Final answer:
SNPs often have no detectable effect on phenotype due to their location in non-coding DNA and the redundancy of the genetic code. GWAS help to identify SNPs associated with diseases, but many SNPs are neutral and do not affect an organism's fitness or characteristics. The complex relationship between genotype and phenotype makes it difficult to link specific SNPs to traits.
Step-by-step explanation:
The reason why single nucleotide polymorphisms (SNPs) generally have no detectable effect on phenotype is largely due to redundancy in the DNA code and the impact of non-coding regions. Many SNPs occur in non-coding DNA, which does not directly code for proteins, and consequently, they do not affect the organism's phenotype. Furthermore, due to the redundancy of the genetic code, where multiple codons can encode the same amino acid, a change in a single nucleotide might not alter the amino acid sequence of a protein, which would have minimal to no impact on the organism's characteristics.
In more detailed terms, we know that within an organism, phenotypes may change while genotypes remain constant. Noncoding DNA, which was once thought to have no biological purpose, often contains regulatory sequences that control gene expression. However, many SNPs within these regions may not lead to phenotypic changes because of the complex interplay between genetic and environmental factors.
It is challenging to identify which SNPs are responsible for specific traits or diseases due to the vast number of them and the subtle effects they may have. Genome-wide Association Studies (GWAS) have been essential in identifying genetic variants that contribute to disease, although interpreting these findings remains complex. SNPs may have evolutionary implications as well, with some conferring advantageous traits subject to the pressures of natural selection. Nonetheless, many SNPs are neutral, having neither beneficial nor deleterious effects on fitness.