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*To*: "'Luis A. Apiolaza'" <luis.apiolaza@utas.edu.au>, asreml@chiswick.anprod.csiro.au*Subject*: RE: Analysis of diallel experiment*From*: "Hardner, Craig (PI, Indooroopilly)" <Craig.Hardner@csiro.au>*Date*: Thu, 10 Jan 2002 09:06:54 +1000*Sender*: asreml-owner@lamb.arm.li.csiro.au

Hi luis i wonder why you dont just have pedigree for additive effects, then 28 sca effects (i.e AxB the same as BxA) and then 56 specific cross effects (AxB different to BxA). Im not sure you need to go through the work of overlaying maternal and paternal design matrices as this would come out by using a pedigree and your Gca effects are 1/2 (I think) the BV's. On the other hand could specific cross effects be treated as maternal effects? Give me a call if you want to chat about this Cheers Craig -----Original Message----- From: Luis A. Apiolaza [mailto:Luis.Apiolaza@utas.edu.au] Sent: Wednesday, 9 January 2002 3:56 PM To: asreml@chiswick.anprod.csiro.au 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?). 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. 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. 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 -- Asreml mailinglist archive: http://www.chiswick.anprod.csiro.au/lists/asreml

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