used for stdents

2. DOCTORAL CREDIT SEMINAR
ON
MARKER ASSISTED SELECTION (MAS): A NOVEL APPROACH
FOR CROP IMPROVEMENT
PRESENTED BY
B. L. MEENA
Ph.D. (GPB)
MAJOR ADVISOR
Dr. N.R. Koli
Department of Genetics & Plant Breeding
College of Agriculture, Ummed ganj Farm,
(Agriculture University) Kota
SEMINAR INCHARGE
Dr. B. Dhaka

3. INTRODUCTION
SELECTION
MOLECULAR MARKER
MARKER ASSISTED SELECTION SCHEMES
ADVANTAGES
DRAWBACK
CASE STUDIES
CONCLUSION

4. The concept of marker-assisted selection (MAS) was suggested 25
years ago by C. Smith and P. Simpson (1986) and by Soller and
Beckmann (1983)
 Marker-Assisted Selection According to Bertrand and Mackill
(2008), ‘The marker assisted Selection (MAS) assume that the
target gene identified and selected based on the closely linked
markers” A successful MAS requires that a gene be mapped
and closely linked to a marker, otherwise which is very difficult
to examine or evaluate by conventional approach.
Why marker assisted selection ?
To reduce the time needed to determine the progeny have desirable trait
Selection at seedling stage possible.
Selection of traits with low heritability
Distinguish homozygotes from heterozygotes
Selection for recessive gene determine traits of interest
Gene Pyramiding for resistant genes
MARKER- ASSISTED SELECTION

5. Marker assisted selection: It involves selecting
desirable plants using molecular markers.
The success of MAS is influenced by the
relationship between the markers and the genes of
interest.(Choudhary et al. 2008)
 Gene assisted selection (GAS)
Marker is in linkage disequilibrium (LD).
Marker is in linkage equilibrium (LE)
SELECTION
Phenotypic selection :It involves selecting desirable
plants by using morphological traits and phenotypic
screening.

6. F2
P2
F1
P1 x
large populations consisting of thousands of plants
PHENOTYPIC SELECTION
Field trials
Glasshouse trials
Donor
Recipient
CONVENTIONAL PLANT BREEDING
Salinity screening in
phytotron
Bacterial blight screening Phosphorus deficiency plot

7. F2
P2
F1
P1 x
large populations consisting of thousands of plants
Resistant
Susceptible
MARKER-ASSISTED SELECTION (MAS)
MARKER-ASSISTED BREEDING
Method whereby phenotypic selection is based on DNA markers

8.  MARKERS : Any part of DNA sequence which is
tightly linked to a gene of interest.
 Since molecular marker is tightly linked to the gene
of interest, so if marker is present in genome then it
is obvious that gene of interest is also present in the
genome .
 There is co segregation of molecular markers and
gene of interest from one generation to another.
 To locate gene of interest we must locate molecular
marker in a whole genome.
 The sequence of molecular marker is already known
to us.

9. Classification of markers

10. Main considerations for the use of DNA markers in
MAS:
Reliability:- Markers should be tightly linked to
target loci.
DNA quantity and quality. Lower quantity & High
quality of DNA.
Technical procedure: Simple and quick methods are
highly desirable.
Level of polymorphism: marker should be highly
polymorphic .
Cost: marker assay must be cost-effective.
The most widely used markers in major cereals are called
simple sequence repeats (SSRs) or microsatellites (Gupta et al.
1999; Gupta & Varshney 2000).

11. Markers must be
tightly-linked to target loci!
 Ideally markers should be <5 cM from a gene or QTL
Marker A
QTL
5 cM
RELIABILITY FOR
SELECTION
Using marker A only:
1 – rA = ~95%
Marker A
QTL
Marker B
5 cM 5 cM
Using markers A and B:
1 - 2 rArB = ~99.5%
• Using a pair of flanking markers can greatly improve reliability
but increases time and cost

12. 1. Marker-assisted backcrossing
2. Marker-assisted Pyramiding
3. Early generation marker
assisted selection
4. ‘Combined’ approaches

13.  MAB has several advantages over conventional backcrossing:
◦ Effective selection of target loci
◦ Minimize linkage drag
◦ Accelerated recovery of recurrent parent (Develop a variety
10-12 years by conventional & 3-4 Years by MAS)
1 2 3 4
Target locus
1 2 3 4
RECOMBINANT
SELECTION
1 2 3 4
BACKGROUND
SELECTION
TARGET LOCUS
SELECTION
FOREGROUND
SELECTION
BACKGROUND SELECTION

14.  Simultaneously combining multiple genes/QTLs
together into a single genotype.
 Pyramiding is extremely difficult to achieve by
using conventional methods.
 Consider: Phenotyping a single plant for multiple forms of
disease resistance – almost impossible
 Important to develop ‘durable’ disease resistance
against different races
CONT.

