Genome mapping

LINKAGE ANALYSIS IN

GENETIC MAPPING

WHAT IS A GENOME?

• It is the entirety of an

organism's hereditary information

• It is encoded either in DNA or,

for many types of viruses, in RNA

GENOME MAPPING

It is the creation of a genetic map assigning DNA fragments

to chromosomes

A genome map provides a guide for the sequencing

experiments by showing the positions of genes and other

distinctive features

DNA sequencing has some major limitation – only 750 bp

can be examined in a single experiment

Two Types Of Genome Mapping

1. Genetic Mapping

2. Physical Mapping

•It is based on use of genetic techniques to construct

maps showing the positions of genes and other

sequence features on a genome.

•It includes cross breeding experiments or examining

the family histories in case of humans

GENETIC MAPPING

MARKERS

Various types of markers were used in mapping the

genome

1. Genes were the 1st markers used

2. DNA markers

RFLPs (Restriction fragment length polymorphisms)

SSLPs (Single sequence length polymorphisms)

SNPs (Single nucleotide polymorphisms)

After obtaining a set of markers to construct a map, mapping

techniques came in the role.

This techniques are based on genetic linkage

Genetic mapping is based on inheritance

Mendel from his breeding experiments with pea plant concluded

that pea plant possesses two alleles for each gene, but displays only

one genotype

He therefore described it as dominant or recessive phenotype

But Mendel did not encounter the other complications like

incomplete and co dominance while performing this experiments

Linkage Analysis Is The Basis Of Genetic Mapping

Incomplete Dominance

• The heterozygous phenotype is somewhere between the two homozygous phenotypes

• Case in which one allele is not dominant over another

Red flower (RR) White flower (WW)Pink flower (RW)

Co dominance

• Both alleles contribute to the phenotype

Apart from dominance recessiveness Mendel carried out

additional experiments by which he established his two laws

Laws Of Genetics :-

1. Alleles segregate randomly

2. Pairs of alleles segregate independently

Inheritance of the alleles of gene T is independent of inheritance of the alleles of gene B

Partial Linkage

Genes reside on chromosome

Chromosomes are inherited as intact units, so it was

reasoned that the alleles of some pairs of genes will be

inherited together because they are on the same chromosome

Pairs of genes were either inherited independently, as

expected for genes in different chromosomes, or, if they

showed linkage, then it was only partial linkage sometimes

they were inherited together and sometimes they were not

Recombination Frequency

Arthur Sturtevant’s, an undergraduate in Morgan laboratory

• The frequency with which the genes are unlinked by crossovers will be

directly proportional to how far apart they are on their chromosome

• The recombination frequency is therefore a measure of the distance

between two genes

• If you work out the recombination frequencies for different pairs of genes,

you can construct a map of their relative positions on the chromosome

• Recombination frequency can be calculated by LOD score method

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.