Genomic signatures of artificial selection in fecundity of Pacific white shrimp, Penaeus vannamei

Quantitative Genetics of Feed-Efficiency-Related Traits for the Pacific Whiteleg Shrimp Penaeus vannamei in a Plant-Based Diet Environment

Selecting shrimp strains that perform well on a plant-based diet holds promise for solving the fishmeal (FM) shortage issue, with genetic improvement of feed efficiency (FE) being a key focus. This study compared a plant-based (fishmeal-free) diet with a 25% FM diet for the Pacific whiteleg shrimp (Penaeus vannamei) to determine whether the FE-related traits, including residual feed intake (RFI), average daily weight gain (ADG), and daily feed intake (DFI), exhibit diet-specific genetic variations and genotype-by-diet (genotype × diet) interactions. Results showed that RFI was significantly higher under the plant-based diet treatment compared to the FM-based diet treatment (0.0049 g/d vs. -0.0045 g/d, p < 0.001), while ADG was notably lower (0.043 g/d vs. 0.110 g/d, p < 0.001), indicating that a plant-based diet may lead to reduced yields and impact the profitability of shrimp culture. In the case of being unable to estimate common environmental effects, the heritability estimates of RFI under the plant-based and FM-based diets were 0.743 ± 0.157 and 0.440 ± 0.125, respectively, and those of ADG and DFI ranged from 0.314 ± 0.121 to 0.947 ± 0.158. Genetic correlations between diets for RFI and DFI were 0.646 ± 0.162 and 0.549 ± 0.163, respectively, suggesting a degree of genotype × diet interactions. In contrast, the genetic correlation between diets for ADG was only 0.296 ± 0.259, indicating a strong genotype × diet interaction. These findings highlight the importance of considering selective breeding for improved feed efficiency in a plant-based diet environment.

Identification of structural variation related to spawn capability of Penaeus vannamei

BACKGROUND

The genetic basis underlying spawning abilities in the Pacific white shrimp, Penaeus vannamei, remains largely unexplored. To investigate genetic variations potentially related to reproductive performance, a systematic bioinformatic analysis was conducted to identify structural variations (SVs) with different polymorphic spectra in P. vannamei with high fertility (HF) and low fertility (LF).

RESULTS

A total of 2,323 and 1,859 SV events were identified exclusively in the HF and LF groups, respectively. These SVs were mapped to 277 genes in the HF group and 231 genes in the LF group. Gene Ontology (GO) enrichment analysis based on SNPs (single nucleotide polymorphism) and SVs revealed several neural-related processes, suggesting the importance of neural regulation in reproduction. Notably, we identified a set of promising genes, including Cttn, Spast, Ppp4c, Spire1, Lhcgr, and Ftz-f1, which may enhance fertility in shrimp.

CONCLUSION

In conclusion, this study is the first to establish a link between SVs and reproductive traits in P. vannamei. The promising genes discovered have the potential to serve as crucial markers for enhancing reproductive traits through targeted genotyping.

Development of DNA Markers for Acute Hepatopancreatic Necrosis Disease Tolerance in Litopenaeus vannamei through a Genome-Wide Association Study

Shrimp aquaculture is facing a serious disease, acute hepatopancreatic necrosis disease (AHPND), caused by Vibrio paraheamolyticus (VpAPHND). For sustainable shrimp aquaculture, massive losses of shrimp infected with VpAPHND must be prevented. Research and selection of shrimp tolerant to VpAPHND infection is a sustainable approach to reducing the risk of AHPND. This study focused on the identification and development of potential DNA markers associated with AHPND using DArT sequencing (DArTSeq) and a genome-wide association study. Three populations of post-larval Litopenaeus vannamei were immersed in VpAPHND to collect susceptible (D) and tolerant (S) samples. The 45 D and 48 S shrimp had their genotypes analyzed using DArTSeq. A total of 108,983 SNPs and 17,212 InDels were obtained from the DArTseq data, while the biallelic 516 SNPs and 2293 InDels were finally filtered with PIC < 0.1, MAF < 0.05, and a call rate ≥ 80%. The filtered variants were analyzed for their association with AHPND tolerance. Although there were no significantly associated SNPs and InDels above the Bonferroni correction threshold, candidate variants, four SNPs and 17 InDels corresponding to p < 0.01, were provided for further validation of the AHPND tolerance trait. The candidate SNPs are located on an exon of the zinc finger protein 239-like gene, an intron of an uncharacterized gene, and in intergenic regions. Most of the candidate InDels are in the intergenic regions, with fewer in the intronic and exonic regions. This study provides information on SNPs and InDels for white shrimp. These markers will support the variant database of shrimp and be useful in shrimp aquaculture for breeding selection.

Reproductive Ability Disparity in the Pacific Whiteleg Shrimp (Penaeus vannamei): Insights from Ovarian Cellular and Molecular Levels

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.