Marker assistant selection

1. PRESENTED BY: Pawan
Nagar
Reg. no.: 04-2690-2015
M.Sc.(Fruit Science)
Marker assisted selection

2. Plant breeding—in combination with developments in agricultural technology such as
agrochemicals—has made remarkable progress in increasing crop yields for over a
century.
However, plant breeders must constantly respond to many changes. First, agricultural
practices change, which creates the need for developing genotypes with specific
agronomic
characteristics. Second, target environments and the organisms within them are
constantly
changing. For example, fungal and insect pests continually evolve and overcome host–
plant
resistance. New land areas are regularly being used for farming, exposing plants to
altered
growing conditions. Finally, consumer preferences and requirements change. Plant
breeders
therefore face the endless task of continually developing new crop varieties.

3. To overcome the demand of food for the world crop improvement in lesser time
duration
is needed, for that DNA markers are very useful to detect the presence of allelic
variation in the genes underlying these traits. By using DNA markers to assist in
plant
breeding, efficiency an d precision could be greatly increased. The use of DNA
markers
in plant breeding is called marker-assisted selection (MAS) and is a component of
the
new discipline of ‘molecular breeding’.


4. 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

5.  Reliability. Markers should be tightly linked to target loci, preferably less
than 5 cM genetic distance. The use of flanking markers or intragenic
markers will
greatly increase the reliability of the markers to predict phenotype
 DNA quantity and quality. Some marker techniques require large
amounts and high quality of DNA, which may sometimes be difficult to
obtain in practice, and this adds to the cost of the procedures.

6.  Technical procedure. The level of simplicity and the time
required for the technique are critical considerations. Highly simple
and quick methods are highly desirable.
 Level of polymorphism. Ideally, the marker should be highly
polymorphic in breeding material (i.e. it should discriminate between
different genotypes), especially in core breeding material.
 Cost. The marker assay must be cost-effective in order for MAS to
be feasible.

7.  Ideally markers should be <5 cM from a gene or QTL
• Using a pair of flanking markers can greatly improve
reliability but increases time and cost
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%

8. 1 2 3 4 5 6 7 8 1 2 3 4 5 6 7 8
RM84 RM296
P1 P2
P1 P2
Not polymorphic Polymorphic!

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

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

11.  more accurate and
efficient selection of
specific genotypes
◦ May lead to accelerated
variety development
 more efficient use of
resources
◦ Especially field trials
Crossing house
Backcross nursery

12. (1) LEAF TISSUE
SAMPLING
(2) DNA EXTRACTION
(3) PCR
(4) GEL ELECTROPHORESIS
(5) MARKER ANALYSIS
Overview of
‘marker
genotyping’

13.  MAB has several advantages over conventional
backcrossing:
◦ Effective selection of target loci
◦ Minimize linkage drag
◦ Accelerated recovery of recurrent parent
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.  Widely used for combining multiple disease
resistance genes for specific races of a
pathogen
 Pyramiding is extremely difficult to achieve using
conventional methods
 Important to develop ‘durable’ disease
resistance against different races

15. F2
F1
Gene A + B
P1
Gene A
x P1
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.  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

17. P1 x F1
P1 x P2
CONVENTIONAL BACKCROSSING
BC1
VISUAL SELECTION OF BC1 PLANTS THAT
MOST CLOSELY RESEMBLE RECURRENT
PARENT
BC2
MARKER-ASSISTED BACKCROSSING
P1 x F1
P1 x P2
BC1
USE ‘BACKGROUND’ MARKERS TO SELECT PLANTS
THAT HAVE MOST RP MARKERS AND SMALLEST %
OF DONOR GENOME
BC2

18.  Simpler method compared to phenotypic
screening
◦ Especially for traits with laborious screening
◦ May save time and resources
 Selection at seedling stage
◦ Important for traits such as grain quality
◦ Can select before transplanting
 Increased reliability
◦ No environmental effects
◦ Can discriminate between homozygotes and
heterozygotes and select single plants

19.  A literature review
indicates thousands of
QTL mapping studies but
not many actual reports of
the application of MAS in
breeding

20.  Resources (equipment) not available
 Markers may not be cost-effective
 Accuracy of QTL mapping studies
 QTL effects may depend on genetic background
or be influenced by environmental conditions
 Lack of suitable marker for polymorphism in
particular breeding material
 Poor integration of molecular genetics and
conventional breeding

21.  Cost-efficiency has rarely been
calculated but MAS is more expensive
for most traits
◦ Exceptions include quality traits
 Determined by:
◦ Trait and method for phenotypic screening
◦ Cost of glasshouse/field trials
◦ Labour costs
◦ Type of markers used

22. Institute Country Crop Cost estimate
per sample*
(US$)
Reference
Uni. Guelph Canada Bean 2.74 Yu et al. (2000)
CIMMYT Mexico Maize 1.24–2.26 Dreher et al. (2003)
Uni. Adelaide Australia Wheat 1.46 Kuchel et al. (2005)
Uni. Kentucky, Uni.
Minnesota, Uni.
Oregon, Michigan
State Uni., USDA-
ARS
United
States
Wheat and
barley
0.50–5.00 Van Sanford et al.
(2001)
*cost includes labour

23.  Large ‘gaps’ remain between marker
development and plant breeding
◦ QTL mapping/marker development have been
separated from breeding
◦ Effective transfer of data or information between
research institute and breeding station may not
occur
 Essential concepts in may not be understood
by molecular biologists and breeders (and
other disciplines)

24.  Improved cost-efficiency
◦ Optimization, simplification of
methods and future innovation
 Design of efficient and
effective MAS strategies
 Greater integration between
molecular genetics and plant
breeding
 Data management

25.  MAS has great
scope, because MAS
saves time and
labour. And these are
the most important
benefits in the
competetive field of
PLANT
BREEDING from
research point of view
and ultimately to give
food security to the
people of the world.