There are quite a few principles to consider when this topic is concerned.
Essentially, you have to understand that along the length of any given chromosome are various gene loci. Genes or alleles on a single chromosome are physically linked and hence tend to be inherited together. Genes located on different chromosomes are usually not linked and this falls back to Mendel's second principle of independent allelic assortment which stipulates that alleles on different chromosomes will assort into gametes independently of each other.
At prophase 1 of meiosis, however, there is a certain probability of exchanging genes between nonsister chromatids of homologous chromosomes thereby generating new allelic combinations or variation. This probability can be estimated based on the distance of the genes under questions along the chromosome. Essentially, genes located close together will be inherited together. Some genes are located so far away from each other along a single chromosome that they will virtually assort independently of each other.
I don't have time to locate the paper atm so if you still struggle posting here the question would really help.