The whole tone, also called the whole step or the major second, is a common musical interval in the music of most modern culture. It is one of the major building blocks of most western scales, and also occurs in pentatonic scales.
In 31-ET, the whole tone is a little bit narrower or smaller than in the standard 12-ET tuning. This difference produces several effects:
31-ET is a meantone tuning, and along with 19 tone equal temperament is one of the two most commonly used equally tempered meantone tunings.
In 12-ET, a whole tone is a very good match for the ratio 9:8 in the harmonic series, and a relatively poor match to the 10:9 ratio. This means that in that tuning, the whole tone implies the bottom note as root.
In 31-ET, the whole tone is more ambiguous, falling close to halfway between the 9:8 and 10:9 ratios. In this tuning, the whole tone can thus imply two different roots, either the bottom note, or a whole step lower than the bottom note. Which root is implied depends on the harmonic context. For example, if you stack a whole tone on top of a septimal whole tone, the middle note would function as the root. Two stacked whole tones, on the other hand, would imply the bottom note as the root. Because the match to either just interval is poor in 31-ET, a whole tone in isolation or with ambiguous harmonic context is harmonically ambiguous and does not imply a clear root.
The whole tone often functions as a dissonant, rather than consonant, interval: in these cases, the root is implied by other notes in a chord. For example, in 13-ET, stacking a major third on top of a whole tone would create a stronger harmonic center in the major third, with the bottom note of the third as the root. The major third would then function as dissonance, which could resolve upwards to unison or downwards to a septimal whole tone.