Download single-nucleotide polymorphism

Synteny
- many distantly related species have colinear maps for portions of their
genomes; co-linearity between maize and
sorghum, between maize and rice.
- Once careful interspecific comparisons
have been made, predictions for gene
locations mapped in one species can be
made in the second
- regions that are sparsely mapped in one
species might be filled by markers from
the molecular map of the second species.
RAPD(randomly amplified pholymorphic DNA)
1) single short oligonucleotides primer (10mer-12mer) can
recognize similar sequences(complementary sequences) that are
opposed to each other at distances close enough for the
intervening sequence to be amplified in the PCR
2) because of the availability of random oligonucleotides and
easy assay, RAPD is simple matter to screen many loci rather
rapidly.
3) limit of RAPD;
priming polymorphism appears to be based on mismatches
with target sequences so that alleles are either present or
absent; no guarantee that the dominant allele will be present in
a second population, not always possible to mapin a new
population
Microsatellite(SSR;simple sequence repeat)
- assay is PCR based; electrophoresis is sufficient to
observe the results; reduce the time to obtain a result
compared with methods based on Southern blotting
- the use of radioisotopes can be avoided because the size
of polymorphism between alleles is large enough to be
seen in agarose gel or PAGE gel.
- co-dominant marker, prevalent in soybean, a species with
limited polymorphic markers in the past
- method is well-established in phage library by screen
with oligonucleotide probes
- quicker approach is to examine sequence databank for
their presence.
- AC repeats, most frequent class in human and mouse, AT
repeats, most prevalent in higher plants.
restriction fragment length
polymorphism (RFLP)
•
The occurrence of variation in the length of
DNA fragments that are produced after cleavage
with a type II restriction endonuclease. The
differences in DNA lengths are due to the
presence or absence of recognition site(s) for
that particular restriction enzyme. RFLPs were
initially detected using hybridization with DNA
probes after separation of digested genomic
DNA by gel electrophoresis (Southern analysis).
Now they are typically detected by
electrophoresis of digested PCR product.
A single-nucleotide polymorphism
• A single-nucleotide polymorphism (SNP, pronounced snip) is
a DNA sequence variation occurring when a single nucleotide
— A, T, C, or G — in the genome (or other shared sequence)
differs between members of a species (or between paired
chromosomes in an individual) which was discovered by Dr.
Steve Ligget. For example, two sequenced DNA fragments
from different individuals, AAGCCTA to AAGCTTA, contain a
difference in a single nucleotide. In this case we say that there
are two alleles : C and T. Almost all common SNPs have only
two alleles.
• Within a population, SNPs can be assigned a minor allele
frequency — the lowest allele frequency at a locus that is
observed in a particular population. This is simply the lesser of
the two allele frequencies for single-nucleotide polymorphisms.
There are variations between human populations, so a SNP
allele that is common in one geographical or ethnic group
may be much rarer in another.