In 1905, the British geneticists William Bateson, Edith Rebecca Saunders and Reginald Punnett cross-bred pea plants in experiments similar to Mendel's. But shortly after Mendel's work was rediscovered, exceptions to this rule were found. Gregor Mendel's Law of Independent Assortment states that every trait is inherited independently of every other trait. A distance of 1 cM between two markers means that the markers are separated to different chromosomes on average once per 100 meiotic product, thus once per 50 meioses. The typical unit of genetic linkage is the centimorgan (cM). Later work revealed that genes are physical structures related by physical distance. At the time, the reason why certain traits tend to be inherited together was unknown. The first experiment to demonstrate linkage was carried out in 1905. Genetic linkage is the most prominent exception to Gregor Mendel's Law of Independent Assortment. Markers on different chromosomes are perfectly unlinked, although the penetrance of potentially deleterious alleles may be influenced by the presence of other alleles, and these other alleles may be located on other chromosomes than that on which a particular potentially deleterious allele is located. In other words, the nearer two genes are on a chromosome, the lower the chance of recombination between them, and the more likely they are to be inherited together.

Two genetic markers that are physically near to each other are unlikely to be separated onto different chromatids during chromosomal crossover, and are therefore said to be more linked than markers that are far apart. Genetic linkage is the tendency of DNA sequences that are close together on a chromosome to be inherited together during the meiosis phase of sexual reproduction.

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