If you require genome-wide coverage with many loci, which marker type is typically favored?

• A. SNPs provide abundant genome-wide coverage.
• B. Microsatellites due to high per-locus polymorphism.
• C. Both provide equal genome-wide coverage.
• D. Neither are suitable for genome-wide coverage.

Answer: (A)

For genome-wide coverage with many loci, you want markers that are abundant across the genome and easy to genotype on a large scale. SNPs fit perfectly here. They occur at a high density throughout the genome, and modern technologies let you assay millions of SNP sites across many individuals quickly and cost-effectively, giving dense, uniform coverage.

Microsatellites offer high variability per locus, but they are far less abundant genome-wide and are more labor-intensive to genotype, making it harder to achieve consistent coverage across the whole genome with a vast number of loci. This is why they’re not typically used when the goal is genome-wide, large-scale marker data.

So, for broad, genome-wide coverage with many loci, SNPs are the best fit.