Theory 1.Gained From The Sage
As we know the sage had the rinnegan so when his sons were born the elder son was born with the sages "eyes"(uchiha) and the younger son(senju) got the sages "body". and before his death he gave his elder son his visual powers. and his younger son his body power. what could have happened was his eyes mixed with the sages eyes mutating them into that swirl like pattern.
Theory 2. He gained them at birth
Another theory is that the elder son was born with the eyes.