The Pacific whiteleg shrimp (Penaeus vannamei) is a highly significant species in shrimp aquaculture. In the production of shrimp larvae, noticeable variations in the reproductive capacity among female individuals have been observed. Some females experience slow gonadal development, resulting in the inability to spawn, while others undergo multiple maturations and contribute to the majority of larval supply. Despite numerous studies that have been conducted on the regulatory mechanisms of ovarian development in shrimp, the factors contributing to the differences in reproductive capacity among females remain unclear. To elucidate the underlying mechanisms, this study examined the differences in the ovarian characteristics between high and low reproductive bulks at different maturity stages, focusing on the cellular and molecular levels. Transmission electron microscopy analysis revealed that the abundance of the endoplasmic reticulum, ribosomes, mitochondria, and mitochondrial cristae in oocytes of high reproductive bulk was significantly higher than that of the low reproductive bulk in the early stages of ovarian maturation (stages I and II). As the ovaries progressed to late-stage maturation (stages III and IV), differences in the internal structures of oocytes between females with different reproductive capacities gradually diminished. Transcriptome analysis identified differentially expressed genes (DEGs) related to the mitochondria between two groups, suggesting that energy production processes might play a crucial role in the observed variations in ovary development. The expression levels of the ETS homology factor (EHF) and PRDI-BF1 and RIZ homology domain containing 9 (PRDM9), which were significantly different between the two groups, were compared using qRT-PCR in individuals at different stages of ovarian maturation. The results showed a significantly higher expression of the EHF gene in the ovaries of high reproductive bulk at the II and IV maturity stages compared to the low reproductive bulk, while almost no expression was detected in the eyestalk tissue of the high reproductive bulk. The PRDM9 gene was exclusively expressed in ovarian tissue, with significantly higher expression in the ovaries of the high reproductive bulk at the four maturity stages compared to the low reproductive bulk. Fluorescence in situ hybridization further compared the expression patterns of EHF and PRDM9 in the ovaries of individuals with different fertility levels, with both genes showing stronger positive signals in the high reproductive bulk at the four ovarian stages. These findings not only contribute to our understanding of the regulatory mechanisms involved in shrimp ovarian development, but also provide valuable insights for the cultivation of new varieties aimed at improving shrimp fecundity.

C-type lectins are known for agglutination activity and play crucial roles in regulating the prophenoloxidase (proPO) activation system, enhancing phagocytosis and encapsulation, synthesizing antimicrobial peptides, and mediating antiviral immune responses. This work cloned a C-type lectin, ladderlectin (LvLL), from Litopenaeus vannamei. LvLL comprised a 531 bp open reading frame (ORF) that encoded 176 amino acids. The predicted LvLL protein included a signal peptide and a CLECT domain. LvLL was predicted to feature a transmembrane region, suggesting it may be a transmembrane protein. LvLL was predominantly expressed in the shrimp’s hepatopancreas. After WSSV infection, LvLL expression in the hepatopancreas increased significantly by 11.35-fold after 228 h, indicating a general upregulation. Knockdown of LvLL resulted in a significant decrease in WSSV viral load and a notable increase in shrimp survival rates. Additionally, knockdown of LvLL led to a significant downregulation of apoptosis-related genes Bcl-2 and caspase 8 and a significant upregulation of p53 and proPO in WSSV-infected shrimp. This study showed that LvLL played a vital role in the interaction between L. vannamei and WSSV.

Penaeus vannamei aquaculture production accounts for the majority of total shrimp aquaculture output, but it has suffered a severe decline in production and economic losses due to WSSV disease. Therefore, elucidating the relationship between the host immune system and pathogens is crucial for shrimp disease prevention and control. Integrins, as receptor-related molecules, have been shown to participate in various physiological functions, including cell migration, organismal development, and the pathogenesis of multiple diseases. However, the regulatory mechanisms of integrin genes in the shrimp immune system remain unclear. This study reports that integrins may regulate the Toll, IMD, and STAT signaling pathways in P. vannamei by influencing Spätzle, TLR, and Domeless, thereby affecting the shrimp’s innate immune system against diseases. Additionally, integrins can inhibit viral entry and replication. Through RNA interference (RNAi) experiments, it was found that knocking down Pv-Integrin β increases the viral load of white spot syndrome virus (WSSV), making shrimp more susceptible to WSSV and giving rise to increasing mortality. Further research indicates that Pv-Integrin β acts as an upstream recognition receptor in the disease resistance immune pathway, influencing other signaling pathway receptors to regulate the innate immune system. Importantly, knocking down Pv-Integrin β upregulates the expression of antimicrobial peptides such as ALF1 and ALF2, but reduces the expression of Crustin1, Crustin2 and prophenoloxidase. In conclusion, this study reveals that Pv-Integrin β regulates the disease resistance immune signaling pathways by affecting the related receptors.

