RE: Diallel

To: asreml@chiswick.anprod.CSIRO.au
Subject: RE: Diallel
From: arthur.gilmour@agric.nsw.gov.au
Date: Thu, 10 Jan 2002 10:27:42 +1000
Sender: asreml-owner@lamb.arm.li.csiro.au

>
> Dear Luis,
> My comments are inserted below.
>
> Arthur
>
> <><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><>
> <><><><><><>
> Arthur Gilmour PhD
> mailto:Arthur.Gilmour@agric.nsw.gov.au
> Principal Research Scientist (Biometrics) fax:
> <61> 2 6391 3899
> NSW Agriculture
> <61> 2 6391 3922
> Orange Agricultural Institute telephone
> work: <61> 215
> Forest Rd, ORANGE, 2800, AUSTRALIA home:
> <61> 2 6364 3288
> mobile:
> <61> 4 1964 7675
> ASREML is available by anonymous ftp from pub/aar on
> ftp.res.bbsrc.ac.uk
> or point your web browser at ftp://ftp.res.bbsrc.ac.uk/pub/aar/
>
> To join the asreml discussion list, send the message
> subscribe
> mailto:asreml-request@chiswick.anprod.CSIRO.au
>
> To send messages to the list, mailto:asreml@chiswick.anprod.CSIRO.au
>
> Asreml list archive: http://www.chiswick.anprod.csiro.au/lists/asreml
>
> <> <> <> <> <> <> <>
> "Blessed are the peacemakers,
> for they shall be called sons of God" Jesus; Matthew 5:9
>
> <><><><><><><><><><><><><><><><><><><><><><><><><><><><><><><>
> <><><><><><>
>
>
>
>
>
> "Luis A. Apiolaza" <Luis.Apiolaza@utas.edu.au>
> Sent by: asreml-owner@lamb.arm.li.csiro.au
> 09-01-02 02:56 PM
> Please respond to "Luis A. Apiolaza"
>
>
> To: asreml@chiswick.anprod.csiro.au
> cc:
> Subject: Analysis of diallel experiment
>
>
> Hi everybody,
>
> We are currently analysing results from a full diallel test of 8
> parents, including reciprocal but no selfs. Well, almost full; there
> are a few missing crosses. I would like to get some comments about the
> coding used for this analysis:
>
> Models for diallel experiment in globulus
> tree !P
> female 670
> male 670
> mum 670
> dad 670
> repl 7
> sca !A
> reciprocal !A
> germ_rate
> ...
> dat2.csv !csv
> dat2.csv !csv !maxit 20 !dopart $A
>
>
> The first model is:
> !part 1
> germ_rate ~ mu repl !r female and(male) sca reciprocal
> 0
>
> where mu is overall mean, repl, replicate for the experiment, female
> and(male) overlays the design matrices for female and male to get a
> unique prediction for gca, sca is a family code where crossing AxB is
> equivalent to crossing BxA, and reciprocal is a unique family code
> where the cross AxB is different from cross BxA. This seems to work
> fine.
>
> *Note 1* although tree is defined as !P we are not using the pedigree
> factor for !part 1 and 2. We will do it with other traits later.
> *Note 2* Although there are only 8 parents, they are coded as
> 550, 570,
> etc.
> We did not use !I here because females and male appear in different
> order and we think that this wouldn't work OK when overlaying the
> design matrices (Arthur: any comments with respect to this?).
>
> *** It seems a bit excessive to set up a 670 level factor
> when all you
> want is
> 8 levels.
> If you were not already using the !P qualifier, you could use this to
> recode
> male and female conformably by creating a pedigree file with
> the 8 parents
> and 0 0 for their parents.
>
> Since there are only eight you could use the !SUB qualifier
> e.g.
> female 8 !SUB 550 570 590 610 630 650 670
> male 8 !SUB 550 570 590 610 630 650 670
> mum 8 !SUB 550 570 590 610 630 650 670
> dad 8 !SUB 550 570 590 610 630 650 670
>
>
> In this case where the codes are equally spaced, you could
> also transform
> them
> using eg
> female 8 !-530 !/20
>
> [It would be safer to use !-529 !/20 just incase rounding
> errors disrupt
> the
> conversion of the recoded values to integers when using
> them as factor
> levels.
>
> END ***
>
> After a few discussions, we extended the model to:
> !part 2
> germ_rate ~ mu repl !r female and(male) mum dad sca reciprocal
> 0
>
> the codes for mum and dad are identical to female and male
> respectively, but we used different names to force ASReml to fit the
> factors, given that were already fitted using female and(male).
> According to our interpretation this would fit common maternal (mum)
> and common paternal (dad) effects. These two extra terms would include
> common environment and any non-nuclear genetic effects.
>
> **** There sould be a singularity in the AI matrix under this model
> because of the association between mum, dad and 'female and(male)'
> Therefore it would be sufficient to include only one of mum and dad.
> CHECK for a singularity. It may be associated with the RESIDUAL.
