CREATE TABLE XtoY (
# No surrogate id for this table
x_id MEDIUMINT UNSIGNED NOT NULL, -- For JOINing to one table
y_id MEDIUMINT UNSIGNED NOT NULL, -- For JOINing to the other table
# Include other fields specific to the 'relation'
PRIMARY KEY(x_id, y_id), -- When starting with X
INDEX (y_id, x_id) -- When starting with Y
) ENGINE=InnoDB;
(See Remarks, below, for rationale.)