15. F2
F1
Gene A + B
P1
Gene A
x P2
Gene B
MAS
Select F2 plants that have
Gene A and Gene B
Genotypes
P1: AAbb P2: aaBB
F1: AaBb
F2
AB Ab aB ab
AB AABB AABb AaBB AaBb
Ab AABb AAbb AaBb Aabb
aB AaBB AaBb aaBB aaBb
ab AaBb Aabb aaBb aabb
Process of combining several genes, usually from 2 different parents,
together into a single genotype
x
Breeding plan

16.  Early generation selection scheme (proposed by Ribaut &
Betran (1999).
 MAS conducted at F2 or F3 stage
 Plants with desirable genes/QTLs are selected and
alleles can be ‘fixed’ in the homozygous state
◦ plants with undesirable gene combinations can be discarded
 Advantage for later stages of breeding program because
resources can be used to focus on fewer lines
CONT.

17. P1 x P2
F1
PEDIGREE METHOD
F2
F3
F4
F5
F6
F7
F8 – F12
Phenotypic
screening
Plants space-
planted in rows
for individual
plant selection
Families grown
in progeny rows
for selection.
Preliminary yield
trials. Select
single plants.
Further
yield trials
Multi-location testing, licensing, seed
increase and cultivar release
P1 x P2
F1
F2
F3
MAS
SINGLE-LARGE SCALE MARKER-
ASSISTED SELECTION (SLS-MAS)
F4
Families grown
in progeny rows
for selection.
Pedigree
selection based
on local needs
F6
F7
F5
F8 – F12
Multi-location testing, licensing, seed
increase and cultivar release
Only desirable
F3 lines planted
in field
Benefits: breeding program can be efficiently
scaled down to focus on fewer lines

18.  In some cases, a combination of phenotypic
screening and MAS approach may be useful
1. To maximize genetic gain (when some QTLs have been
unidentified from QTL mapping)
2. Level of recombination between marker and QTL (in
other words marker is not 100% accurate)
3. To reduce population sizes for traits where marker
genotyping is cheaper or easier than phenotypic
screening

19. BC1F1 phenotypes: R and S
P1 (S) x P2 (R)
F1 (R) x P1 (S)
Recurrent
Parent
Donor
Parent
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 …
SAVE TIME & REDUCE
COSTS
*Especially for quality traits*
MARKER-ASSISTED SELECTION (MAS)
PHENOTYPIC SELECTION
(Also called ‘tandem selection’)
Use when markers are
not 100% accurate or
when phenotypic
screening is more
expensive compared to
marker genotyping

20.  Simpler method compared to phenotypic screening
◦ Especially for traits with laborious screening
◦ May save time , resources and may cost effective.
 Selection at seedling stage
◦ Important for traits such as grain quality
◦ Can select before transplanting in rice
 Single plants may be selected with high reliability.
◦ No environmental effects
◦ Can discriminate between homozygotes and
heterozygotes and select single plants
◦ May be reduced the number of lines that need to be
tested.

21.  More accurate and efficient selection of specific
genotypes
◦ May lead to accelerated variety development
 More efficient use of resources
◦ Especially field trials
 Molecular markers permit the identification of putative
resistant plants in absence of disease tests . e.g. assay
for resistance to soybean cyst nematode (SCN) is very
difficult due to problem in inoculation and scoring.

22.  linkage map of two chromosome showing position
of two resistance gene and near by marker
 MAS may be more expensive than conventional
technique.
 Recombination between marker and the gene of
interest may be occur, leading to the false
positives.
 Marker developed for MAS in one population may
not be transferable to another Population.

23.  MAS has been initiated in India in several major crops for targeted
traits that include resistance to biotic and abiotic stresses and some
quality traits.
 Introgression of gene for disease resistance
 Crops Disease Improved variety
Rice Bacterial blight PB-1 & Samba Masuri
Rice Sub emergence tolerance Swarna-sub-1
Maize improved for lysine & Threonine Hybrid (Vivek QPM9)
Pear millet Resistant to downy mildew HHB-67-2
Chickpea Fusarium Wilt and Ascochyta Blight
Outstanding success stories on the deployment of the marker(s)
/QTL(s) in routine breeding programme are available in several
crops including rice, maize, wheat, pearl millet and mustard (Gupta
et al. 2012a ).

25.  Molecular marker assisted selection offer great
scope for improving the efficiency of conventional
plant breeding.
 Gene pyramiding may not be the most suitable
strategy when many QTL with small effects control
the traits and other methods such marker-assisted
recurrent selection should be consider.
 This will help breeder get around problems related
to larger breeding population, replications in
diverse environments, and speed up the
development of advance line.