Transcriptome differential expression analysis reveals the activated genes in Litopenaeus vannamei shrimp families of superior growth performance

Santos, Camilla A.; Andrade, Sónia Cristina da Silva; Teixeira, Ana Karina; Farias, Flávio; Guerrelhas, Ana C.; Rocha, J. L.; Freitas, Patrícia Domingues de

doi:10.1016/j.aquaculture.2020.735871

Cited by 27 publications

(16 citation statements)

References 60 publications

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“…This indicates that the Toll pathway may be involved in the process of regulating growth. Santos et al (2020) reported that several immune‐related genes were up‐regulated in the high‐growth group, suggesting that these animals may potentially display more efficient and faster immune responses when eventually in contact with pathogens (Santos et al, 2020). This is consistent with the results presented here.…”

Section: Discussionmentioning

confidence: 99%

Comparative analysis of different density restrictions reveals the potential influence mechanism on the compensatory growth of Litopenaeus vannamei

Liu

Jiang

et al. 2022

Aquaculture Research

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Shrimp nursery rearing technology is increasingly being used by aquatic farmers and enterprises. Determining an appropriate density restriction in order to obtain a greater compensatory growth potential is the key to this technology. Based on the industry standards for indoor shrimp farming, three densities for Litopanaeus vannamei nursery rearing were examined (D1 [control] = 10,000 PL/m3, D3 = 30,000 PL/m3, and D5 = 50,000 PL/m3). The results showed that the D5 group had an over‐compensation growth effect, whereas the D3 group showed a full‐compensation growth effect. A preliminary investigation of the mechanism of compensatory growth was explored. The results showed that during the compensation stage, the SGR (Special Growth Rate) and FCE (Feed Conversion Efficiency) of the D5 group were significantly higher (p < 0.05) than the control. T‐SOD enzyme activity was not significantly different (p > 0.05) from the control. Antioxidants such as CAT, GSH‐PX and MDA all had compensatory changes. In addition, the relative mRNA expression of several genes was measured. The results showed that growth‐related genes (EGFR, MSTN), molting‐related genes (MIH), immune‐related genes (Toll) and digestion‐related genes (α‐amylase) had a relative compensation of mRNA expression. Meanwhile, transcriptome analysis of shrimps after different density restrictions in the compensation stage was performed. Totally 237 and 348 differentially expression genes (DEGs) were identified in the D5‐ and D3‐treated shrimps, respectively. In D5‐treated shrimps, DEGs were annotated and grouped into nine processes or pathways related to animal metabolic response. With respect to D3‐treated shrimps, DEGs were mainly annotated to 15 processes or pathways related to animal metabolic response. Therefore, this study provides a basis for the theory and practice of compensatory growth during the nursery rearing of commercial shrimp.

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Section: Discussionmentioning

confidence: 99%

Comparative analysis of different density restrictions reveals the potential influence mechanism on the compensatory growth of Litopenaeus vannamei

Liu

Jiang

et al. 2022

Aquaculture Research

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“…Based on the transcriptome data, myosin, myosin heavy chain, and chitinase were proved to be related to growth performance in L. vannamei (Santos et al, 2018). Transcriptome comparison between the families with high growth rate and low growth rate also illustrated that the genes related to cuticle, chitin, and muscle proteins were upregulated exclusively in higher growth families (Santos et al, 2021). Besides, the gene profiles of the Vibrioresistant and Vibrio-susceptible Meretrix petechialis families were analyzed, and several genes such as Big-Def, CTL9, and Bax were identified as candidate resistance-associated genes (Jiang et al, 2017).…”

Section: Introductionmentioning

confidence: 96%

Comparison of Gene Expression Between Resistant and Susceptible Families Against VPAHPND and Identification of Biomarkers Used for Resistance Evaluation in Litopenaeus vannamei

Zhang

Luo

et al. 2021

Front. Genet.