> If you chose to include dad, then you could infact include it
> as 'male'
> since 'male' is not the same as 'and(male)'
>
> You could infact use female and(male) male and(female,-1)
>
> Of cource, the 'reciprocal' model term is just 'female.male'
>
> You could create the 'sca' term as 'male.female and(female.male)'
>
> END ****
> Running part 2 we get that mum is significant, while dad isn't. This
> would be expected with our experience in controlled pollination.
>
> At the same time sca appears to be non-significant for this
> trait, but the reciprocal is significant (the same happens with !part
> 1). I'm not yet fully convinced that what you are crossing is not
> significant but that the order matters, but it seems that there are
> some special cases where this could be true.
>
> Upto this stage I have mentioned models fitting only the parental
> values, but not producing results for all individuals. I assume that
> a way to get predicted values for all individuals (for the case of
> growth, for example) would be to change the beginning of the model
> equation to:
>
> !part 3
> germ_rate ~ mu repl !r tree mum dad sca reciprocal
> 0
>
> where tree would have the role of female and(male) on terms of taking
> into account additive effects. A question here, would this be
> different from running !part 2 but defining the factors at the
> beginning as:
> tree
> female !P
> male !P
> ...
>
> I would really appreciate to receive your comments on the models and
> any other alternative models that you have tried for this type of
> mating design.
>
> *****
> This final model would be equivalent but the predictions for the
> individual
> trees would be different. In the latter case, they would be based
> purely on the parental values. In the former case, they would include
> their own information.
>
> END *****
> Best regards,
>
>
> Luis
>
> --
> Dr Luis A. Apiolaza
> Quantitative Geneticist
> CRC for Sustainable Production Forestry
> School of Plant Science
> University of Tasmania
> GPO Box 252-55
> Hobart TAS 7001
> Australia
>
> phone: +61-3-6226 2213
> fax: +61-3-9229 2698
> email: mailto:luis.apiolaza@utas.edu.au
>
> 'There is no intellectual exercise which is not
> ultimately useless' --Jorge Luis Borges
> http://www.scieng.utas.edu.au/plantsci/
> http://www.geocities.com/uncronopio/
> ;-)
>
> --
> Asreml mailinglist archive:
> http://www.chiswick.anprod.csiro.au/lists/asreml
>
>
>
> --=_alternative 000AD829C9256B3D_=
> Content-Type: text/html; charset="us-ascii"
>
>
> 
> Dear Luis,
> My comments are inserted
> below.
> 
> Arthur
> 
> face="sans-serif"><><><><><><
> ><><><><><><><>&l
> t;><><><><><><><>
> <><><><><><><><&g
> t;<><><><><><><><> 
> Arthur Gilmour PhD            
>      mailto:Arthur.Gilmour@agric.nsw.gov.au 
> Principal Research Scientist (Biometrics)    
>        fax: <61> 2 6391 3899 
> NSW Agriculture            
>                
>               <61> 2
> 6391 3922 
> Orange Agricultural Institute        
>             telephone work:
> <61> 215 
> Forest Rd, ORANGE, 2800, AUSTRALIA      
>            home: <61> 2
> 6364 3288 
>                
>                
>                
>  mobile: <61> 4 1964 7675 
> ASREML is available by anonymous ftp from pub/aar on
> ftp.res.bbsrc.ac.uk 
>    or point your web browser at
> ftp://ftp.res.bbsrc.ac.uk/pub/aar/ 
> 
> To join the asreml
> discussion list, send the message   
>     subscribe 
> mailto:asreml-request@chiswick.anprod.CSIRO.au
> 
> To send messages to the
> list, mailto:asreml@chiswick.anprod.CSIRO.au
> 
> Asreml list archive:
> http://www.chiswick.anprod.csiro.au/lists/asreml
> 
>      
>                
>   <> <> <> <> <> <>
> <> 
> "Blessed are the peacemakers, 
>        for they shall be called sons of
> God"   Jesus; Matthew 5:9
> 
> face="sans-serif"><><><><><><
> ><><><><><><><>&l
> t;><><><><><><><>
> <><><><><><><><&g
> t;<><><><><><><><
> >
> 
> 
> 
> 
> <table width=100%>
> <tr valign=top>
> <td>
> <td>"Luis A.
> Apiolaza" <Luis.Apiolaza@utas.edu.au>
> Sent by:
> asreml-owner@lamb.arm.li.csiro.au
> 09-01-02 02:56 PM
> Please respond to
> "Luis A. Apiolaza"
> 
> <td>        
>      
>   To:      
>  asreml@chiswick.anprod.csiro.au
>      
>   cc:        
>      
>   Subject:        Analysis of
> diallel experiment</table>
> 
> 
> Hi everybody, 
> 
> We are currently analysing results from a full diallel test of 8 
> parents, including reciprocal but no selfs. Well, almost
> full; there 
> are a few missing crosses. I would like to get some comments
> about the 
> coding used for this analysis: 
> 
> Models for diallel experiment in globulus 
> tree   !P 
> female 670 
> male   670 
> mum    670 
> dad    670 
> repl   7 
> sca        !A 
> reciprocal !A 
> germ_rate 
> ... 
