Re: QTL mapping

Valeria,
You need a program to calculate your IBD and then you can fit the QTL as
a random effect eg

  animal !P
  fixed1 !I
  fixed2 !I
  fixed3 !I
  variate1 !M0
  variate2 !M0
   nqtl 800
pedigree.prn
invm5.giv

Datafile.txt !MAXIT 100
 
# Model 1 (Animal)
variate1 ~ mu fixed1 fixed2... !r animal nqtl
0 0 2
animal 1
animal 0 AINV 0.1 !GP
 
nqtl 1
nqtl 0 GIV1 0.1 !GP
 
 
I hope that will help. you then can plot -2log likelihood ratio test
values to map the QTL.
 
Ozzie
 

Oswald Matika

Oswald Matika
Div. Genetics and Genomics
The Roslin Institute and R(D)SVS,
University of Edinburgh
Roslin
Midlothian EH25 9PS
Scotland, UK

Tel: + (131) 527 4325
Fax: + (131) 440 0434
E-Mail: Oswald.Matika_at_roslin.ed.ac.uk

Web: www.roslin.ed.ac.uk

The University of Edinburgh is a charitable body, registered in
Scotland, with registration number SC005336
Disclaimer: This e-mail and any attachments are confidential and
intended solely for the use of the recipient(s) to whom they are
addressed. If you have received it in error, please destroy all copies
and inform the sender.

________________________________

From: ASReml users discussion group [mailto:ASREML-L_at_DPI.NSW.GOV.AU] On
Behalf Of valepacc
Sent: 02 October 2008 01:32
To: ASREML-L_at_DPI.NSW.GOV.AU
Subject: Re: QTL mapping

As I said above, if I had an answer I would post it to everyone...
These are then ones I get till this moment...
Thanks Jocelyn Poissant and Dr Gilmour

Please if someone else has something to add it would be so kind of
him/her to send it to the forum.
Valeria.

Hi Valeria,
Regarding your ASREML QTL mapping question you should contact Jon Slate
(j.slate_at_shef.ac.uk).
Jocelyn Poissant

_____________________________________________________

Dear Valeria,
A recent related paper is http://dx.doi.org/10.1016/j.csda.2008.04.004
It may have some useful references.
The main issue in association studies is to create the IBD matrix based
on genotyping an incomplete (unknown) pedigree.
The NRM represents the average relationship of an individual with its
relatives based on pedigree.
The IBD matrix looks at the specific inheritance of a particular allele
at a particular locus.
So far I have not worked on the issue of forming the IBD matrix, just
utilising it in ASReml.
May Jesus Christ continue to be gracious to you,
Arthur Gilmour, His servant .

-------------------- m2f --------------------

Sent using Mail2Forum (http://www.mail2forum.com).

Read this topic online here:
http://www.vsni.co.uk/forum/viewtopic.php?p=250#250

-------------------- m2f --------------------

This message is intended for the addressee named and may contain
confidential information. If you are not the intended recipient, please
delete it and notify the sender. Views expressed in this message are
those of the individual sender, and are not necessarily the views of
their organisation.
Received on Sat Oct 02 2008 - 07:50:35 EST