Analyzing the data at the top left corner, the box comparing the M2 sample on x-axis and M2 sample on y-axis is dark blue indicating self compared to self as zero variability.
Looking at the Leaf samples, similar to the information on the PCA plot L2 compared to L1 and L3 is a lighter blue indicating more variability (~200) and the Meristem samples compared to Leaf samples is high variability (~350)