Re: Format of pedigree data in BLUP-analysis

Hi,
Basically, as Greg said, individuals without a pedigree are treated as
founders yet they are not founders. These individuals should appear as
outlier (compared to the real founders) because they potentially include
all the genetic changes since the population was founded. Since the
variance component estimates only apply to the base/founder population,
these individuals artificially increase estimates because that genetic
change is unaccounted for. Thus the requirement of genetic groups.

For example, see
C. Pieramati and L. D. Van Vleck 1993. Effect of genetic groups on
estimates of additive genetic variance
http://jas.fass.org/cgi/content/abstract/71/1/66

Díaz, C.; Moreno, A.; Carabaño, M. J. 2002. Effects of genetic groups on
estimates of variance components for a maternally influenced trait in
the Spanish Limousine
Journal of Animal Breeding and Genetics, Volume 119, Number 5, October
2002 , pp. 325-334(10)
http://www3.interscience.wiley.com/journal/118922871/abstract?CRETRY=1&SRETRY=0

If you have very few unknown individuals relative to known contemporary
individuals then you should just remove these unknown individuals as the
contemporary mean should be well estimated.

Bruce

On 10/13/2009 06:19 PM, Greg Dutkowski wrote:
>
> Joao Costa e Silva has found in the forestry context that including
> such individuals in the analysis can lead to quite large differences
> in the estimates of the additive variance. We standardly apply an
> extra units variance with a possible positive or negative variance
> (sorry, don't know the R way of doing that) to such analysis to avoid
> bias in the variance estimates. Or we exclude them from variance
> estimation.
>
> I don't know why this happens, but presumably as individuals with no
> parents these are treated as unrelated founders in the pedigree and
> are somehow given high weight in the variance estimation. They may,
> in fact, be related, or they may come from different populations.
>
> Greg Dutkowski
>
> Quantitative Geneticist
>
> PlantPlan Genetics http://www.plantplan.com
>
> c/- School of Plant Science
>
> University of Tasmania
>
> Private Bag 55
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>
> *From:* ASReml users discussion group [mailto:ASREML-L_at_DPI.NSW.GOV.AU]
> *On Behalf Of *Christof Pietsch
> *Sent:* Tuesday, 13 October 2009 7:41 PM
> *To:* ASREML-L_at_DPI.NSW.GOV.AU
> *Subject:* Format of pedigree data in BLUP-analysis
>
> Dear all,
> I'd like to know, if entries with no pedigree information but with
> phenotypes have to be incorporated in the pedigree-data for the
> calculation of the numerator relationship matrix in a BLUP-analysis
> using the VPEDIGREE-directive.
> Thank you very much in advance!
> Christof
>
>
>
>
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Received on Thu Oct 14 2009 - 11:50:02 EST