CRISPR-Cas9 sgRNA design and outcome assessment: Bioinformatics tools and aquaculture applications

The CRISPR-Cas9 genome editing has many advantages over its counterparts and could ultimately assist in disease control and molecular breeding in aquaculture. Single-guide RNA (sgRNA) design is presumably the most crucial task in a typical CRISPR-Cas9 experiment; an understanding of algorithms behind sgRNA design programs is thus essential for improved efficacy and specificity. We focus this review on the bioinformatics aspects in genome editing experiments and describe commonly used computational approaches and tools of sgRNA design and outcome assessment. We show an example of sgRNA design with optimal parameter settings and appropriate interpretation of results and present a brief overview of CRISPR-Cas9 applications, such as genetic improvement and sustainability in aquaculture. We discuss challenging issues, particularly in the context of computational biology, in the use of computational tools in CRISPR-based genome editing. This review provides a synthesis of bioinformatics tools used for CRISPR-Cas9 sgRNA design and outcome assessment and offers a general view of CRISPR-based applications in farmed fish, which are expected to facilitate genome editing programs and hence improve aquaculture breeding, production, and sustainability.