Background Largemouth bass ( Micropterus salmoides ) has significant economic value as a high-yielding fish species in China’s freshwater aquaculture industry. Determining the major genes related to growth traits and identifying molecular markers associated with these traits serve as the foundation for breeding strategies involving gene pyramiding. In this study, we screened restriction-site associated DNA sequencing (RAD-seq) data to identify single nucleotide polymorphism (SNP) loci potentially associated with extreme growth differences between fast-growth and slow-growth groups in the F 1 generation of a largemouth bass population. Results We subsequently identified associations between these loci and specific candidate genes related to four key growth traits (body weight, body length, body height, and body thickness) based on SNP genotyping. In total, 4,196,486 high-quality SNPs were distributed across 23 chromosomes. Using a population-specific genotype frequency threshold of 0.7, we identified 30 potential SNPs associated with growth traits. Among the 30 SNPs, SNP19140160, SNP9639603, SNP9639605, and SNP23355498 showed significant associations; three of them (SNP9639603, SNP9639605, and SNP23355498) were significantly associated with one trait, body length, in the F 1 generation, and one (SNP19140160) was significantly linked with four traits (body weight, height, length, and thickness) in the F 1 generation. The markers SNP19140160 and SNP23355498 were located near two growth candidate genes, fam174b and ppip5k1b , respectively, and these candidate genes were closely linked with growth, development, and feeding. The average body weight of the group with four dominant genotypes at these SNP loci in the F 1 generation population (703.86 g) was 19.63% higher than that of the group without dominant genotypes at these loci (588.36 g). Conclusions Thus, these four markers could be used to construct a population with dominant genotypes at loci related to fast growth. These findings demonstrate how markers can be used to identify genes related to fast growth, and will be useful for molecular marker-assisted selection in the breeding of high-quality largemouth bass.

The common strain black carp (Cyprinus carpio var. baisenensis) is a culturally important carp strain that is raised and cultured in Guangxi Province, China. Its color reflects the interactions between the Burau people and their surrounding environment. The population of the common carp black strain was isolated and cultured in a rice-fish integration system. To explore the genetic diversity and protection of germplasm resources, we analyzed mitochondrial DNA (mtDNA) sequences, specifically the displacement loop (D-loop) and cytochrome b (Cytb), using single-nucleotide polymorphisms (SNP). We compared these sequences with those from four other local common carp populations. The study included a total of 136 adult common carps from five strain populations: the common black carp strain (HJ = 31), Jian (F = 30), Heilongjiang (H = 10), Songpu (S = 31), and Saijiang (SJ = 34). The results of the Cytb and D-loop analyses showed that the Heilongjiang carp (H) and Saijiang (SJ) populations had the highest levels of haplotype diversity (0.867±0.034785) and nucleotide diversity (π = 0.0063±0.000137 and 0.0093±0.000411), respectively. On the other hand, the Common carp black strain population (HJ) exhibited the lowest haplotype diversity in both Cytb and D-loop, with haplotype 2 being the most commonly observed among the populations. Private haplotypes dominated the five common carp populations, which were significantly different at P<0.001. Furthermore, analyzing the coefficient of genetic differentiation (Fst), the highest genetic difference was observed between Saijiang (SJ) and Heilongjiang (H) (Fst = 0.963), whereas the lowest was observed between Songpu (S) and the Common carp black strain population (HJ) (Fst = 0.019) for the Cytb gene sequences. For the D-loop, the Common carp black strain population (HJ) and Songpu (S) (Fst = 0.7) had the highest values, and Heilongjiang (H) and Common black carp strain (HJ) had an Fst of 0.125. Additionally, the AMOVA analysis revealed a higher level of variance for the Cytb and D-loop genes, indicating lower genetic diversity within the local carp community. On the other hand, the phylogenetic tree analysis showed that the five carp populations were closely related and formed a distinct cluster. The distinct cluster of populations suggests a common ancestor or recent gene flow, possibly due to geographic proximity or migration history, and unique genetic characteristics, possibly due to adaptations or selective pressures. The results of this study provide valuable insights into the genetic diversity of the common strain black carp, which can have implications for conservation, breeding programs, evolutionary studies, and fisheries management.

The Common Black Carp Strain (Cyprinus carpio var. baisenensis), known for its black skin, is commonly cultured in the integrated rice-agriculture (IRA) system in Guangxi province, China. This study aimed to compare the genetic diversity of three common carp strains/populations (Common Black Carp Strain, Huanghe, and Songpu) using resequencing data. The genome-based method reveals a significant difference (p < 0.05) in identified loci and SNP frequency (p < 1 × 10−6) between the Songpu (Sp) or mirror carp and Huanghe (Hh) new strain. Additionally, the Common Black Carp Strain (Bk) exhibits a higher number of Tajima’s D values, possibly due to its population size and mutations within its entire genome. The average value of population nucleotide diversity (π) for the Bk is 1.706 × 10−4 while the mean number for the Hh and Sp strains is 1.691 × 10−4 Heterozygosity analysis results indicate that the Bk has the highest F coefficient compared to the Sp and Hh hybrids. This suggests that the isolated population of the Bk may have experienced a decrease in population size as a result of environmental disturbances in the IRA system. PCA results further reveal that all individuals of the Bk, except for one, are clustered together, while individuals of the Hh form a separate group. On the other hand, Sp displays a distinct distribution pattern. The comparative study of the genetic diversity of the Bk provides baseline data on its genome makeup. Assessing genetic diversity and genetic structure is critical for fisheries management and the conservation of critically endangered fish species.

