The chromosomal location (where A and a are located) may control the color of the individual's eyes, or some other simple trait.
(a; are located; ) (The chromosomal location (where A and a are located; may control; the color of the individual's eyes, or some other simple trait)
a The chromosomal location (where A and a are located
are located may control
the color of the individual's eyes, or some other simple trait