Dear all,

I would like to investigate the linkage disequilibrium in maize collection with TASSEL in order to determine the marker number for population structure and GWA analysis.

Our maize collection have been genotyped with maize DArTseq (1.0) by the Diversity Arrays Technology Ltd. So I have two types of markers:

(1) dominant silicoDArT markers (Presence/Absence variation of restriction fragment)

(2)  codominat SNP markers in the restriction fragments

Can I mix this two types of marker data in the hapmap file and run the LD analysis?

Is it appropriate to mix two different marker data when I perform LD analysis?

Or should I make one hapmap file for silicoDArT markers and one for SNP markers and perform the LD analysis for the two marker sets independetly?

Thanks for your help!