Incomplete linkage is due to

Genes present in the same chromosome have a tendency to separate due to crossing over and hence produce recombinant progeny besides the parental type. The number of recombinant individuals is usually less than the number expected in independent assortment. In independent assortment, all the four types (two parental types and two recombinant types) are each 25%. In case of linkage, each of the two parental types is more than 25% while each of the recombinant types is less than 25%.