PRESENTED BY: Pawan NagarReg. no.: 04-2690-2015M.Sc.(Fruit Science)

Marker assisted selection

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.

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’.

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

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.

 

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.

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

QTL5 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%

1 2 3 4 5 6 7 8 1 2 3 4 5 6 7 8RM84 RM296

P1 P2

P1 P2

Not polymorphic Polymorphic!

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

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

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

(1) LEAF TISSUE SAMPLING

(2) DNA EXTRACTION

(3) PCR

(4) GEL ELECTROPHORESIS

(5) MARKER ANALYSIS

Overview of ‘marker

genotyping’

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

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

F2

F1Gene A + B

P1Gene A

x P1Gene B

MAS

Select F2 plants that have Gene A and Gene B

Genotypes

P1: AAbb P2: aaBB

F1: AaBb

F2AB 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

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

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

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

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

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

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

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

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)

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

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.