BSA-seq and transcriptome analysis identification candidate genes associated with Pseudomonas plecoglossicida resistance in the large yellow croaker (Larimichthyscrocea).

Visceral white-nodule disease (VWND), caused by Pseudomonas plecoglossicida, poses a significant threat to the development of the Larimichthys crocea aquaculture industry. Breeding disease-resistant strains offers a potential solution, but the underlying mechanisms of disease resistance in L. crocea remain unclear, and relevant functional markers are still lack. In the present study, 243 full-sibling F populations of L. crocea were infected with P. plecoglossicida. Whole-genome resequencing, bulk segregant analysis (BSA) mapping, and spleen transcriptome analysis were performed on two extreme phenotype pools, which defined by survival time (AT) and spleen bacterial load (BL) as disease-resistance indicators. Candidate genes were validated through infection experiments. A total of 5,576,771 SNPs were identified, and Δ(SNP-index), Euclidean distances (ED), and G-statistics were applied to locate two stable disease resistance-related QTLs on Chr 02 (2.6 Mb) and Chr 24 (4.9 Mb) with 99 % confidence, containing 278 candidate genes. Transcriptomic analysis revealed 4811 genes involved in the immune response, with 949 genes linked to P. plecoglossicida resistance variation in L. crocea. Integrated analysis identified 17 core immune gene, and subsequent validation confirmed that 6 genes (Phf11, CYBB, PTK2B, STAT1, Adamts1, and NRP2) play a consistent role in L. crocea resistance. Our findings highlight the utility of BSA-seq for genetic analysis of disease resistance and provide insights for molecular-assisted breeding in L. crocea.