Potential loci and candidate genes associated with Vibrio anguillarum resistance in black rockfish (Sebastes schlegelii) revealed by BSA-seq analysis

Selection for resistant lines is an important part in black rockfish (Sebastes schlegelii) breeding program. The identification of markers closely linked to disease-resistance is an essential step for the improvement of the resistance in S. schlegelii through marker-assisted selection (MAS). However, lack of parental genomic infor-mation increased the difficulty for MAS. In the present study, by using whole genome re-sequencing strategy and bulked segregant analysis (BSA), 704,630 SNPs and 253,436 in/del within the two extreme phenotypes were identified in S. schlegelii. Furthermore, using combination of SNP frequency difference and Eucildean distance, we conducted linkage analysis of SNPs located in immune-related genes, and identified markers associated with Vibrio anguillarum resistance. A total of 64 SNPs was identified as candidate SNPs between susceptible and resistant groups, 48 SNPs located in 43 genes were selected for further genotyping analysis in verification population and 7 of them showed significant association with V. anguillarum-resistance (P < 0.05). Generalized multifactor dimensionality reduction (GMDR) was performed to analyze the SNP-SNP interaction. The best three-factor model consisted of loci from Casp8, Pglyrp2 and Gnb1 was considered to be associated with V. anguillarum resistance in S. schlegelii. Combining the actual phenotype with predicted phenotype, the best three-factor model was proved to have 69.1% identification accuracy. Our study demonstrated that the genetic analysis with the application of BSA-seq has propelling effect in disease resistance and will assist the selective breeding of S. schlegelii with V. anguillarum resistance.