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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]

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    $\begingroup$ a link to a reference paper on "Griffing and Hayman diallel analysis" would be very helpful for non geneticists $\endgroup$ – RockScience Apr 4 '11 at 4:32
  • $\begingroup$ please how can i use SAS for diallel analysis involving three (3) parents. $\endgroup$ – user35611 Dec 3 '13 at 9:22
  • $\begingroup$ Welcome @Musa. this is not an answer to the OP's question. If you have a question yourself, please ask it via the Ask Question button. If you do, please make sure to accurately describe your problem, include a reproducible example or a (toy) data set and perhaps share what you tried so far. $\endgroup$ – Momo Dec 3 '13 at 9:49
  • $\begingroup$ If you have a new question, please ask it by clicking the Ask Question button. Include a link to this question if it helps provide context. $\endgroup$ – Momo Dec 3 '13 at 9:50
  • $\begingroup$ This does not really answer the question. If you have a different question, you can ask it by clicking Ask Question. You can also add a bounty to draw more attention to this question once you have enough reputation. $\endgroup$ – Glen_b -Reinstate Monica Dec 3 '13 at 11:26
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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:

http://rplantbreeding.blogspot.com/

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 
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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).

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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.

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