Marker Assisted Back Crossing

(MABC)

Dr. Md. Nasim Ali

 Definition:
Marker assisted selection (MAS)
refers to the use of DNA markers
that are tightly-linked to target loci as
a substitute for or to assist
phenotypic screening

Assumption: DNA markers can reliably

predict phenotype
 Main Features of MAS
1. Application: applicable to Self pollinated,
cross pollinated and asexually propagated
species.
2. High Accuracy
3. Rapid method
4. Free from Environmental Effects
5. Permits QTL tagging
6. Requires sophisticated Laboratory
7. Health Hazards: in case radio active labelling
markers.
 DNA markers
• Restriction Fragment Length Polymophism
(RFLP)
• Random Amplified Polymorphic DNA (RAPD)
• Inter Simple Sequence Repeats (ISSR)
• Microsatellites or Simple sequence repeats.
• Amplified Fragmnent Length Polymorphism
(AFLP)
• Cleasved Amplefied Polymorphic Sequence
(CAPS)
 Linked Markers
One type of molecular marker is called a linked marker.
Using well-designed experiments, scientists can find
molecular markers that are located very close to major
genes of interest. The molecular marker is said to be
linked to that gene. Linked markers are only near the
gene of interest on the chromosome and are not part of
the DNA of the gene of interest.
 Markers must be
tightly-linked to target loci!
• Ideally markers should be <5 cM from a gene or QTL
RELIABILITY FOR
SELECTION
Marker A

QTL Using marker A only:

5 cM
1 – rA = ~95%

Marker A Marker B
Using markers A and B:
QTL
5 cM 5 cM 1 - 2 rArB = ~99.5%

• Using a pair of flanking markers can greatly improve reliability but increases time
and cost
Markers must be polymorphic
RM84 RM296

1 2 3 4 5 6 7 8 1 2 3 4 5 6 7 8

P1 P2
P1 P2

Not polymorphic Polymorphic!

 CONVENTIONAL PLANT BREEDING

P1 x P2

Recipient Donor

F1
large populations consisting of thousands
F2 of plants

PHENOTYPIC SELECTION

Phosphorus deficiency plot

Salinity screening in phytotron Bacterial blight screening

Glasshouse trials Field trials

 MARKER-ASSISTED BREEDING

P1 x P2
Susceptible Resistant

F1

large populations consisting of thousands

F2
of plants

MARKER-ASSISTED SELECTION (MAS)

Method whereby phenotypic selection is based on DNA markers

Mapping population
 Concept of ‘linkage drag’
• Large amounts of donor chromosome remain even after many backcrosses
• Undesirable due to other donor genes that negatively affect agronomic
performance

LINKED DONOR
GENES
TARGET c TARGET
LOCUS
LOCUS

Donor/F1 BC1 BC3 BC10

RECURRENT PARENT
CHROMOSOME

DONOR CHROMOSOME
 • Markers can be used to greatly minimize the amount of donor
chromosome….but how?

Conventional backcrossing

TARGET
GENE c c

F1 BC1 BC2 BC3 BC10 BC20

Marker-assisted backcrossing

TARGET
GENE
c

Ribaut, J.-M. & Hoisington, D. 1998 Marker-assisted selection: new

tools and strategies. Trends Plant Sci. 3, 236-239.

F1 BC1 BC2
MAS BREEDING SCHEMES

1. Marker-assisted backcrossing
2. Pyramiding
3. Early generation selection
4. ‘Combined’ approaches
Marker-assisted backcrossing (MAB)
• MAB has several advantages over conventional
backcrossing:
– Effective selection of target loci
– Minimize linkage drag
– Accelerated recovery of recurrent parent
1 2 3 4 1 2 3 4 1 2 3 4

Target
locus

TARGET LOCUS RECOMBINANT BACKGROUND

SELECTION SELECTION SELECTION

FOREGROUND
BACKGROUND SELECTION
SELECTION
 Pyramiding
• Widely used for combining multiple disease
resistance genes for specific races of a
pathogen
• Pyramiding is extremely difficult to achieve using
conventional methods
– Consider: phenotyping a single plant for multiple
forms of seedling resistance – almost impossible

• Important to develop ‘durable’ disease

resistance against different races
Marker assisted pyramiding of two disease
resistance genes.
P1
Resistant to Race 1
Susceptible to Race 2
x P2
Susceptible to Race 1
Resistant to Race 2

F1

F2

Line number 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20
Phenotype Race 1 R S R R S R R S R R R R S R R R R R S R

Phenotype Race 2 S R S R R R R S R S R R R R R S S R R R

P1 P2 F1 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20

MARKER 1 R1
S

P1 P2 F1 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20

R2
MARKER 2
S

Note that homozygotes can be selected from the F2 population.

 Merits
• Early selection of traits that are expressed late in the
life of plants.
• It permits screening of traits that are extremely difficult
, expensive or time consuming to score phenotypically.
e g. Root morphology, resistance to biotic and abiotic
stress.
• It helps in distinguishing the homozygous and
heterozygous condition of many loci in a single
generation without the need of progeny testing,.
• DNA markers permits marker aided selection for
several characters at one time.
• Accuracy is very high.
 Demerits
• Required sophisticated and well equipped
laboratory.
• Very expensive.
• Required well trained manpower
• The detection of various DNA markers (RFLP,
AFLP and RAPD) is aborious and time
consuming work,
• Radio-lebelling in case of RFLP amy create
health hazards.