linkage analysis and genome mapping

1. Linkage analysis
Rajpal Choudhary
161103004
M.Sc. Biotechnology

2. Linkage
• Linkage is defined genetically as the failure of two genes to assort
independently.
• Linkage is the association of genes on the same chromosome.
• Linkage occurs when two genes are close to each other on the same
chromosome.
• However, two genes on the same chromosome are called syntenic.

3. • Linked genes are syntenic, but syntenic genes are not always linked.
Genes far apart on the same chromosome assort independently: they
are not linked.
• Linkage is based on the frequency of crossing over between the two
genes. Crossing over occurs in prophase of meiosis I, where
homologous chromosomes break at identical locations and re-join
with each other.
• A linkage group is a group of genes which is known to be linked. A
chromosome can be called as linkage group.

4. Process of Recombination
• From an evolutionary point of view, the purpose of sex is to re-shuffle the
combinations of alleles so the offspring receive a different set of alleles
than their parents had.
• Natural selection then causes offspring with good combinations to survive
and reproduce, while offspring with bad combinations don’t pass them on.
• Genes are on chromosomes. Meiosis is a mechanism for re-shuffling the
chromosomes: each gamete gets a mixture of paternal and maternal
chromosomes.
• However, chromosomes are long and contain many genes. To get individual
genes re-shuffled, there needs to be a mechanism of recombining genes
that are on the same chromosome. This mechanism is called “crossing over.

5. • Crossing over occurs in prophase of meiosis 1, when the homologous
chromosomes synapse, which means to pair closely with each other. DNA
strands from the two chromosomes are matched with each other.
• During synapsis, an enzyme, recombinase, attaches to each chromosome
at several randomly chosen points. The recombinase breaks both DNA
molecules at the same point, and re-attaches them to opposite partners.
• The result of crossing over can be seen in the microscope as prophase
continues, as X shaped structures linking the homologues.
• The genetic consequence of crossing over is that each chromosome that
goes into a gamete is a combination of maternal and paternal
chromosomes.

6. Recombination Process

8. No Linkage: Independent Assortment

9. Linkage without Recombination

10. Linkage with Recombination

11. 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 mattings 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.

12. • Only mattings 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).

15. • 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).

16. Linkage analysis techniques
• Recombination fraction
• LOD score
• Haldane mapping function

17. 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 are on the same
chromosome = linked

18. Calculation of Recombination Frequency
The percentage of recombinant progeny produced in a cross is called the
recombination frequency, which is calculated as follows:

19. Recombination Frequency

20. LOD SCORE
• The LOD score is calculated as follows:
• 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.
• On the other hand, a LOD score less than -2.0 is considered evidence
to exclude linkage.

21. Mapping function
• The genetic distance between locus A and locus B is defined as the
average number of crossovers occurring in the interval AB.
• Mapping function is use to translate recombination fractions into
genetic distances.
• In 1919 the British geneticist J, B. S. Haldane proposed such Mapping
function Haldane defined the genetic distance, x, between two loci as
the average number of crossovers per meiosis in the interval between
the two loci.

22. Haldane’s mapping function
• Assumptions: crossovers occurred at random along the chromosome
and that the probability of a crossover at one position along the
chromosome was independent of the probability of a crossover at
another position.
• Using these assumptions, he derived the following relationship
between
• Ø, the recombination fraction and
• x ,the genetic distance (in morgans):
• Ø=1/2(1-e-2x) or equivalently,
• X=-1/2ln(1-2Ø)

23. • Genetic distance between two loci increases, the recombination
fraction approaches a limiting value of 0.5.
• Cytological observations of meiosis indicate that the average number
of crossovers undergone by the chromosome pairs of a germ-line cell
during meiosis is 33.
• Therefore, the average genetic length of a human chromosome is
about 1.4 morgans, or about 140 centimorgans.

25. LIMITATIONS
• A map generated by genetic techniques is rarely sufficient for directing the
sequencing phase of a genome project. This is for two reasons:
• The resolution of a genetic map depends on the number of crossovers that
have been scored.
• Genes that are several tens of kb apart may appear at the same position on
the genetic map.
• Genetic maps have limited accuracy .
• Presence of recombination hotspots means that crossovers are more likely
to occur at some points rather than at others.
• physical mapping techniques has been developed to address this problem.

26. Thank you