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.

This study evaluated the genetic parameters for growth and Vibrio parahaemolyticus (Vp_AHPND) resistance in both the introduced MK strain and the self-constructed GK strain of Penaeus vannamei, investigating the impact of genotyped female parents on trait estimates under a single-parent nested mating design. A total of 32 families from the MK strain and 44 families from the GK strain were analyzed. Fifty-four female parents from both strains were genotyped using the “Yellow Sea Chip No. 1” containing 10.0 K SNPs. In the MK strain, heritability estimates ranged from 0.439 to 0.458 for body weight (Bw) and from 0.308 to 0.489 for survival time (ST) and survival rates at 36 h (36 SR), 50% mortality (SS₅₀), and 60 h (60 SR). In the GK strain, heritability for Bw ranged from 0.724 to 0.726, while ST, 36 SR, SS₅₀, and 60 SR had heritability estimates between 0.370 and 0.593. Genetic correlations between Bw and ST were 0.601 to 0.622 in the MK strain and 0.742 to 0.744 in the GK strain. For Bw and survival rates, correlations ranged from 0.120 to 0.547 in the MK strain and from 0.426 to 0.906 in the GK strain. The genetic correlation between ST and survival rates was not significantly different from 1 (p > 0.05) in both strains. High Pearson correlations (0.853 to 0.997, p < 0.01) were observed among survival rates at different points. Predictive accuracies for Bw, ST, and survival rates using single-step genomic best linear unbiased prediction (ssGBLUP) were comparable to pedigree-based best linear unbiased prediction (pBLUP) in the MK strain, while in the GK strain, ssGBLUP improved predictive accuracies for Bw, ST, and SS₅₀ by 0.20%, 0.32%, and 0.38%, respectively. The results indicate that both growth and Vp_AHPND resistance have significant breeding potential. Although the genetic correlation between weight and resistance varies across different populations, there is a positive genetic correlation between these traits, supporting the feasibility of multi-trait selection. To enhance genetic accuracy, breeding programs should include more genotyped progeny. These findings also suggest that infection frequency and observation time influence resistance performance and breeding selection, emphasizing the need for a tailored resistance evaluation program to improve breeding efficiency and reduce costs.

The Indian Ocean is globally significant in terms of capture fisheries, and understanding the species composition of fish in the Indian Ocean is of great importance for the protection and development of its fishery resources. While coastal fish communities in the Indian Ocean are relatively well-documented, studies on pelagic zones remain sparse, especially for non-target species constituting fishery bycatch. Traditional biodiversity surveys rely on labor-intensive, inefficient trawling methods. To address these limitations, this study aims to apply environmental DNA (eDNA) metabarcoding for a species diversity survey in the Western Indian Ocean, offering a more reliable, efficient, and non-invasive alternative to traditional methods. The results will provide important insights into the region’s fish biodiversity, supporting sustainable management and conservation of fisheries resources in the area. Samples were collected from 130 stations in different water layers in the Western Indian Ocean, and species diversity was analyzed through 12S rRNA gene amplicon sequencing. The results showed that 98 fish species were detected from 176 seawater eDNA samples, belonging to two classes (Actinopteri and Chondrichthyes), 20 orders, 35 families, and 60 genera. Within a depth range of 300 m, there were no significant differences in species diversity parameters among samples from different depths. The orders with the highest relative abundance detected include Scombriformes, Aulopiformes, and Myctophiformes. The species with the highest relative abundance include Thunnus albacares, Alepisaurus ferox, Xiphias gladius, Diaphus fragilis, Decapterus macarellus, Thunnus maccoyii, and Platycephalus cultellatus. The species composition and relative abundance of economic species observed in this study showed, as expected, differences from fishery catch statistics. These results suggest that eDNA technology can not only monitor marine fish diversity more efficiently but also complement the lack of fisheries data. Integrating eDNA technology into routine monitoring in the Western Indian Ocean in the future could promote sustainable management of fisheries resources in the region.

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.

Reproductive inefficiency remains a major constraint in Penaeus vannamei hatcheries due to high rates of non-spawning females. This study presents the first two-generational quantitative genetic analysis of female reproductive performance under standardized SPF (Specific Pathogen-Free) conditions. A total of 986 females across two generations (2021–2022) from 198 full-sib and 68 half-sib families were evaluated. Traits analyzed included spawning frequency (SF), mean spawning interval (MSI), number of eggs laid for the first time (NE1), average spawning (AS), total spawning (TS), and spawning success (SS). Heritability estimates for SF, SS, and TS were moderate (0.30 ± 0.06, 0.23 ± 0.06 and 0.28 ± 0.07, respectively), while MSI, NE1, and AS showed low heritability (0.10–0.16). When analyzed separately by year, heritability estimates declined substantially for most traits in the second generation. Strong positive genetic correlations were observed between SF, MSI, NE1, AS, and TS, with pairwise estimates ranging from 0.82 to 0.99, indicating that these traits are under shared genetic control. Despite not being direct selection objects, all reproductive traits exhibited relative genetic progress (246–488% per generation), which is attributable to the high selection intensity applied to the parental generation. Our findings provide a robust foundation for integrating reproductive performance into breeding programs for P. vannamei, particularly under biosecurity and commercial feed-dominated conditions.

Litopenaeus vannamei, commonly known as the Pacific white shrimp, is one of the most economically significant species in global aquaculture, valued for its rapid growth and adaptability. However, the mechanisms regulating its growth, especially under high-density farming and environmental stress, remain poorly understood. Previous study predicted that LvSlc12A2 was involved in growth regulation. To further reveal the function of this gene in the growth regulation of the whiteleg shrimp, in this study, we explore its function using RT-qPCR, RNA interference, overexpression, and tissue in situ hybridization. RT-qPCR results showed that LvSlc12A2 was highly expressed in gills (about 62%), followed by the hepatopancreas, with the lowest expression in muscle (0.08%, compared to the gills). Myostatin (LvMstn) was mainly expressed in the heart, and molt-inhibiting hormone (LvMIH) in the ventral nerve. In situ hybridization of gill tissues using the mRNA of the gene as a probe revealed strong LvSlc12A2 signals in the gill stratum and epithelial cells. Overexpression of LvSlc12A2, significantly decreased the osmotic gene aquaporin (LvAqp), while knockdown increased its expression. Additionally, levels of growth-related inhibitory genes LvMstn and LvMIH increased significantly after LvSlc12A2 overexpression and were downregulated after its knockdown, suggesting LvSlc12A2 negatively regulates growth, possibly in synergy with LvMstn and LvMIH. These findings indicate LvSlc12A2 influences growth both by negative regulation and by modulating osmotic balance in gill tissues.