[Jun Jian Ni]

Dear Dr. Sabu,

I would like to briefly answer your question. Maybe Dr. Noel Yap
(curator for map and marker in Gramene) will give you additional
comments.

While constructing genetic map and mapping QTL, first factor we should
consider is a good coverage of markers over the genome (we hope to
detect most QTLs on genome for particular traits). Thus, probably we
should consider distance on chromosome first (the position of the marker
on chromosome). From 600 SSR markers, you can pick up around 150 markers
based on their position on the map (the distance between markers had
better be less than 20 cM). You can use this marker set to do parental
survey and the polymorphic markers from parental survey can be used for
population genotypic analysis.

Other info from SSR table will be also helpful for your study. From
Number of alleles and PIC value, you can have general info on
polymorphic rate for markers. Anneal temperature can be help you to do
PCR amplification. You can get more detail description of those
parameters from the following papers:

1.Temnykh-S, DeClerck-G, Lukashova-A, Lipovich-L, Cartinhour-S,
McCouch-S.
Computational and experimental analysis of microsatellites in rice
(Oryza sativa L.): frequency, length variation, transposon associations,
and genetic marker potential. Genome research, 2001, vol.11, pp1141-1451

2. Temnykh-S, Park-W-D, Ayres-N-M, Cartinhour-S, Hauck-N, Lipovich-L,
Cho-Y-G, Ishii-T, McCouch-S-R. Mapping and genome organization of
microsatellite sequences in rice (Oryza sativa L.)  Theoretical and
applied genetics, 2000, vol.100, pp697-712
3. Chen-X, Temnykh-S, Xu-Y, Cho-Y-G, McCouch-S-R. Development of a
microsatellite framework map providing genome-wide coverage in rice
(Oryza sativa L.)  Theoretical and applied genetics, 1997, vol.95,
pp553-567

We hope this info helpful and please let's know if you have further
questions.

Junjian Ni
Phenotype curator in Gramene


Sabu wrote:

> Hello,
>
> My question is on the selection of microsatellite
> markers for QTL mapping in rice. We would like to
> analyse, say 150 RM markers and from the available
> list of 600 markers in the gramene site
> (http://www.gramene.org/microsat/RM_primers.html)
> which ones we can select? What are the criteria? There
> are things like Distance on chromosome, Repeat type
> and length, No. of alleles, PIC, PCR product in, Size
> range, Anneal temp (ºC) etc. Can you please comment on
> this problem.
>
> Thanks.. Sabu
>
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