There are several things one should consider when selecting a RRS method. One consideration is to evaluate the genome coverage provided by each RRS method. Some methods may target specific genomic regions or focus on regions of interest, while others offer more comprehensive coverage of the genome. Thus, different RRS methods may be better suited for different research objectives. The number of markers needed for a study varies based on its purpose. For comprehensive genome-wide investigations like GWAS, tens of thousands of high-density markers are necessary. However, studies focusing on phylogenetic relationships or gene mapping may require only a few hundred to a few thousand markers. The choice between RRS methods depends on the desired marker density.
One should also consider the number of samples they plan to analyze and the throughput capabilities of each RRS method, as methods may differ between one another. Additionally, high-quality DNA samples are essential for efficient enzyme digestion, and the required sample volume varies depending on the method used. RAD-seq is typically the most widely used method for reduced-representation library sequencing. It simplifies complex genomes by focusing on fragments near restriction sites, enabling deep sequencing coverage and SNP detection. When dealing with species lacking a reference genome or with a poorly assembled reference genome, RAD technology becomes more preferable. This is because RAD can generate fragments up to 400-500 bp in size.