Genomics Terms

Morphological Markers

Identifying individuals with a desired trait by phenotype (shape, size, color, etc)

• These happen due to variation in alleles of individuals within a population

Molecular Markers

Identifying differences among individuals by the DNA sequences present

• uses RFLP/AFLPs, SNPs, and VNTRs

• can be due to base pair changes, insertions, deletions, rearrangements, variation in repeat numbers etc

Physical maps (restriction maps)

are based on physical distance between markers (restriction enzyme cut sequences)

• DNA sequence gives the order/spacing of genes

DNA sequence variation

• Harmless (but may change phenotype)

• Harmful (diabetes, cancer, heart disease, Huntington’s disease, and hemophilia)

• Latent (sequence variation who are not harmful on their own, but only become apparent under some conditions)

  • Ex: chances of lung cancer become increase if one smokes

Polymorphism

Changes in the DNA sequence

• May or may not affect gene function

• Originally result form mutations

Types of Polymorphism

• SNP (Single Nucleotide Polymorphism)

• VNTR (Variable number Tandem Repeats)

SNP (Single Nucleotide Polymorphism)

Single base pair change present in at least 1% of the population

• Has to be in the population

VNTR (Variable number of tandem requests)

Tandemly repeated short DNA sequence

• Also called SSR’s. micro-satellites and STR’s

RFLP

Restriction fragment length polymorphism

• changes in the DNA sequence that adds or removes a restriction enzyme recognition site

• Variation in restriction site locations between individuals in a population

• Used to detect polymorphisms in DNA sequences.

AFLP

Amplified Fragment Length Polymorphism

• Variations in restriction site locations of DNA amplified by PCR between individuals in a population

Separating DNA by Electrophoresis

DNA is highly negatively charged and Electrophoresis pulls the DNA through the gel towards a positive charge

2 common ways to identify RFLPs in people

• PCR then running gel for AFLP

• Southern Blot for RFLP

Steps for Electrophoresis

1- Isolate the DNA from the individual

2- PCR amplify part of the genome

3- cut PCR DNA with RE

4- Run DNA on agar gel

PCR

Polymerase Chain Reaction

• Selectively amplifies a small region of DNA exponentially; once a small part is cut and copied to keeps doing it till there is many

PCR reaction requires

• Template DNA

• Primer specific to region you want to amplify

• Nucleotides (dNTPs)

• Taq Polymerase

Southern Blot

Technique to identify DNA fragments that are complementary to a known DNA sequence

Steps of a southern bolt

1- Isolate the DNA

2- Digest DNA with RE

3- Run DNA on gel

4- Transfer DNA to membrane → southern blot

• DNA strain is in the same position

• detects DNA

5- Add probe

• Band (hybridized) to complementary DNA sequence

• has identified label to find bound probe

Gene probe

Short fragment of known sequence of DNA that will base-pair (hybridize) with a stretch of DNA that is complementary

Hybridization

Single stranded DNA probe binds with complementary single-stranded DNA on membrane