how to get population structure

[xiang lin]

Hi everyone,

I'm going to run GLM and MLM analysis on Tassel 5. I have all genotyping data from Cornell University. However, when I check GLM and MLM analysis online, it mentions that I need population structure to run the test. How do I get population structure data? Thank you very much.

[Ana Etch]

Hi Xiang,

you can include PCA analysis results to MLM/GLM : Analysis->PCA in Toolbar, and join PCA file to geno and pheno files.

Another option, for example, is joining results from some soft like STRUCTURE (Q matrix), or PCA/PCO from R package (like {ecodist}).

For MLM you also need Kinship (Analysis->Kinshipl).

Good luck!:)

Anna.

[xiang lin]

Hi Ana,

Thanks for your help. I did PCA analysis in Tassel; however, each PC only explains small proportion of variance. Attached is the PCA analysis. Shall I try STRUCTURE to get Q matrix? Thank you.

Best

Xiang