Finger printing using RM primer

[Junjian Ni]

Dear Narottam,

Here are two coins from me for your issue:

1. Firstly, I would like to say, for assessing genetic diversity and
cluter analysis, SSR (SSLP) should be much more informative and better
than RAPD. RAPD was developped after RFLP in quite early stage and
generally the results include a lot of false positive results. Currently
we have more than 2000 SSR markers available for rice, andexcept for some
special reasons such as screening library, I don't think there are too
many reasons to use RAPD markers for mapping or fingerprinting purpose.

2. You need some special data transferring and treatment for SSR marker
beforing generating genetic distance matrix. The basic procedure could be
as follows:

1) For each SSR marker, you can generate 1/0 matrix for germplasm which
are involved in your experiment base on whether they share same bands or
not.

Let's say, you have germplasm (G1, G2, G3, G4, ..., Gn), and for SSR
marker RM1, the matrix could be like this:

RM1---G1---G2---G3---G4...
G1---1---0---1---1...
G2---1---1---0---1...
G3---0---0---0---1...
G4---1---1---1---0...
...

"1" stand for if sharing same band for two germplam, "0" stand for having
different bands.
For m SSR markers, you can generate m sheets of 1/0 matrices.

2) Based on individual and separate sheets, you can generate a summerary
sheet [add 1 or 0 values of different sheets in same position (same row
and column if using spreadsheet)]. If two germplasm have more "1", that
means they are more closely related.

3) Following procedures would be very similar to using RAPD markers,
generate genetic distance matrix, doing cluster analysis based on that,
...
I assume you have no problem there.

You might get some ideas from the following paper:
http://www.gramene.org/perl/pub_search?ref_id=6996

You also can get more info from the following book:
Nei and Kumar: Molecular Evolution and Phylogenetics, Oxford Univ. Press 2000

Hope this info helpful to you. Good luck.

Junjian Ni
Gramene Curator



> Dear Rajkumar,
>        Here I am trying to tell u the actual problem. Look at the two
> attahed figure.
> In Figure RM-559 (Polymorphism scoring of  RILs of F-9) there is no
problem regarding scoring as the paprents shows disticts polymirphism,
But
> problem arise when we want to score a germplasm collection say two
variety
>  giving a specific band of same mole wt (fig RM-112) , then we can not
> differetite them by SSLP but in RAPD one variety giving 5 band and
another
> giving 4 so we can easily differetiate them.Now question is that thogh
in
> case RIL scoring (with SSLP)we give 1,2,3 score But in  case of
germplasm
> we give 1,0.And again in case of RAPD for every band produced by a
particular primer we give 1,0 scre.
> So, it is clear that for assessment genetic diversity and cluter
analysis
> RAPD is more informative than that of SSLP. But RAPD is random, which do
not take any information from genome sequence whereas SSLP primers are
in
> most cases Mapped marker but became less informative .
> Can you solve this paradox.
> 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)