The highlighting list allows you to select which degrees of the scale/arpeggio being displayed are highlighted.
When you select an option from this list the markers on the guitar neck are highlighted/un-highlighted accordingly. Note that depending on the type of scale, some of these options may not do anything, e.g. for notes from a Harmonic Minor mode, pentatonic highlighting won't apply.
If you're viewing a chord/arpeggio, then only a limited set of annotation options are available.
No Highlighting: Does exactly as it says - no degrees are highlighted.
Highlight Root Note: The root degree of the scale is highlighted.
Chord Tones (Triads): Degrees from the scale which belong to the corresponding triad are highlighted.
Chord Tones (7th Chords): Degrees from the scale which belong to the corresponding 7th chord are highlighted.
Pentatonic Notes: Degrees from the scale which belong to the corresponding pentatonic scale are highlighted.
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