I'm studying Nan Laird's Fundamentals of Modern Statistical Genetics book. In the book it says we use linkage analysis in order to estimate the physical linkage between a marker and a Disease Susceptibility Locus (DSL) by using recombination fraction. Now, I assume that we know the positions of the markers and we don't know the position of DSL. Although we know the allele at the marker we don't know the allele at the DSL; however, here is my first question, we can guess the allele of the DSL by checking the phenotype, right? If that's so, and here is my second question, do we need to use linkage analysis only on Mendelian diseases since we associate the phenotype with only one locus?