Tilapia (Oreochromis spp.) is a globally important farmed fish. Analyses of genetic variation across different types of tilapia are essential for the development of superior breeding populations. We investigated the genetic structures of breeding populations of blue tilapia (Oreochromis aureus) (OA), Nile tilapia (Oreochromis niloticus) (ON), and red tilapia (Oreochromis spp.) (OS) by whole-genome resequencing. The results showed that the OS population had maintained high genetic diversity but significant genetic differentiation from the OA population. Principal component analysis, phylogenetic analysis, and genetic clustering analysis revealed a clear pattern of genetic differentiation among the three populations. The genetic structure of the ON population differed from that of the OA population but was similar to that of the OS population. Population kinship analysis revealed a close relationship between the ON and OS populations. Selective scanning analyses of three comparison groups (OA vs. ON, OA vs. OS, and ON vs. OS) revealed population-selected regions related to metabolism, endocrine, and immune systems, harboring key genes (qrsl1, pde4d, hras, ikbkb, prkag1, prkaa2, prkacb, irs2, and eif4e2). These key genes were related to growth, reproduction, and disease resistance, indicating that breeding programs have selected for these traits. Due to the lack of stable morphological characteristics of juvenile fish and the changes in external environmental conditions that lead to changes in individual morphological characteristics, SNP fingerprints were successfully constructed for the identification of the three populations based on the differences in SNPs. Based on the five core SNP markers, two combinations of SNP markers were developed to accurately identify the three populations of tilapia at the genomic level. These results provide new information about tilapia genetic resources and reference data for identification and breeding purposes.

This study presents the development of a quantitative evaluation method utilizing machine vision technology to characterize the extent of body surface damage in largemouth bass (Micropterus salmoides) infected with largemouth bass ranavirus (LMBV). High-resolution, multi-angle images (6000 × 4000 pixels) of the body surface from 239 infected specimens were acquired at a fixed distance of 40 cm using a SONY ILCE-7RM3 digital camera within a GODOX-LST60 softbox. Key parameters, including the number of segmented injury areas, the count of body surface lesions, and the total lesion area, were analyzed. These parameters were integrated through principal component analysis (PCA) to construct a comprehensive damage scoring model. The severity of viral-induced body surface damage was categorized into four grades: uninjured (0), minor injury (1), moderate injury (2), and severe injury (3). Histopathological examination revealed that early-stage infection (grade 1) predominantly exhibited localized hemorrhagic spots in the muscular region of the body side (B/E region) with limited lesion area. In contrast, moderate to severe infections (grades 2–3) were characterized by extensive ulceration, muscle necrosis, and visceral lesions, including hepatic fibrosis and splenic granulomatous formations. Quantitative real-time PCR (qRT-PCR) analysis demonstrated a progressive upregulation of pro-inflammatory cytokines (IL-6, IL-8, TNF-α, CXCL2) in immune organs, concomitant with increased expression of apoptosis-related genes (CASP8, CYC). This study successfully established a rapid and objective quantitative grading system for ranavirus infection, offering a novel technical approach for early diagnosis and precise prevention and control strategies against largemouth bass ranavirus.

Crossbreeding often results in heterosis. In this study, we generated hybrids from largemouth bass from geographically isolated populations. Growth, digestive enzyme activity, and muscle nutrient composition were compared between the hybrid groups (NC and CN) and the purebred groups (NN and CC), and the gut microbiota was investigated. The heterosis rates of body length, body height, and body thickness in hybrid largemouth bass were statistically significant. Digestive enzyme activity was higher in the hybrid groups than in the purebred groups. Compared with the CN and CC groups, the NC group had significantly higher levels of essential amino acids and total amino acids in the muscle. The polyunsaturated fatty acid content was lower in the hybrid groups than in the purebred groups. The gut microbiota in the hybrid groups predominantly exhibited a non-additive inheritance pattern, characterized by a reduced abundance of Proteobacteria and an increased abundance of Fusobacteria. Microbial taxa showing differences in abundance between the hybrid and purebred groups harbored genes enriched in multiple amino acid and fatty acid metabolism pathways. Cetobacterium, Pseudomonas, and Stenotrophomonas were more abundant in the hybrids, and were positively correlated with multiple amino acids and fatty acids. These results highlight the critical role of gut microbiota in heterosis.

In this study, we systematically analyzed the dynamic changes in chromatin accessibility and the transcriptional responses in the spleen of largemouth bass (Micropterus salmoides) following infection with iridovirus (LMBV) using the assay for transposase-accessible chromatin with sequencing (ATAC-seq) and transcriptome sequencing (RNA-seq). Based on post-infection survival status, largemouth bass were classified into a resistant group (SR) and a susceptible group (SS). A total of 11,317 differentially accessible regions were identified between the two groups, among which the chromatin accessibility of core promoter regions was entirely increased in the SR group, suggesting that chromatin remodeling in these regions may directly participate in the transcriptional regulation of immune-related genes. Functional enrichment analysis revealed that genes associated with differentially accessible regions were significantly enriched in immune-related pathways such as autophagy, apoptosis, Toll-like receptor signaling, and NOD-like receptor signaling. Motif analysis further identified that transcription factors significantly enriched in the SR group included CTCF and heterodimers composed of multiple members of the ETS and FOX transcription factor families. Through integrative analysis, seven transcription factors (CTCF, Spi1, ETV2::FOXI1, FOXJ2::ELF1, FOXO1::ELK1, SPIC, and FOXO1::ELF1) were found to be significantly enriched in core promoter regions. To further screen for differentially expressed genes directly regulated by chromatin accessibility changes, an overlapping analysis was performed between 629 predicted target genes and 2656 differentially expressed genes (DEGs), resulting in the identification of 71 candidate genes. Among these, three immune-related genes (irf4a, btk, and nfil3-2) belonging to the ETS and FOX families were identified. This study reveals the dynamic chromatin accessibility landscape of largemouth bass in response to LMBV infection and demonstrates that increased chromatin accessibility in core promoter regions is closely associated with the resistant phenotype. Heterodimers of ETS and FOX family transcription factors may participate in antiviral immune responses by regulating the expression of key immune genes such as irf4a, btk, and nfil3-2, providing potential epigenetic molecular markers for disease resistance breeding in fish.