Genetic Polymorphisms and Techniques in Genomics

These flashcards cover key terms and concepts related to genetic polymorphisms and various molecular techniques used in genomics.

Probe

A molecule (DNA, RNA, protein, or lectin) with specific interactions used to detect or bind to a target.

Genetic Polymorphism

The coexistence of multiple alleles at a locus

Single Nucleotide Polymorphism (SNP)

A change in a single nucleotide between alleles, impacting gene function and phenotype.

Restriction Fragment Length Polymorphisms (RFLPs)

Polymorphisms detectable through restriction digest analysis, used for genetic mapping and linking markers to phenotypes.

Molecular Marker

An identifiable DNA sequence at a specific genome location, transmitted by Mendelian inheritance, but does not represent a gene.

target

molecule of interest, can be DNA, RNA, protein, or a chemical

what can a target be bound to

a membrane, microtitre plate, or a microscope slide

original mendelian view of genome

alleles are either wild type or mutant

Polymorphic

any site at which multiple alleles exist as stable components of the population

when is an allele defined as polymorphic

if present >1% frequency in the population

Mutations that result in different protein function give a change in

phenotype

restriction digests maps of alleles may also be polymorphic therefore

different from eachother - a phenotype

how do alleles differ in nucleotides

in single or multiple nucleotides

what gives a polymorphism when deleted

a restriction site may be deleted or added

RFLP analysis: restriction map

independent of gene function, and a polymorphism at this level can be detected irrespective of whether the sequence change affects the phenotype

RFLP analysis: where is recombinant frequency measured

between a restriction marker and a visible phenotypic marker

RFLP analysis: what can a genetic map include

a genotype and a phenotype

what can be the basis for linkage maps

RFLPs and SNPs

what are RFLPs and SNPs useful for

establishing parent-offspring relationships

RFLP analysis: what is the tight linkage of a restriction marker to a mutant phenotype used for

to link a marker to a target gene

RFLP analysis: what would be ideal for a marker and phenotype

to have 100% linkage and not be separated by a recombination event

RFLP analysis: what can RFLP markers be used for?

diagnostic procedure for disease detection and map based cloning

RFLP analysis: how does RFLP detect disease

a marker is linked to a phenotype

what can be used to identify heredity unequivocally

the variation between microsatellites or minisatellites

what is a short tandem repeat (STR) in DNA

polymorphism resulting from a pattern of microsattelite DNA

STR: What are repetitive regions in the genome?

Repetitive regions in the genome are areas that consist of two or more nucleotides repeated in tandem.

what sequence is usually found in non coding genomic DNA

CATG

how can a unique genetic profile of an individual be created

examination of several STR loci and counting the repeats of a specific STR sequence

how many published STR sequences are there in the human genome

over 10,000

prevalent analysis method for determining genetic profiles in forensic cases

what is a pro of STR analysis

give a high degree of error free data while being robust enough to survive degradation in non-ideal condidtions

what is RAPD

random amplified polymorphic DNA

RAPD: what happens because of its short sequence

the oligonucleotide will pair with chromosomal DNA at many sites

RAPD: when do the strands get amplified

when the stands face each other in opposite directions

RAPD: What conditions allow for amplification of target DNA using primers?

A primer can hybridize to both strands of the target DNA in the proper orientation when the two sites are about 100-3000bp from each other.

RAPD: can PCR be used to generate polymorphisms

9-10bp PCR olignucleotide primers, no palindrome sequences, GC content of 50-80%

why is selecting the right sequence for the primer important

because different sequences will produce different band patterns and possibly allow for a more specific recognition of individual strains

SCAR

sequence characterized amplified region

what is a scar

RAPD fragments that map close to a trait of interest

what size primers are used for SCAR

15-30bp primers

why does SCAR need longer primers

so they do not face the problem of low reproducibility generally encountered with RAPDs

AFLP

amplified fragment length polymorphism

what is AFLP-PCR

a highly sensitive method for detecting polymorphisms that includes the restriction digest of RFLP and the PCR-based protocol of RAPD

a method of generating even greater numbers of unique polymorphisms

AFLP-PCR

what are the 3 basic steps of AFLP

1. digest genomic DNA with one or more restriction enzymes, and ligate to linker adaptors to a restriction fragment

2. PCR primers made for the adapters and a small selective sequence are used to amplify specific regions. the additional small sequence with the adapters allows for selective amplification of some of these fragments

3. gel electrophoresis of the amplicons to visualize the band pattern