Marine animals possess genomes of considerable complexity and heterozygosity. Their unique reproductive system, characterized by high fecundity and substantial early mortality rates, increases the risk of inbreeding, potentially leading to severe inbreeding depression during various larval developmental stages. In this study, we established a set of inbred families of Fenneropenaeus chinensis, with an inbreeding coefficient of 0.25, and investigated elimination patterns and the manifestations of inbreeding depression during major larval developmental stages. Reduced-representation genome sequencing was utilized to explore the genotype frequency characteristics across two typical elimination stages. The results revealed notable mortality in hatching and metamorphosis into mysis and post-larvae stages. Inbreeding depression was also evident during these developmental stages, with depression rates of 24.36%, 29.23%, and 45.28%. Segregation analysis of SNPs indicated an important role of gametic selection before hatching, accounting for 45.95% of deviation in the zoea stage. During the zygotic selection phase of larval development, homozygote deficiency and heterozygote excess were the main selection types. Summation of the two types explained 82.31% and 89.91% of zygotic selection in the mysis and post-larvae stage, respectively. The overall distortion ratio decreased from 22.37% to 12.86% in the late developmental stage. A total of 783 loci were identified through selective sweep analysis. We also found the types of distortion at the same locus could change after the post-larvae stage. The predominant shifts included a transition of gametic selection toward normal segregation and other forms of distortion to heterozygous excess. This may be attributed to high-intensity selection on deleterious alleles and genetic hitchhiking effects. Following larval elimination, a greater proportion of heterozygous individuals were preserved. We detected an increase in genetic diversity parameters such as expected heterozygosity, observed heterozygosity, and polymorphic information content in the post-larvae stage. These findings suggest the presence of numerous recessive deleterious alleles and their linkage and suggest a major role of the partial dominance hypothesis. The results provide valuable insights into the mechanisms of inbreeding depression in marine animals and offer guidance for formulating breeding strategies in shrimp populations.

Anti-lipopolysaccharide factors (ALFs) are an important molecular category within the antimicrobial peptide family. They play a crucial role in resisting pathogen infections and are of importance in the innate immune system of shrimp. A novel ALF-like gene was identified from L. vannamei in this study. Its expression profile was investigated after WSSV infection. Results demonstrated that the mRNA transcription level of the ALF-like gene was significantly upregulated in hemocytes, hepatopancreas, gills, and intestines of L. vannamei. When the mRNA transcription level of the ALF-like gene was inhibited, the expression levels of key WSSV genes (VP 28 and IE 1) were significantly upregulated, accompanied by a decrease in shrimp survival rate. Meanwhile, the expression of genes involved in the apoptotic pathway (Lv-Caspase 3, Lv-Caspase 8, and Lv-Bcl 2) and antioxidant enzyme pathway (Lv-GST, Lv-CAT, Lv-Prx, Lv-GPX, and Lv-SOD) was also significantly increased. Flow cytometry further revealed that the hemocyte apoptosis rate induced by WSSV infection was reduced when the transcription level of the target gene was inhibited. These results indicate that the Lv-ALF-like gene plays an important regulatory role in the resistance of L. vannamei to WSSV infection, and studying the function of this gene is of great significance for disease prevention and control of shrimp.

Harvest weight uniformity is a critical economic trait in the production of Pacific white shrimp (Penaeus vannamei). Social interactions among individuals can significantly influence both uniformity and productivity in aquaculture. To improve harvest weight uniformity through selective breeding, it is essential to accurately partition the genetic component of social effects, known as an indirect genetic effect (IGE), from purely environmental factors. Since IGEs cannot be estimated when all individuals are kept in a single group, a specialized experimental design, such as the grouping design with three families per group (3FAM), is required. With this experimental design, the shrimp population is divided into multiple groups (cages), each containing three families. Individuals from each family are then evenly subdivided and placed in three cages, thereby enabling the estimation of both direct and social genetic effects. Additionally, integrating genomic information instead of relying solely on pedigree data improves the accuracy of genetic relatedness among individuals, leading to more precise genetic evaluation. This study employed a 3FAM experimental design involving 40 families (36 individuals per family) to estimate the contribution of direct and indirect genetic effects on harvest weight uniformity. The genotypes of all tested individuals obtained using the 55K SNP panel were incorporated into a hierarchical generalized linear model to predict direct genetic effects and indirect genetic effects (IGE) separately. The results revealed that the heritability of harvest weight uniformity was low (0.005 to 0.017). However, the genetic coefficient of variation (0.340 to 0.528) indicates that using the residual variance in harvest weight as a selection criterion for improving uniformity is feasible. Incorporating IGE into the model increased heritability estimates for uniformity by 150% to 240% and genetic coefficient of variation for uniformity by 32.11% to 55.29%, compared to the model without IGE. Moreover, the genetic correlation between harvest weight and its uniformity shifted from a strongly negative value (−0.862 to −0.683) to a weakly positive value (0.203 to 0.117), suggesting an improvement in the genetic relationship between the traits and better separation of genetic and environmental effects. The inclusion of genomic data enhanced the prediction ability of single-step best linear unbiased prediction for both harvest weight and uniformity by 6.35% and 10.53%, respectively, compared to the pedigree-based best linear unbiased prediction. These findings highlight the importance of incorporating IGE and utilizing genomic selection methods to enhance selection accuracy for obtaining harvest weight uniformity. This approach provides a theoretical foundation for guiding uniformity improvements in shrimp breeding programs and offers potential applications in other food production systems.