Dissolved oxygen (DO) is a key factor affecting the health of aquatic organisms in an intensive aquaculture environment. In this study, largemouth bass (Micropterus salmoides) were subjected to acute hypoxic stress for 96 h (DO: 1.00 mg/L) followed by recovery under sufficient DO conditions (DO: 7.50 mg/L) for 96 h. Serum biochemical indices, intestinal histomorphology, the transcriptome, and intestinal microbiota were compared between hypoxia-treated fish and those in a control group. The results showed that hypoxia caused oxidative stress, exfoliation of the intestinal villus epithelium and villus rupture, and increased cell apoptosis. Transcriptome analyses revealed that antioxidant-, inflammation-, and apoptosis-related pathways were activated, and that the MAPK signaling pathway played an important role under hypoxic stress. In addition, 16S rRNA sequencing analyses revealed that hypoxic stress significantly decreased bacterial richness and identified the dominant phyla (Proteobacteria, Firmicutes) and genera (Mycoplasma, unclassified Enterobacterales, Cetobacterium) involved in the intestinal inflammatory response of largemouth bass. Pearson's correlation analyses showed that differentially expressed genes in the MAPK signaling pathway were significantly correlated with some microflora. The results of this study will help to develop strategies to reduce damage caused by hypoxic stress in aquacultured fish.

Intestinal microbiota plays an important role in promoting digestion, metabolism, and immunity. Intestinal microbiota and fatty acids are important indicators to evaluate the health and nutritional composition of Procambarus clarkii. They have been shown to be strongly influence by environmental and genetic factors. However, it is not clear whether environmental factors have a greater impact on the intestinal microbiota and fatty acid composition of crayfish. The link between the intestinal microbial communities and fatty acid (FA) compositions of red swamp crayfish from different geographical has not yet been studied. Thus, the current paper focuses on the influence of different environments on the fatty acids in muscles of crayfish and the possible existence between gut microbiota and fatty acids. Therefore, in this study, we compared the fatty acid compositions and intestinal microbiota of five crayfish populations from different geographical locations. The results were further analyzed to determine whether there is a relationship between geographical location, fatty acid compositions and intestinal microbiota. The gut microbial communities of the crayfish populations were characterized using 16S rRNA high-throughput gene sequencing. The results showed that there were significant differences in FA compositions of crayfish populations from different geographical locations. A similar trend was observed in the gut microbiome, which also varied significantly according to geographic location. Interestingly, the analysis revealed that there was a relationship between fatty acid compositions and intestinal microbes, revealed by alpha diversity analysis and cluster analysis. However, further studies of the interactions between the P. clarkii gut microbiota and biochemical composition are needed, which will ultimately reveal the complexity of microbial ecosystems with potential applications in aquaculture and species conservation.

Abstract Intestinal flora plays an important role in promoting digestion, metabolism and immunity. It is an important basis for assessing the health and nutritional content of Procambarus clarkii. Fatty acids are also important indicators for assessing the P.clarkii. They are strongly related to environmental and genetic factors. However, whether environmental factors or genetic factors have a greater impact on the health and nutrition of crayfish is currently a hot topic, and it is unclear whether there is a link between the intestinal flora and the distribution of fatty acid (FA) compositions of red swamp crayfish.This paper focuses on the influence of different environments on the fatty acids in muscles of crayfish and the possible existence between gut microbiota and fatty acids. Therefore, we compared and clustered fatty acid compositions of crayfish populations in five different geographical locations to determine the relationship between geographical location and fatty acid compositions. We also characterized the gut microbial communities of these crayfishes using 16S rRNA high-throughput gene sequencing. We found that there were significant differences in FA compositions of crayfish populations in different geographical locations. Similar trends were observed in the gut microbiome, which also varied significantly according to geographic phenotypes. In addition, the relationship between fatty acid compositions and intestinal microbes was revealed by alpha diversity analysis and cluster analysis. However, further studies of the interactions between the P.clarkii gut microbiome and biochemical composition are needed, which will ultimately reveal the complexity of microbial ecosystems with potential applications in aquaculture and species conservation.

Aquaculture feed containing olive oil (OO) instead of fish oil (FO) can cause oxidative stress and impair gonad development in fish. We determined the effect of dietary OO-induced oxidative stress on ovarian development, and explored whether vitamin E (VE) could mitigate negative effects. Female Nile tilapia (Oreochromis niloticus) were fed for 10 weeks with four diets: 5% OO + 70 mg/kg VE, 5% OO + 200 mg/kg VE, 5% FO + 70 mg/kg VE, or 5% FO + 200 mg/kg VE. Dietary OO reduced the specific growth rate and gonadosomatic index, inhibited superoxide dismutase and catalase, delayed ovarian development, decreased serum sex hormone levels, and reduced ovarian triglyceride and n-3 highly unsaturated fatty acid contents. The transcript levels of genes encoding sex hormone receptors (erα, fshr, lhr) and components of the lipid metabolism pathway (pparα, pparγ, hsl, accα, elovl6), the nrf2 signaling pathway (nrf2, keap1), and the nf-κb signaling pathway (nf-κb, tnfα, infγ, il1β) differed between the 70VE/OO and 70VE/FO groups. Supplementation with 200 mg/kg VE mitigated the adverse effects of OO by improving antioxidant capacity and alleviating inflammation and abnormal lipid metabolism. This may be because VE is an antioxidant and it can regulate the nrf2-nf-κb signaling pathway.