Identification and characterization of disease resistance-related SNPs using transcriptome analyses in sea cucumber Apostichopus japonicus.

Apostichopus japonicus is a commercially significant aquaculture species. However, in recent years, frequent outbreaks of skin ulcer syndrome (SUS) caused by Vibrio splendidus have resulted in substantial economic losses for the A. japonicus industry. Molecular breeding techniques, such as marker-assisted selection and genomic selection, are effective methods for accelerating breeding programs aimed at enhancing disease resistance. In the present study, we aimed to identify single nucleotide polymorphism (SNP) markers associated with disease-resistance by characterizing SNPs from the transcriptomes of two phenotypically distinct groups: a disease-resistant group (RG) and a disease-susceptible group (SG). We identified 5400 significantly differentially expressed genes (DEGs; p < 0.05) and 5,600,281 single nucleotide polymorphism (SNP) markers between the RG and SG groups. Association analysis revealed 503 SNPs across 365 genes exhibiting significant allelic imbalance (adjusted p < 0.05). Functional annotation revealed that immune-related genes harboring these significant SNPs were markedly enriched in lysosomal pathways, implicating their crucial role in defense mechanisms against V. splendidus. Six candidate SNPs derived from immune-related genes were successfully validated by Sanger sequencing, with three demonstrating statistically significant associations with disease-resistance. These functionally validated SNPs represent promising molecular markers for implementing marker-assisted selection in the breeding of disease-resistant A. japonicus.