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Dr N.I. Leaves nleaves at hgmp.mrc.ac.uk
Tue Jan 23 07:44:40 EST 2001

Hi Raja, I'm not sure about plant systems and SNPs.

In human populations SNPs have advantages and disadvantages in
genetic mapping studies.

In the last ten years or so di-, tri-, and tetranucleotide
repeat microsatellites have been widely used in mapping. These are
extremely informative in linkage studies where the large number of alleles
are exploited. However, their mutability makes them less useful in studies
of linkage disequilibrium where association between marker and disease
mutation might have drifted. In contrast SNPs are much more stable in
populations and are likely to be useful in studies of linkage
disequilibrium, especially if used in haplotypes. However, their
informativity is much lower when considered as single markers. In
humansib-pair studies, I think genome wide estimates of 8 or so SNPs to
replace a single microsatellite have been made.

SNPs occur at a greater frequency (>1 SNP/kb) than microsatellites so
there are plenty out there. Typing SNPs is however generally problematic
in mapping studies of outbred populations where large numbers of SNPs 
(many 1000s) typed on large numbers of DNAs would be needed in a genome
wide application. Currently, there are many commercial organisations
fighting to prove their technology is capable of large scale SNP genetic

I hope these ramblings are of some help

Best wishes

Nick Leaves

Dr N I Leaves
Mouse Sequencing - Production Manager
MRC HGMP Resource Centre
Cambridge CB10 1SB
tel: 01223 494557 (office) or 01223 494541 (lab)
email: nleaves at hgmp.mrc.ac.uk


On Mon, 22 Jan 2001, Dr Raja Kota wrote:

> Dear Netters,
> So far what I have read about SNPs, they are generally biallelic in a given
> population.  I am not sure whether this hold true in plant systems as well.
> in any case, is it advantageous in mapping studies to employ biallelic
> systems???.  If so, why?.
> Thanks in advance,
> Raj

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