Final answer:
Limited genome coverage, reduced sample size, and excessive SNP variations are challenges in using GWAS for SNP-trait association.
Step-by-step explanation:
One challenge in using GWAS for SNP-trait association is limited genome coverage. GWAS examines a large number of genetic variations in the genome, but it doesn't cover the entire genome. It focuses on specific regions that are more likely to have associations with traits or diseases. This means that some potentially important genetic variations may be missed.
Another challenge is reduced sample size. Ideally, GWAS requires a large sample size to have enough statistical power to detect significant associations. Smaller sample sizes can lead to lower statistical power and increase the risk of false positive or false negative results.
Excessive SNP variations can also pose a challenge in GWAS. It can be challenging to accurately analyze and interpret the vast amount of SNP data generated from GWAS. Additionally, the presence of many SNP variations in the genome can complicate the identification of specific variations associated with a particular trait.