Final answer:
Incomplete penetrance is the genetic phenomenon that complicates determining the mode of inheritance in pedigree analysis because not all individuals with a dominant allele will express the phenotype, making the inheritance pattern unclear.
Step-by-step explanation:
The genetic phenomenon that would make it difficult to determine the mode of inheritance from analysis of a pedigree is incomplete penetrance. When a genotype does not always produce the corresponding phenotype, this is known as incomplete penetrance. With this phenomenon, not all individuals with a dominant allele will express the trait, which can obscure patterns of inheritance in a pedigree chart. For autosomal or X-linked dominant traits, it may seem like the affected genotype is skipping generations, challenging the ability to discern the mode of inheritance accurately.
For context, X-linked recessive inheritance occurs when a trait is determined by an allele on the X chromosome. Males (XY) who inherit the affected X chromosome will express the trait because they don't have a second X chromosome to mask the effect of the recessive allele. Females (XX) must inherit two affected X chromosomes—one from each parent—to express the trait fully. If they inherit only one such X, they become carriers without necessarily showing symptoms of the condition.
X-linked dominant inheritance patterns are also complex, where affected males pass the trait to all daughters but no sons. An affected female has a 50% chance of passing the trait onto each child, regardless of gender. This pattern can resemble autosomal dominant inheritance when examining a pedigree.