Split plot analysis and BLUP's

DaisyA — Mon, 27 Jan 2020 20:39:33 GMT

Hello,

I am using SAS version 9.4

I am analysing freezing tolerance in plants as measured by the percentage of electrolyte leakage (EL) after freezing treatment.
All the genotypes tested are siblings.
My experimental design is a split plot design with 5 replications.
My main factor is freezing treatment or temperature (3 levels) and my subfactor is plant genotype (100 levels).
In each experiment (or replication) I measured EL on 3 stem sections per genotype and per temperature.
I consider that stem section is a factor nested within genotype but I think that I still need to specify the residuals 'Block*FactorA*FactorB' in the model since I have multiple data point for each genotype*temperature.
My ultimate goal here is to compute BLUP's for each genotype and temperature across 5 replications, to be used in genetic mapping.
I consider temperature as a fixed effect, while I consider both replication and genotype as random effects in a mixed model.
Indeed, the 100 genotypes represent a sub-sample of the entire bi-parental population.

My response variable (EL) is a percentage, so I chose to indicate a beta distribution with the linked scale Logit using proc glimmix and laplace approach.

Please see my script below:

data first;
input Rep$ Temperature$ Genotype$ Stem_Section$ EL;
datalines;
[...]
proc glimmix data = first method=laplace;
EL = EL/100;
class Temperature Genotype Rep Stem_Section;
model EL= Temperature/ dist = beta link=logit ;
random Rep Rep*Temperature Genotype Genotype*Temperature Rep*Temperature*Genotype / solution;
output out=second pred(ilink blup)=pblup ;
proc print data=second;
title 'Mixed model analysis with Random Genotype effect computing BLUPs'
Run;

In the random statement, 'Rep Rep*Temperature Genotype Genotype*Temperature' specify the G matrice
while 'Rep*Temperature*Genotype' specifies the residuals associated with the presence of multiple measurements and then the R matrice.

With 100 genotypes, SAS never ends processing the data.

I have no problems when I run the model with only 5 genotypes and I obtain Subject=1 in the Dimensions table, which makes sense to me since I have specified both the G and R matrices.
I also obtain blup estimates for Genotype*Temperature*Rep.
I would then pursue by calculating the mean of Blup's per genotype and temperature across 5 replications to obtain Blups for each genotype and temperature to be used in mapping.

My questions are:
1) Is my approach for estimating BLUP's correct and did I stated my random effects properly without overspecifying my split plot design?
2) I already increased my SAS memory, how can I process all 100 genotypes at once to compute BLUP's using SAS?

Thank you so much for any help you could provide.

Sincerely,
Daisy

topic Split plot analysis and BLUP's in Statistical Procedures

Split plot analysis and BLUP's