How are linked genes an exception to Mendel's law of independent assortment?

Answer 1

The alleles are on the same chromosome, for the simplistic answer. No independent assortment.

Answer 2

Independent assortment is really dependent on physical distance, and it's really independent assortment of chromosomes. If two genes are linked (linkage disequalibrium) and on the same chromosome, it means they are very close to each other and thus during meitoic crossing-over are likely to remain together. However even strongly linked genes can be seperated by rare recombination events. What we look for in genetics though is the rare recombinant when trying to link disease genes to marker locations/genes in the genome to determine the locus/region where our disease gene resides.

Answer 3

The law says that the way one pair of genes separates does not affect the way another pair of genes separates when gametes are made.

Linked genes are genes that are found on the same chromosome. They are not going to segregate independently. Where one chromosome goes, all of its genes will go (ignoring crossing over). It's kind of like cars on a train. If the train is going to Chicago, then the second car is going to Chicago and the fourth car is going to Chicago. They're together in the same train.