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Molecular Markers

This document discusses different types of genetic markers that can be used as tools to identify species and individuals. It describes phenotypic markers, biochemical markers, and genetic/DNA/molecular markers. Molecular markers are further classified based on mode of gene action as co-dominant or dominant, and method of detection as hybridization-based or PCR-based. Commonly used molecular markers like RFLP, AFLP, RAPDs, SSRs, SCAR, CAPs, and SSCP are also outlined. The document discusses applications of molecular markers in plants, including construction of linkage maps, QTL mapping, marker-assisted selection, marker-assisted backcrossing, and marker-assisted pyramiding.

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saroj Burlakoti
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192 views42 pages

Molecular Markers

This document discusses different types of genetic markers that can be used as tools to identify species and individuals. It describes phenotypic markers, biochemical markers, and genetic/DNA/molecular markers. Molecular markers are further classified based on mode of gene action as co-dominant or dominant, and method of detection as hybridization-based or PCR-based. Commonly used molecular markers like RFLP, AFLP, RAPDs, SSRs, SCAR, CAPs, and SSCP are also outlined. The document discusses applications of molecular markers in plants, including construction of linkage maps, QTL mapping, marker-assisted selection, marker-assisted backcrossing, and marker-assisted pyramiding.

Uploaded by

saroj Burlakoti
Copyright
© © All Rights Reserved
We take content rights seriously. If you suspect this is your content, claim it here.
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Download as PPTX, PDF, TXT or read online on Scribd
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Markers

Gene or DNA sequence at known location on a chromosome, that can


be used as tool for identifying a species or individual
Identify either presence or absence of any character in the individual
Keys to unravel the genetic basis of quantitative traits
Usually inherited
1. Phenotypic/Morphological/classical/visible markers
usually identified visually
eg: traits such as flower color, seed shape,
growth habits or pigmentation
2. Biochemical Markers
Exploits variation in expressed product
Eg: proteins, isozymes
• Diff in enzymes that are detected by electro-
phoresis and specific staining.
Phenotypic Markers
• Influenced by environment or developmental stage of plant
• Limited in number
3. Genetic/DNA/
molecular markers
• substitution mutations
• rearrangements
(insertions or deletions)
• errors in replication
of tandemly repeated
DNA
Classification of molecular markers
Mode of gene action
co-dominant: SSR, STR, RFLP
Dominant: ISSR,RAPD,AFLP
Method of detection
Hybridization based molecular markers
PCR based markers
Widely used molecular markers

• Restriction fragment length polymorphism (RFLP)


• Amplified fragment length polymorphism (AFLP)
• Random amplified polymorphic DNAS (RAPDs)
• Micro satellite markers ( simple sequence repeats- SSRs)
• Sequence characterized amplified region markers (SCAR)
• Cleaved amplified polymorphic sequences (CAPs)
• Single strand conformational polymorphism (SSCP)
Advantages
1) time saving
2) stability and reliability
3) Biosafety
4) Performance
5) Precise selection of the complex traits
Desirable genetic markers features
• show high level of genetic polymorphism;
• be co-dominant (heterozygous individuals can be distinguished from homozygous one);
• allelic features should be clearly distinguished in them (so, the different alleles can be
easily detected);
• have appropriate distribution throughout the genome;
• have neutral selection;
• have an easy tracking (the entire process can be automated easily);
• low-cost genotyping;
• have a high repeatability (the data can be stored and shared between laboratories)
• Suitable DNA markers should be polymorphic in the DNA level and can be expressed in
all tissues, organs, and various developmental stages
Applications of Molecular Markers in
Plants
1. Construction of linkage maps
Linkage maps are used to identify chromosomal
regions that contain single gene traits
(controlled by a single gene) and
quantitative traits using QTL analysis

In order to use the genetic information that has been


provided by molecular markers, it is important to know
the relative location of molecular markers on chromosomes
Indicate position & genetic distances between markers along
chromosomes

Main use: find location of genes and QTLs


2. Construction of QTL mapping
QTL mapping is based on marker segregation via chromosome
recombination during meiosis
in which those markers which are tightly linked with each other will be
transferred together more commonly during recombination as
compared to those which are away from each other.
Principle of QTL Mapping
Methods to detect QTLs using single
marker Analysis
• T test
Describing QTLs detected from interval
mapping
• Flanking markers used
• selection based on
two markers more reliable
• Recombination chance low
3. Marker Assisted Selection
Method in which phenotype is selected on the genotype of markers.
Steps required for the development of markers for use in MAS includes:
I. High resolution mapping
II. Validation of markers
III. Marker conversion
I. High resolution mapping of QTLs
population sized use greater than 1000 to minimize distance <1cM
II. Validation of Markers
testing reliability of markers to predict phenotype
Testing effectiveness in determining target phenotype in independent
populations and different genetic backgrounds
III. Marker Conversion
problems of reproducibility
marker technique complicated, time consuming or expensive
4. Marker Assisted Back Crossing
• Conventional breeding methods takes 6-8 backcrosses to fully recover
parent genome
• Though average % of recurrent parent genome is 75% ( for entire BC1
population) some individuals may possess more
• Tightly linked marker flanking QTLs and evenly spaced markers from
other chromosomes can be used
5. Marker Assisted Pyramiding
 Evolution and phylogeny
dependent on chloroplast genome sequence data
 Investigation of heterosis
various crops such as in rice, wheat, maize and rape seed
SSRs mainly used
 Identification of haploid/diploid plants and cultivars genotyping
haploid/DH plants used as mapping population for QTL
integration of physical and genetic maps allowing accurate detection of
candidate genes of interest
R1-nj (Navajo) anthocyanin color marker, SSR, SNP
Thank you !!!

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