PCR product with RM-473D

[Pankaj Jaiswal]

Dear Narottam,

If you search for marker name "RM337" at
http://www.gramene.org/db/markers/marker_view

You will get to a record e.g. 
http://www.gramene.org/db/markers/marker_view?marker_name=rm337&marker_type=&Submit=

On this page though the image is not available, look for the section 
Expected PCR Product Size  	192
Source Germplasm 	IR36

It suggests that the band size authors Temnykh et. al got was 192bp band 
from IR36.

Similarly if you click at the
Genome Positions  	 Search for Genome Positions
If the marker has been mapped on the sequenced rice genome based on our 
electronic PCR (computational), you will see a bp position  (146952 bp - 
147138 bp). This will help you to find that you are expected to get a 
product of 187bp from Nipponbare, which is a japonica cultivar.

In any case you do not need a sophisticated instrumentation for 
determining the band size. Just run a DNA ladder marker in the size 
range next to your amplified band in the same gel and then calculate the 
bp length based on the rf distance and mol size in bp plotted on the log 
paper. I am sure any good molecular biology protocol book would help.


Pankaj



narottam dey wrote:
>   
> Respected all,
>          I am getting a PCR product of arround 143 bp in IR-36 rice variety using RM-337.I have no sophisticated instrumental facility for determination of mol wt. so I request you all if somebody have already used that RM primer please tell me the PCR product size expected.
> Thanking you.
> With regards,
> Narottam 
> 
> Narottam Dey.
> Senior Research Fellow.
> Dept Of Botany
> Bose Institute.
> 93/1,APC road,
> Kolkata-700009,(W.B)
> India.
> Ph-91-33-23679670 (R),23506619-ext-330(o)

-- 
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Pankaj Jaiswal, PhD
G15-Bradfield Hall
Dept. of Plant Breeding
Cornell University
Ithaca, NY-14853, USA

Tel: +1-607-255-3103
      +1-607-255-4109
Fax: +1-607-255-6683
http://www.gramene.org
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