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.

Penaeid shrimp, with its genomes enriched in short tandem repeats (STRs), presents an ideal model for studying the distribution and biological functions of STRs. In this study, we systematically identified and compared STRs across multiple species, confirming a significantly higher prevalence of STRs (26–32%) in penaeid shrimp, which is markedly higher than that observed in other species, such as mammals (1.3–2.1%) and plants (0.21–0.73%). Further analysis utilizing a cohort of 326 Pacific white shrimp revealed a total of 672,507 high-quality STRs evenly distributed across the genome, with a notably lower frequency of SNPs within these STR regions. Focusing on growth traits as a case study, we conducted a genome-wide association study (GWAS) and correlation analyses to identify the regulatory relationship of STRs on complex traits. We discovered 84 STRs that showed a significant association with body weight. Interestingly, eleven of these STRs, with 81% being composed of an A/T base, showed a significant linear correlation with body weight, revealing the key role of A/T-related STRs in shrimp weight regulation. For instance, a significant association and a negative correlation were found between the copy number of the STR [(A)n] at NW_020872788.1:580574 and body weight. The cytokinesis protein 7-like (LOC113800912) gene, which contains this STR in its splice region, exhibits differential expression associated with body weight variation. These findings introduce a model for STR copy number regulation in non-human species, illuminating the influence of STRs on growth traits. It offers a valuable framework for investigating complex traits and the biological functions of STRs in agricultural animals.

Overcoming fishmeal dependence is crucial for the sustainable development of Penaeus vannamei aquaculture, yet the molecular mechanisms underlying the efficient utilization of plant-based diets remain poorly understood. In this study, residual feed intake (RFI) was used as an indicator to investigate these mechanisms. Transcriptome sequencing of the intestine, hepatopancreas, and muscle was performed on shrimp fed a plant-based diet, followed by weighted gene co-expression network analysis (WGCNA) and validation in an independent population. Phenotypic analysis revealed extensive variation in growth performance and RFI among individuals fed the plant-based diet. WGCNA identified four tissue-specific modules significantly associated with RFI, from which 20 hub genes were screened. Independent validation confirmed that seven genes were significantly differentially expressed between high- and low-feed-efficiency groups (q < 0.1): five in the intestine (LOC113811628, LOC113811631, LOC113824170, LOC113817752, LOC113811632) and two in the hepatopancreas (LOC113809216, LOC113820990). These genes are involved in mitochondrial function, energy metabolism, intracellular pH homeostasis, and nucleic acid metabolism, suggesting potential coordination between the intestine and hepatopancreas in response to plant-based diets. Collectively, these findings provide insights into the genetic basis of shrimp adaptation to plant-based diets and offer candidate molecular targets that may inform selective breeding efforts aimed at improving feed efficiency in P. vannamei.

Low-density SNP panels are widely used to reduce genotyping costs in genomic selection (GS) in aquaculture, but sparse marker density can constrain prediction accuracy, particularly in species with rapid linkage disequilibrium decay. In this study, we evaluated a locally enriched multi-SNP (mSNP) strategy derived from a conventional 1K SNP panel in a family-based breeding population of Pacific white shrimp (Penaeus vannamei). Targeted sequencing was used to recover multiple nearby variants surrounding each marker locus, and conventional SNP and mSNP panels were compared for genomic features, imputation performance, and genomic prediction accuracy for body weight. The mSNP panel exhibited higher polymorphism and broader gene-region coverage than the corresponding SNP panel. The original mSNP panel improved prediction accuracy by 11.6% over the original 1K SNP panel. This advantage was maintained or slightly improved when mSNPs were restricted to on-target variants within ±300 bp of the target markers. A locus-matched comparison further showed that enriched mSNPs consistently outperformed conventional SNPs derived from the same target loci, with a 12.0% improvement at the full 961-locus panel. Although imputation improved the 1K SNP panel, the original mSNP panel already outperformed the imputed SNP panel and reached 0.509 after imputation. These findings demonstrate that locally enriched mSNP markers provide an effective and practical strategy for improving low-density GS in aquaculture species with rapid LD decay.