Reda,, I have just yesterday discovered RG has an option to ask questions. I have not run MTGSAM for threshold traits. I do know more than one threshold can be used. Most programs don't do that. Have you tried the one threshold option? Often what I do for a trait such as calving ease is to create 2 categories out of how many were possible. For example, combine the first 2 categories into a new category 1 and the others into a new category 2. Then use the usual linear model. If the frequency of new 1's is between 0.25 and 0.75 ranking of animals will be much the same as with  threshold model. In case you want to contact me by e-mail my address is [email protected]      Dale  .