> dat2.csv   !csv 
> dat2.csv   !csv !maxit 20 !dopart $A 
> 
> 
> The first model is: 
> !part 1 
> germ_rate ~ mu repl !r female and(male) sca reciprocal 
> 0 
> 
> where mu is overall mean, repl, replicate for the experiment,
> female 
> and(male) overlays the design matrices for female and male to
> get a 
> unique prediction for gca, sca is a family code where
> crossing AxB is 
> equivalent to crossing BxA, and reciprocal is a unique family code 
> where the cross AxB is different from cross BxA. This seems
> to work 
> fine. 
> 
> *Note 1* although tree is defined as !P we are not using the
> pedigree 
> factor for !part 1 and 2. We will do it with other traits later. 
> *Note 2* Although there are only 8 parents, they are coded as
> 550, 570, etc. 
> We did not use !I here because females and male appear in
> different 
> order and we think that this wouldn't work OK when overlaying the 
> design matrices (Arthur: any comments with respect to this?).
> 
> *** It seems a bit
> excessive to set up a 670 level factor when all you want is
> 8 levels.
> If you were not already
> using the !P qualifier, you could use this to recode
> male and female
> conformably by creating a pedigree file with the 8 parents
> and 0 0 for their parents.
> 
> Since there are only
> eight you could use the !SUB qualifier
> e.g.  
>  female 8  !SUB
> 550 570 590 610 630 650 670 
> male   8  !SUB 550 570 590 610 630 650 670 
> mum    8  !SUB 550 570 590 610 630 650 670 
> dad    8  !SUB 550 570 590 610 630 650 670 
> 
> 
> In this case where the
> codes are equally spaced, you could also transform them
> using    eg
>   
>  female 8 !-530 !/20
> 
> [It would be safer to use
> !-529 !/20  just incase rounding errors disrupt the
>   conversion of the
> recoded values to integers when using them as factor levels.
> 
> END ***
> 
> After a few discussions, we extended the model to: 
> !part 2 
> germ_rate ~ mu repl !r female and(male) mum dad sca reciprocal 
> 0 
> 
> the codes for mum and dad are identical to female and male 
> respectively, but we used different names to force ASReml to
> fit the 
> factors, given that were already fitted using female and(male). 
> According to our interpretation this would fit common
> maternal (mum) 
> and common paternal (dad) effects. These two extra terms
> would include 
> common environment and any non-nuclear genetic effects. 
> 
> ****   There sould
> be a singularity in the AI matrix under this model
> because of the
> association between mum, dad and 'female and(male)'
> Therefore it would be
> sufficient to include only one of mum and dad.
> CHECK for a singularity.
>  It may be associated with the RESIDUAL.
> If you chose to include
> dad, then you could infact include it as 'male'
> since 'male' is not the
> same as 'and(male)'
> 
> You could infact use
>   female and(male)  male and(female,-1)
> 
> Of cource, the
> 'reciprocal' model term is just 'female.male'
> 
> You could create the
> 'sca' term as  'male.female and(female.male)'
> 
> END **** 
> Running part 2 we get that mum is significant, while dad
> isn't. This 
> would be expected with our experience in controlled pollination. 
> 
> At the same time sca appears to be non-significant for this 
> trait, but the reciprocal is significant (the same happens
> with !part 
> 1). I'm not yet fully convinced that what you are crossing is not 
> significant but that the order matters, but it seems that
> there are 
> some special cases where this could be true. 
> 
> Upto this stage I have mentioned models fitting only the parental 
> values, but not producing results for all individuals. I
> assume that 
> a way to get predicted values for all individuals (for the case of 
> growth, for example) would be to change the beginning of the model 
> equation to: 
> 
> !part 3 
> germ_rate ~ mu repl !r tree mum dad sca reciprocal 
> 0 
> 
> where tree would have the role of female and(male) on terms
> of taking 
> into account additive effects. A question here, would this be 
> different from running !part 2 but defining the factors at the 
> beginning as: 
> tree 
> female !P 
> male !P 
> ... 
> 
> I would really appreciate to receive your comments on the
> models and 
> any other alternative models that you have tried for this type of 
> mating design. 
> 
> *****
> This final model would be
> equivalent but the predictions for the individual
> trees would be different.
>  In the latter case, they would be based
> purely on the parental
> values.  In the former case, they would include
> their own information.
> 
> END ***** 
> Best regards, 
> 
> 
> Luis 
> 
> -- 
> Dr Luis A. Apiolaza 
> Quantitative Geneticist 
> CRC for Sustainable Production Forestry 
> School of Plant Science 
> University of Tasmania 
> GPO Box 252-55 
> Hobart TAS 7001 
> Australia 
> 
> phone:   +61-3-6226 2213 
> fax:     +61-3-9229 2698 
> email:   mailto:luis.apiolaza@utas.edu.au 
> 
> 'There is no intellectual exercise which is not 
> ultimately useless' --Jorge Luis Borges 
> http://www.scieng.utas.edu.au/plantsci/ 
> http://www.geocities.com/uncronopio/ 
> ;-) 
> 
> -- 
> Asreml mailinglist archive:
http://www.chiswick.anprod.csiro.au/lists/asreml 

 
 
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