How did Thomas Hunt Morgan connect genes with chromosomes?

Thomas Hunt Morgan established the chromosome theory of heredity by demonstrating that genes are physically located on chromosomes.1

Initially skeptical of both Mendelian and chromosome theories, Morgan’s perspective shifted through his experimental research with the fruit fly (Drosophila). In 1910, he observed a white-eyed male fly and discovered that the trait was inherited in a pattern linked to the fly's sex. He concluded that the gene for eye color was located on the X chromosome, a phenomenon known as sex-linkage.12

Because multiple sex-linked traits were inherited together, Morgan deduced that genes were arranged in a linear fashion on chromosomes. He and his collaborators, including A.H. Sturtevant, C.B. Bridges, and H.J. Muller, further solidified this by creating chromosome "maps" that assigned specific genes to precise positions. This work provided definitive proof that Mendel’s hereditary factors had a physical basis in chromosome structure.1