The chromosome theory of inheritance states that chromosomes contain genes and are responsible for Mendel's principles of segregation and independent assortment during meiosis. Thomas Hunt Morgan's experiments with fruit flies led to the discovery of sex linkage, where genes on the X chromosome show different inheritance patterns between males and females. Nettie Stevens' analysis of beetle karyotypes revealed that females have two X chromosomes while males have one X and one Y chromosome, establishing the sex chromosome system. Morgan then used this information to propose X-linked inheritance for white eye color in fruit flies, providing support for the chromosome theory of inheritance.