BY__

WADIWALA PRACHI
M.Sc (MICROBIOLOGY)
SEM-II
 CONTENT
DEFINATION OF GENOME

TYPES OF GENOME
MAPPING

GENOME MAPPING BY---

RFLP
SNP
AFLP
 WHAT IS GENOME ?

The genome refers to the total genetic composition of an

organism.

WHAT IS GENOMICS ?

The term refers the molecular analysis of the entire genome

of a species.

Genome analysis is a molecular dissection process applied to

a complete set of chromosomes. During genome analysis ,
segments of chromosomes are cloned and analyzed in
progressively smaller pieces , the locations of which are
known on the intact chromosomes. This is the “mapping
phase” of genome analysis.
 WHAT IS GENOME MAPPING?

The determination of the sequence of genes and

their relative distances from one another on a
specific chromosome.

The mapping of the genome ultimately progresses

to the determination of the complete DNA
sequence, that provide the most detailed
description of an organism’s genome.
Three types of mapping……

1.Cytogenetic mapping

2.Genetic linkage mapping

3.Physical mapping

Genetic linkage mapping uses molecular markers RFLPs,

SNPs & AFLPs.
 RFLP
Restriction Fragment Length
Polymorphism
 HOW RFPL GENERATED ?
The genetic variability at a particular locus (gene)
due to even minor base changes can alter the
pattern of restriction enzyme digestion fragments
that can be generated.

Pathogenic alterations to the genotypic can be due

to deletions or insertions within the gene being
analyzed or even single nucleotide substitutions
that can create or delete a restriction enzyme
recognition site.
 HOW RFPL GENERATED ?

1. Loss of an endonuclease cleavage site, most

probably as a result of a base change

2. By insertion or deletion of a stretch of DNA

3. By variation in the number of repeats of

microsatellite
RFLP arise from differences in the
number and locations of restriction
enzyme sites among individuals
THE DISTANCE BETWEEN
TWO RFLPs CAN BE
DETERMINED
An RFLP Map Describes The Locations Of
Many Different RFLPs Throughout The
Genomes; Functional Genes Can Be
Located Within An RFLP Map
Applications of RFLP
In the detection of the genetic diseases and other
human diseases

In forensic lab for doing paternity test

• Sickle cell anemia results (at the level of the gene)
from a single nucleotide change (A --> T) at codon 6
within the b-globin gene.

• This alteration leads to a glu ----> val amino acid

substitution, while at the same time abolishing a MstII
restriction site.

• As a result a b-globin gene probe can be used to detect

the different MstII restriction fragments.

• It should be recalled that there are two copies of each

gene in all human cells, therefore, RFLP analysis
detects both copies: the affected alelle and the
unaffected allele.
SINGLE NUCLEOTIDE
POLTMORPHISM
(SNP)
• SNP are single base-pair positions in genomic DNA at
which different sequence alternative (alleles) exist in a
population

• In human, polymorphisms are considered to be SNPs

only if the least abundant allele has a frequency of 1%
or more. This is to distinguish the SNP from very rare
mutation

• When SNP occurs at the restriction site , it alters the

sensitivity of a sequence to be cleavage by restriction
endonuclease. These are known as RFLPs.
SNPs are the most important sequence markers bcz they
have the potential to provide the greatest density of
markers.

For example, their frequency is estimated to be 1 per 1000

basepairs which , in the case of the human genome,
means 3 million in total.

Originally the HUMAN SNP CONSORTIUM planned to map

3,00,000 of them but the latest version of the SNP
database contains 10 million.
•Many different methods for detecting SNPs have
been developed.

•This divided into 2 different activities : Scanning DNA

sequences for previously unknown polymorphism to
facilitate mapping , and screening of individual for
known polymorphism.

•Scanning further divided into the global or random

approach and the regional or targeted approach---
relies on dHPLC.
Techniques that detect mutation based on the
differences in mobility of partially denatured include---

•Constant gradient gel electrophoresis (CGGE)

•Denaturing gradient gel electrophoresis (DGGE)

•Temperature gradient gel electrophoresis (TGGE)

POLYMORPHIC DNA CAN BE DETECTED IN
THE ABSENCE OF SEQUENCE
INFORMATION

• RAPD (Randomly amplified polymorphic DNA)

• CAPS (cleaved amplified polymorphic

sequences)
THANK YOU