Lecture 4: Molecular Markers and Primer Design

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Total cards: 24•Content version: v4•Public deck•Updated: 8/1/2026

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Front (Question)

• DNA-based genetic markers occupying specific genomic loci

Back (Answer)

Molecular Markers

Front (Question)

• Acts as “flags” or sign of variation

Back (Answer)

Molecular Markers

Front (Question)

• Unaffected by environment; selectively natural

Back (Answer)

Molecular Markers

Front (Question)

Molecular markers acts as ____ or sign of _____

Back (Answer)

Flags; variation

Front (Question)

Different sources of variation detected by Molecular markers

Back (Answer)

• Substitution mutations (point mutations • Rearrangements • insertions or deletions (InDels) • Errors in replication of tandemly repeated DNA

Front (Question)

Advantages of Molecular Markers

Back (Answer)

• Practically unlimited in number • not affected by the environment • selectively natural

Front (Question)

Uses/applications of Molecular Markers

Back (Answer)

Genetic diversity analysis determination of population genetic structure linkage and association mapping for identification determination of hybridity parentage analysis phylogenetic/evolutionary relationships marker assisted selection (MAS) marker assisted breeding (MAB)

Front (Question)

refers to the presence of two or more variant forms of a specific DNA sequence that can occur among different individuals or populations

Back (Answer)

Polymorphism

Front (Question)

refers to the presence of two or more variant forms of a specific ____ ____ that can occur among ____ individuals or populations

Back (Answer)

DNA sequence; different

#10

Front (Question)

Types of Molecular Markers

Back (Answer)

• Restriction Fragment Length polymorphism • Random Amplified Polymorphic DNA (RAPD) • Amplified Fragment Length Polymorphism (AFLP) • Simple Sequence Repeats (SSRs) or Microsatellites • Variable Numbers Tandem Repeats (VNTR) • Single Nucleotide Polymorphism (SNPs)

#11

Front (Question)

• involves restriction digestion and hybridization Co-dominant marker • Single nucleotide alteration can create or destroy a restriction site

Back (Answer)

Restriction Fragment Length Polymorphism

#12

Front (Question)

Advantages of RFLP

Back (Answer)

Robust and Reliable

#13

Front (Question)

Disadvantage of RFLP

Back (Answer)

time-consuming, laborious, expensive Large amounts of DNA required Limited Polymorphism

#14

Front (Question)

Also known as Restriction Endonucleases - molecular scissors that cut DNA into fragments at specific sites in their sequence

Back (Answer)

Restriction Enzymes

#15

Front (Question)

What type of RFLP that cuts DNA at random far from their recognition sequences?

Back (Answer)

Type I

#16

Front (Question)

What type of RFLP that : cuts DNA at defined positions close to or within their recognition sequences

Back (Answer)

Type II

#17

Front (Question)

What type of RFLP cuts DNA outside of two recognition sequences in opposite orientations

Back (Answer)

Type III

#18

Front (Question)

What type of RFLP cuts modified DNA

Back (Answer)

Type IV

#19

Front (Question)

a type of Molecular Markers that is PCR based

Back (Answer)

RAPD (Random Amplified Polymorphic DNA)

#20

Front (Question)

advantage of RAPD

Back (Answer)

Quick and Simple Inexpensive Multiple loci from a single primer possible small amounts of DNA required

#21

Front (Question)

Disadvantages of RAPD

Back (Answer)

Problems with reproducitibility Generally not transferrable

#22

Front (Question)

• combines the accuration of restriction enzyme digestion with the precision of PCR • Dominant marker

Back (Answer)

Amplified Fragment Length Polymorphism (AFLP)

#23

Front (Question)

Three steps of AFLP

Back (Answer)

• Digestion of gDNA with one or more REs • Selective amplification • Electrophoretic seperation and visualization

#24

Front (Question)

Advantage of AFLP

Back (Answer)

Multi loci High levels of polymorphism generated