Single-Nucleotide Polymorphism (SNP) array: an array of hope for genetic improvement of aquatic species and fisheries management

Abstract

In recent years, significant progress in genomic technologies has revolutionized the field of aquaculture. These advancements have facilitated the utilization of DNA markers, particularly single nucleotide polymorphisms (SNPs), to enhance the genetic characteristics of aquatic species, leading to overall improvements in economically important traits. A SNP array or panel is a DNA microarray designed with probes for SNP locations, allowing the identification of specific alleles in a DNA sample through hybridization with fragmented DNA. SNP arrays are known for their efficiency, cost-effectiveness, and automation, making them a high-throughput method for genotyping. Thus, genome scale SNP genotyping, aided by SNP arrays and genotyping-by-sequencing (GBS), has transformed aquaculture genetics. Recently, multi-species arrays allow researchers to study closely related species simultaneously, reducing costs and enabling comparative genomics and resource sharing. In this paper, we reviewed the global advancements in SNP array development for key aquaculture species and highlighted their applications in genetic selection and fisheries management. SNP panels, commonly used in genome-wide association studies (GWAS), leverage population linkage disequilibrium (LD) to pinpoint genetic variants associated with production or performance traits. Using genomic estimated breeding values (GEBVs) derived from SNP data offers enhanced selection accuracy compared to traditional pedigree based methods, especially when dealing with challenging traits in aquatic species. Overall, the study indicates that high-density SNP panels offer a consistent and reliable tool for genotyping across diverse breeding populations. This technology has demonstrated versatility and efficiency, being applied in genomic selection, genome characterization, population genomics, and QTL mapping in aquatic species. The growing accumulation of genomic information and the abundance of SNPs in aquaculture species have driven the demand for efficient and cost effective genotyping techniques in genetic improvement programs and fisheries management.