Lecture 18 - Molecular Markers | Plant Biotechnology - Botany PDF Download

 Page 1


Molecular Markers 
 
                                                                                              
 
 
 
 
 
Discipline: Botany 
Paper: Plant Biotechnology 
Lesson: Molecular Markers 
Lesson Developer: Ms. Namrata Dhaka 
Department/College: Department of Genetics, University of Delhi South 
Campus 
 
 
Page 2


Molecular Markers 
 
                                                                                              
 
 
 
 
 
Discipline: Botany 
Paper: Plant Biotechnology 
Lesson: Molecular Markers 
Lesson Developer: Ms. Namrata Dhaka 
Department/College: Department of Genetics, University of Delhi South 
Campus 
 
 
Molecular Markers 
 
2 
Institute of Lifelong learning, University of Delhi 
Learning Outcomes 
After reading this chapter, the readers should be able to understand the following: 
? What are molecular markers? 
? The basic terminology used with reference to markers like – polymorphism, 
dominant/codominant markers, indels, SNPs etc. 
? Different types of marker systems. 
? Hybridization based and PCR based markers. 
? The principle, methodology and relative advantages and disadvantages of five most 
commonly used type of molecular markers – RFLP, RAPD, AFLP, SSR and SNP. 
? Application of molecular markers, especially in context of plant breeding.
Page 3


Molecular Markers 
 
                                                                                              
 
 
 
 
 
Discipline: Botany 
Paper: Plant Biotechnology 
Lesson: Molecular Markers 
Lesson Developer: Ms. Namrata Dhaka 
Department/College: Department of Genetics, University of Delhi South 
Campus 
 
 
Molecular Markers 
 
2 
Institute of Lifelong learning, University of Delhi 
Learning Outcomes 
After reading this chapter, the readers should be able to understand the following: 
? What are molecular markers? 
? The basic terminology used with reference to markers like – polymorphism, 
dominant/codominant markers, indels, SNPs etc. 
? Different types of marker systems. 
? Hybridization based and PCR based markers. 
? The principle, methodology and relative advantages and disadvantages of five most 
commonly used type of molecular markers – RFLP, RAPD, AFLP, SSR and SNP. 
? Application of molecular markers, especially in context of plant breeding.
Molecular Markers 
 
3 
Institute of Lifelong learning, University of Delhi 
Table of Contents  
 
Chapter: Molecular Markers 
? Introduction  
? Advantages of molecular markers over morphological and 
biochemical markers 
? How can we visualize DNA? 
? Types of molecular markers 
? Restriction Fragment Length Polymorphism (RFLP) 
? Principle 
? Discovery 
? Method 
? Advantages 
? Disadvantages 
? Random Amplified Polymorphic DNA (RAPD) 
? Principle 
? Discovery 
? Method 
? Advantages 
? Disadvantages 
? Amplified Fragment Length Polymorphism (AFLP) 
? Principle 
? Discovery 
? Method 
? Advantages 
? Disadvantages 
? Simple Sequence Repeats (SSR) 
? Principle 
? Discovery 
? Method 
? Advantages 
? Disadvantages 
? Single Nucleotide Polymorphism (SNP) 
Page 4


Molecular Markers 
 
                                                                                              
 
 
 
 
 
Discipline: Botany 
Paper: Plant Biotechnology 
Lesson: Molecular Markers 
Lesson Developer: Ms. Namrata Dhaka 
Department/College: Department of Genetics, University of Delhi South 
Campus 
 
 
Molecular Markers 
 
2 
Institute of Lifelong learning, University of Delhi 
Learning Outcomes 
After reading this chapter, the readers should be able to understand the following: 
? What are molecular markers? 
? The basic terminology used with reference to markers like – polymorphism, 
dominant/codominant markers, indels, SNPs etc. 
? Different types of marker systems. 
? Hybridization based and PCR based markers. 
? The principle, methodology and relative advantages and disadvantages of five most 
commonly used type of molecular markers – RFLP, RAPD, AFLP, SSR and SNP. 
? Application of molecular markers, especially in context of plant breeding.
Molecular Markers 
 
3 
Institute of Lifelong learning, University of Delhi 
Table of Contents  
 
Chapter: Molecular Markers 
? Introduction  
? Advantages of molecular markers over morphological and 
biochemical markers 
? How can we visualize DNA? 
? Types of molecular markers 
? Restriction Fragment Length Polymorphism (RFLP) 
? Principle 
? Discovery 
? Method 
? Advantages 
? Disadvantages 
? Random Amplified Polymorphic DNA (RAPD) 
? Principle 
? Discovery 
? Method 
? Advantages 
? Disadvantages 
? Amplified Fragment Length Polymorphism (AFLP) 
? Principle 
? Discovery 
? Method 
? Advantages 
? Disadvantages 
? Simple Sequence Repeats (SSR) 
? Principle 
? Discovery 
? Method 
? Advantages 
? Disadvantages 
? Single Nucleotide Polymorphism (SNP) 
Molecular Markers 
 
