Q-K association analysis with SSR

Question

Hello,

I am a new user of JMP, and the issue is that I have a collection of inbred lines of a crop they are genotyped with 150 SSR markers, and the phenotype is a binary trait (0 and 1), since I plan to do Q-K association analysis I have expanded the markers format using JMP Genomics 7.0 and I am using logistic regression to do association test. My case is similar to the example of the "Step-by-step guide to association analysis with SSR markers". The issue is that I have follow most of the step of the guide but I have not been able to get successful results.

What I did is:

1) Expanding the format of the mult-iallelic SSR markers (eg. 150/150, 167/150, 167/167) to 0, 1, and 2 format (where 0 and 2 are the homozygous and 1 the heterozygous).

2) Compute PCA in order to account for population structure

3) Compute a based marker relationship matrix (IBS).

4) Q-K association analysis using the Marker-Trait Association option of JMP Genomics.

4.1 I have tried using the multi-allelic markers (not the EG_ markers) as suggested the guide and cheking the "Genotypes" box in the "Options" tap and "/" as genotype delimiter. The result is the following error message "ERROR: File WORK.GENOTYPES.DATA does not exist"

4.2 I have tried using the extended markers (with the prefix EG_) and checking the "Numeric Genotypes" box in the "Options" tap but when I run the analysis It seems like it is running well but the process never ends, it is more like frozen.

Could anyone help me with this analysis?

Thanks

LF

Fers · Answer

Dear Kelci,

Thank you for your support, I have tried different specifications to get

the compressed K matrix, I always get an error when I place the pca1 pca2

and pca3 in the "Q Matrix Variables" box of the "Model Variables" tab.

However:

1. when I place pca1, pca2 and pca3 in the "Q Matrix Variable" box and

also checking the "Columns of Q sum to 1" box, I get as result a K matrix

(of 420 lines) compressed in 11 groups.

2. when I only check on the "Columns of Q sum to1" box without placing the

three first principal components in the "Q Matrix Variable" box, or either

when both boxes are left blank the result is a K matrix compresed in 8

groups.

So I have used either of the two compressed K matrices in the association

tests but the results are still unsatisfactory.

LF

kelci_miclaus · Answer

Hi LF,

Our development team tried and couldn't duplicate the error you're seeing. I'm going to put you in touch with our Genetics processes developer to try to help trouble shoot this further via your email!  That way you can more easily share log/settings files etc so we can help figure out the problems!

The error in K matrix compression is a little more helpful, when a trait is binary, the GLIMMIX procedure is used and it is more sensitive to models that don't fit/converge well so it could be the model you are trying to fit to your data is not possible.

Fers · Answer

Also It is not possible to reproduce the analysis of the of the example in the "Step-by-step guide to association..." using the same data set and the same specifications, I get the following error in the first step (expansion genotype).

ERROR: The file WORK.AF (memtype=DATA) already exists. Rename was not done.

Thanks

LF