Mendel’s law of independent assortment relates to the genetic mixing that occurs between prophase 1 and metaphase 1 in meiosis, sexual reproduction. The homologous chromosomes are paired up and proximate to each other. Mendel’s law states that alleles in distant locales on genes or on different chromosomes are inherited independently. This results in genetically unique gametes at the end of meiosis 2.
Plant and Soil Sciences eLibrary. 2017. Mendel’s law of independent assortment. CGIAR Integrated Breeding Platform
In this diagram of Mendel’s peas, you can see that wrinkle/round and yellow/green phenotypes, which are derived from different alleles, can be dispersed independently among offspring. This is a classic example of independent assortment.
Genetic Science Learning Center. (2014, December 2) Genetic Linkage
The alternatives are linked genes that reliably travel together during meiosis. The important thing to realize is that this is essentially a principle of physics, not biology. Laws of physics describe how matter behaves in relative position to other matter. When the alleles are physically close to each other, they are more likely to travel together because the action of “crossing over” is literally a shift in position that is solidified through chemical bonding. A section of a chromosome is a super molecule that when cleaved from its original chromosome, is perturbed in only one or two positions in the molecule. The rest of the molecules remains intact, ie alleles close together are not perturbed.