombination can be detected. The overall result of genetic mapping is to produce a picture of the locations of the marker loci on the chromosomes – rather like establishing the order of the cities and large town between two points on a map.

5. Physical Mapping 1.Physical mapping is required to add some more of the detail to what is obtained by genetic mapping 2.As with genetic maps, construction of a physical map requires markers that can be mapped to a precise location on the DNA sequence. 3.The distance between markers is usually expressed as a number of nucleotides in a physical map. 4. A physical map can be made by isolating DNA from a chromosome then cutting it using restriction enzymes (also known as restriction endonucleases)to construct a pattern.

6. 5. Different restriction enzymes cut the DNA at different points as each recognises a particular short sequence of bases occurring in the DNA. Where the sequence is recognised, the enzyme cuts the DNA so that it is cut into fragments. 6. By using combinations of restriction enzymes and working out the size of the fragments it is possible to recognise a pattern. The fragments can be identified by their size or by using a specific DNA probe to bind to its complementary sequence. Warning - The following example is difficult. Try not to freak out but follow it carefully as a problem of this sort appeared in the 2001 paper

7. G G G G G G G G C C C C C C C C CUT FRAGMENT Physical Restriction Mapping - Example 1. Genes do not exist as separate entities but as part of the larger DNA molecule 2. DNA can be broken up into fragments by ENDONUCLEASES which cut at specific base sequences - look up page 316 of your textbook for more examples

8. C G G G G G G C C C C C G G G G G G G G G G G G C C C C C C C C C C C C G G G G G G C C C C C C Not 1 - always cuts at the following sequence of eight pairs. This happens on average every 65536 nucleotide pairs ( 1 in 48 ) and produces much larger fragments The resulting fragments can be separated using GEL ELECTROPHORESIS and used to physically map the sections of DNA - See textbook p317 The following table shows the fragments produced from a 15kbp fragment Bam H1 EcoR1 EcoR1 plus Pst1 Pst1 Bam H1 plus EcoR1 Bam H1 plus Pst1 Bam H1 plus EcoR1 plus Pst1 7 5 3 11 3 1 8 6 1 12 3 8 7 14 1 6 5 3 1

9. 15 12 9 3 6 0 kbp ANALYSING THE FRAGMENTS A) BAM H1 (14 +1) 14 1 B) EcoR1 (12 +3) 12 3 Option 1 12 3 Option 2 C) BAM H1 plus Eco R1 (11 +3 +1) 3 11 1 Option 1 12 1 2 Option 2 Option 2 for EcoR1 above would give 12 +2 +1 with the double digest which is INCORRECT. This means that the fragment must have been cut with the following orientation EcoR1 BAM H1

10. Pst 1 EcoR1 BAM H1 By repeating this procedure it is possible to build up a RESTRICTION MAP for this section of DNA - this lets us know the base sequence at each point of cut, 15 12 9 3 6 0 kbp A) BAM H1 (14 +1) 14 1 B) Pst 1 (8 +7) 8 7 Option 1 8 7 Option 2 C) BAM H1 plus Pst1 (8 +6 +1) 8 6 1 Option 1 7 7 1 Option 2 Option 2 for EcoR1 above would give 7 +7 +1 with the double digest which is INCORRECT. This means that the fragment must have been cut with the following orientation

11. 1 1 1 1 2 3 A 1 2 3 B 1 2 3 C • Checking the results of the triple digest EcoR1 plus Pst1 plus Bam H1 show that are • map is correct. • Since each cut with a known enzyme is a specific base sequence comparing restriction • maps allows biologists to look for the numbers and locations of these base sequences. • The theory is that the greater the number of sequences and the closer their location on • the DNA the more closely related the individuals • In the following example three endonucleases have been used (1-3) and have cut the strands • at the points shown. The reults indicate that individuals A and B are more closely related • that individuals A and C or B and C Physical Mapping relies on the availability of many copies of the DNA fragment. This is only possible because of the technique known as POLYMERASE CHAIN REACTION or PCR which allows many copies of the section of DNA to be produced