PCA analysis

[MRS]

Hi everybody,
somebody knows how to manage a large group of related individuals (F2 population) in PCA analysis? I have a database, including parental lines of the F2 population.
I have added 140 individuals (F2) in one step. I got a plotting where all the F2 lines are grouped outside of database line.
Is it strange?
Is it the right way to analyse population like that, if not what is the best way?
Thanks for any hint