This was Mendel's demonstration that genes segregated independently. This happens when two genes lie on different chromosomes, or lie sufficiently far apart on a chromosome that the frequency with which recombination occurs decouples them. Although noticed in 1902, genetic linkage was largely elucidated in Morgan's 'fly lab' at Columbia from 1910 through the 1920s. Genetic linkage is the tendency for genes which are close to one another on a chromosome to be more frequently transmitted together to progeny than genes which are far apart or on different chromosomes. Meiotic recombination and its companion 'Interference' are responsible for this tendency.
Linkage is estimated by determining how far deviated from expectation are gamete frequencies.
While I was a graduate student, it was impossible to reasonably consider cloning an actual gene in which any reasonable person might be interested. Goldman and his students produced the estimate that about 100,000 genes were expressed during the lifetime of an average plant. While perhaps off by a factor of two, it's still a decent estimate. While I was a student perhaps 100 plant genes were cloned, sequenced and generally understood. Currently over 40,000 genes have been at least partially cloned and sequenced.