Final answer:
A recessive allele is responsible for a decrease in the production of a functional protein and is only visible in homozygous genotypes. This contrasts with a dominant allele which manifests in both homozygous and heterozygous genotypes.
Step-by-step explanation:
The type of allele that often leads to a decrease in the production of a functional protein is the recessive allele. A recessive allele causes a phenotype that is only observed in the homozygous condition (when an individual has two copies of the same allele). In many cases, such alleles are defective and do not produce a normal amount of gene product or a functional protein, resulting in the recessive trait being masked by the presence of a dominant allele in heterozygous individuals.
If two individuals present the same phenotype, it does not necessarily mean they have the same genotype, due to the existence of both homozygous dominant and heterozygous genotypes displaying the same phenotype in the case of dominant traits. For instance, a tall, green plant that is homozygous for each trait with T representing the tall allele and G representing the green allele, would have the genotype TTGG and the phenotype of being tall and green.