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Acute hepatopancreatic necrosis disease (AHPND) has caused a heavy loss to shrimp aquaculture since its outbreak. Vibrio parahaemolyticus (VPAHPND) is regarded as one of the main pathogens that caused AHPND in the Pacific white shrimp Litopenaeus vannamei. In order to learn more about the mechanism of resistance to AHPND, the resistant and susceptible shrimp families were obtained through genetic breeding, and comparative transcriptome approach was used to analyze the gene expression patterns between resistant and susceptible families. A total of 95 families were subjected to VPAHPND challenge test, and significant variations in the resistance of these families were observed. Three pairs of resistant and susceptible families were selected for transcriptome sequencing. A total of 489 differentially expressed genes (DEGs) that presented in at least two pairwise comparisons were screened, including 196 DEGs highly expressed in the susceptible families and 293 DEGs in the resistant families. Among these DEGs, 16 genes demonstrated significant difference in all three pairwise comparisons. Gene set enrichment analysis (GSEA) of all 27,331 expressed genes indicated that some energy metabolism processes were enriched in the resistant families, while signal transduction and immune system were enriched in the susceptible families. A total of 32 DEGs were further confirmed in the offspring of the detected families, among which 19 genes were successfully verified. The identified genes in this study will be useful for clarifying the genetic mechanism of shrimp resistance against Vibrio and will further provide molecular markers for evaluating the disease resistance of shrimp in the breeding program.

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“…This heterosis could improve the survival rate of hybrids, which is important for aquaculture. However, compared to shrimp, mollusks, and other aquatic animals [ 73 , 74 ], the molecular mechanisms of heterosis in immunity and antioxidant capacity in fish hybrids remain unclear. We report disease and cellular process pathways to be mostly enriched from ELD-NL and ELD-AR genes, including “apoptosis”, “hepatitis C”, “p53 signaling pathway”, and “platinum drug resistance”.…”

Section: Discussionmentioning

confidence: 99%

Integration of mRNA and miRNA Profiling Reveals Heterosis in Oreochromis niloticus × O. aureus Hybrid Tilapia

Xiao

Chen

Wang

et al. 2022

Animals

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Heterosis is a widespread biological phenomenon in fishes, in which hybrids have superior traits to parents. However, the underlying molecular basis for heterosis remains uncertain. Heterosis in growth and survival rates is apparent in hybrid tilapia (Oreochromis niloticus ♀ × O. aureus ♂). Comparisons of growth and hematological biochemical characteristics and mRNA and miRNA transcriptional analyses were performed in hybrid and parents tilapia stocks to investigate the underlying molecular basis for heterosis. Growth characteristics and hematological glucose and cholesterol parameters were significantly improved in hybrids. Of 3097 differentially expressed genes (DEGs) and 120 differentially expressed miRNAs (DEMs) identified among three stocks (O. niloticus, O. aureus, and hybrids), 1598 DEGs and 62 DEMs were non-additively expressed in hybrids. Both expression level dominance and overdominance patterns occurred for DEGs and DEMs, indicating that dominance and overdominance models are widespread in the transcriptional and post-transcriptional regulation of genes involved in growth, metabolism, immunity, and antioxidant capacity in hybrid tilapia. Moreover, potential negative regulation networks between DEMs and predicted target DEGs revealed that most DEGs from miRNA-mRNA pairs are up-regulated. Dominance and overdominance models in levels of transcriptome and miRNAome facilitate the integration of advantageous parental alleles into hybrids, contributing to heterosis of growth and improved survival. The present study provides new insights into molecular heterosis in hybrid tilapia, advancing our understanding of the complex mechanisms involved in this phenomenon in aquatic animals.

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Transcriptome differential expression analysis reveals the activated genes in Litopenaeus vannamei shrimp families of superior growth performance

Cited by 27 publications

References 60 publications

Comparative analysis of different density restrictions reveals the potential influence mechanism on the compensatory growth of Litopenaeus vannamei

Comparative analysis of different density restrictions reveals the potential influence mechanism on the compensatory growth of Litopenaeus vannamei

Comparison of Gene Expression Between Resistant and Susceptible Families Against VPAHPND and Identification of Biomarkers Used for Resistance Evaluation in Litopenaeus vannamei

Integration of mRNA and miRNA Profiling Reveals Heterosis in Oreochromis niloticus × O. aureus Hybrid Tilapia

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