Skin mucus DNA with MIG-seq: a valuable combination for genome-wide SNP typing in aquaculture fish

Abstract

Genome-wide SNP typing has garnered significant interest related to the growing demands for genetic research in farmed fish species. This study validated skin mucus-derived DNA from red sea bream Pagrus major, a major aquaculture species in Japan as a viable source for the genotyping-by-sequencing technique MIG-seq. Skin mucus samples were collected by swab from juvenile red sea bream, and DNA was subsequently extracted using Serapure magnet beads. The DNA sourced from mucus was more degraded than that obtained from fin samples. MIG-seq amplification of mucus-derived DNA was successful, albeit resulting in shorter amplicons relative to those derived from fin samples. Approximately 14,000 SNPs were identified from both DNA sources, with ~ 50% of the SNPs in common. Phylogenetic analysis using UPGMA clustering indicated that mucus- and fin-derived samples from the same individual were closely grouped. Furthermore, a Mantel test comparing genetic relationship matrices (GRM) of fin- and mucus-derived samples showed a significant correlation (r = 0.684, P < 0.001) suggesting strong but imperfect genetic similarity. The observed heterozygosity of the mucus samples was significantly greater than that of the fin, suggesting potential contamination. The applicability and effectiveness of this methodology were further corroborated through a field trial using adult farmed red sea bream. Although less DNA was extracted in the field trial, MIG-seq library construction was successful, yielding 17,474 high-quality SNPs. These results indicate that mucus-derived DNA, when combined with MIG-seq, is a promising non-invasive alternative for genome-wide SNP typing in fish. However, further optimization is required to minimize contamination risks and standardize protocols before its application in genome-wide SNP typing in fish.