# How to perform diallel analysis in R?

Diallel Analysis using the Griffing and Hayman approach is so common in plant breeding and genetics. I'm wondering if someone can share R worked example on Diallel Analysis. Is there any good referenced book which covered worked examples? Thanks

References:

Griffing B (1956) Concept of general and specific combining ability in relation to diallel crossing systems. Aust J Biol Sci 9:463-493 [pdf]

Hayman BI (1954) The analysis of variance of diallel tables. Biometrics 10:235-244 [JSTOR]

Hayman BI (1954) The theory and analysis of diallel crosses. Genetics 39:789-809 [pdf]

• a link to a reference paper on "Griffing and Hayman diallel analysis" would be very helpful for non geneticists Apr 4 '11 at 4:32
• please how can i use SAS for diallel analysis involving three (3) parents.
– user35611
Dec 3 '13 at 9:22
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– Momo
Dec 3 '13 at 9:49
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– Momo
Dec 3 '13 at 9:50
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There is beta package plantbreeding, which can do diallel analysis.

https://r-forge.r-project.org/projects/plantbreeding/

They has a blog:

The following is example from this package:

require(plantbreeding)
data(fulldial)
out <-diallele1(dataframe = fulldial, male = "MALE", female = "FEMALE",
progeny = "TRT", replication = "REP", yvar = "YIELD" )

print(out)
out$anvout # analysis of variance out$anova.mod1 # analysis of variance for GCA and SCA effects
out$components.model1 # model1 GCA, SCA and reciprocal components out$gca.effmat # GCA effects
out$sca.effmat # SCA effect matrix out$reciprocal.effmat # reciprocal effect matrix

out$varcompare # SE for comparisions out$anovadf.mod2   # ANOVA for model 2
out\$varcomp.model2  # variance components for model 2


I think it's unlikely that you'll find worked examples in R for the analysis of diallels.

I did find some references for diallel analysis in SAS (e.g., here, and there's a chapter on DIALLEL-SAS in the book Handbook of formulas and software for plant geneticists and breeders).

There's a nice worked example in the book Statistical and Biometrical Techniques in Plant Breeding by Jawahar R. Sharma on about page 184. Visible in Google books.