4 
Institute of Lifelong learning, University of Delhi 
? Principle 
? Method 
? Advantages 
? Disadvantages 
? Comparison of different molecular marker systems 
? Applications of molecular markers 
? Mapping genes of interest 
? Marker assisted breeding 
? Assessment of genetic diversity 
? DNA fingerprinting 
? Summary  
? Exercise/ Practice 
? Glossary 
? References/ Bibliography/ Further Reading 
 
 
 
 
 
 
 
 
 
 
 
 
 
Page 5


Molecular Markers 
 
                                                                                              
 
 
 
 
 
Discipline: Botany 
Paper: Plant Biotechnology 
Lesson: Molecular Markers 
Lesson Developer: Ms. Namrata Dhaka 
Department/College: Department of Genetics, University of Delhi South 
Campus 
 
 
Molecular Markers 
 
2 
Institute of Lifelong learning, University of Delhi 
Learning Outcomes 
After reading this chapter, the readers should be able to understand the following: 
? What are molecular markers? 
? The basic terminology used with reference to markers like – polymorphism, 
dominant/codominant markers, indels, SNPs etc. 
? Different types of marker systems. 
? Hybridization based and PCR based markers. 
? The principle, methodology and relative advantages and disadvantages of five most 
commonly used type of molecular markers – RFLP, RAPD, AFLP, SSR and SNP. 
? Application of molecular markers, especially in context of plant breeding.
Molecular Markers 
 
3 
Institute of Lifelong learning, University of Delhi 
Table of Contents  
 
Chapter: Molecular Markers 
? Introduction  
? Advantages of molecular markers over morphological and 
biochemical markers 
? How can we visualize DNA? 
? Types of molecular markers 
? Restriction Fragment Length Polymorphism (RFLP) 
? Principle 
? Discovery 
? Method 
? Advantages 
? Disadvantages 
? Random Amplified Polymorphic DNA (RAPD) 
? Principle 
? Discovery 
? Method 
? Advantages 
? Disadvantages 
? Amplified Fragment Length Polymorphism (AFLP) 
? Principle 
? Discovery 
? Method 
? Advantages 
? Disadvantages 
? Simple Sequence Repeats (SSR) 
? Principle 
? Discovery 
? Method 
? Advantages 
? Disadvantages 
? Single Nucleotide Polymorphism (SNP) 
Molecular Markers 
 
4 
Institute of Lifelong learning, University of Delhi 
? Principle 
? Method 
? Advantages 
? Disadvantages 
? Comparison of different molecular marker systems 
? Applications of molecular markers 
? Mapping genes of interest 
? Marker assisted breeding 
? Assessment of genetic diversity 
? DNA fingerprinting 
? Summary  
? Exercise/ Practice 
? Glossary 
? References/ Bibliography/ Further Reading 
 
 
 
 
 
 
 
 
 
 
 
 
 
Molecular Markers 
 
5 
Institute of Lifelong learning, University of Delhi 
Introduction 
Often, you may have come across a situation where a passer-by asks you the way to reach 
a particular location. The way you generally answer them is through the help of certain 
landmarks and directions. For example, you may answer somewhat in this manner - you 
say, go straight take left from the school building, go straight till the traffic light signal, take 
right and then take a second right from under the flyover and if you go straight a little 
further, you shall reach your destination. In this case, you have used ‘school building’, 
‘traffic light signal’ and ‘flyover’ as landmarks to help the passer-by to reach his destination. 
In a similar way, in biology, one may define such landmarks called as ‘markers’ to 
characterize individuals or differentiate between any two individuals, for various research 
purposes especially plant and animal breeding, human genetics and forensics. 
The question that arises next is – what are we actually trying to ‘mark’ with these 
‘markers’? Markers are basically used to find the locations of genes of interests. The exact 
purpose and the overall methodology employing the markers to find a desired gene in any 
organism vary according to the different research goals. We shall discuss ahead, what are 
the various applications of markers.  
Taking the concept ahead, the next question that may arise in your mind is what is the 
exact nature of these markers? What are they actually – chemicals, molecules or any other 
attribute? Practically, any trait which exhibits variation between individuals can be used as a 
marker. Markers may be - 
? Morphological – Any trait visible to naked eye, example, plant height, flower color, fruit 
shape and so on. 
? Biochemical – Allozymes (isozymes) which are structurally different forms of the same 
enzyme. 
? Molecular – DNA markers. (allozymes are proteins, they may also be grouped as 
molecular markers but these days, the term ‘molecular markers’ is synonymously used 
for DNA markers and therefore allozymes are separately referred to as biochemical 
markers).  These DNA markers are essentially nothing but the landmarks on the genome 
of an individual, which can be visualized through various techniques to detect differences 
between small stretches of DNA of any two individuals.