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Molecular Genetics and Genomics of Aquatic Crustaceans

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A Special Issue of International Journal of Molecular Sciences (ISSN 1422-0067) belonging to the section "Molecular Genetics and Genomics".

Deadline for manuscript submissions: 23 April 2027 | Viewed by 4084

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Editors

Prof. Dr. Xianhong Meng

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Guest Editor

State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China
Interests: aquaculture; breeding; molecular
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Prof. Dr. Falin Zhou

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Guest Editor

Key Laboratory of South China Sea Fishery Resources Exploitation and Utilization, Ministry of Agriculture, South China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510300, China
Interests: germplasm resource evaluation; breeding; genetic improvement
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Prof. Dr. Lingbo Ma

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Guest Editor

Key Laboratory of East China Sea Fishery Resources Exploitation, Ministry of Agriculture and Rural Affairs, East China Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Shanghai 200090, China
Interests: aquaculture; genetics; breeding

Special Issue Information

Dear Colleagues,

Genomics and molecular genetics have revolutionized our understanding of biological systems, providing insights into genome structure, function, and evolution and their applications in breeding and biotechnology. In recent years, advances in sequencing technologies and bioinformatics tools have greatly enhanced genomic research, enabling comprehensive studies on genotype–phenotype relationships across diverse species. While significant progress has been made in plant and terrestrial animal genomics, aquatic crustaceans—a highly diverse and ecologically significant group—remain relatively understudied at the genomic level.

This Special Issue, “Molecular Genetics and Genomics of Aquatic Crustaceans”, will highlight recent advancements in genomic research on crustaceans, including crabs, lobsters, shrimp, and other aquatic arthropods. We welcome contributions covering a wide range of topics, such as genome sequencing and assembly, comparative genomics, genome evolution, gene editing (e.g., CRISPR), transcriptomics (RNA-seq), expression profiling, functional genomics, epigenetics, SNP discovery, genome-wide association studies (GWASs), and genomic selection. By showcasing cutting-edge research articles in this field, we hope to foster a deeper understanding of crustacean biology and support applications in aquaculture, conservation, and evolutionary studies.

Prof. Dr. Xianhong Meng
Prof. Dr. Falin Zhou
Prof. Dr. Lingbo Ma
Guest Editors

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Keywords

genome sequencing
epigenomics
CRISPR/Cas9 gene editing
transcriptomics
gene expression profiling
genome-wide association studies (GWASs)
quantitative trait loci (QTL) mapping
genomic selection
marker-assisted selection (MAS)
molecular markers

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Published Papers (4 papers)

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Research

14 pages, 1138 KB

Open AccessArticle

Identification of Growth-Related Single-Nucleotide Polymorphisms in the cAMP-Dependent Protein Kinase Type I Regulatory Subunit-like Gene of the Oriental River Prawn, Macrobrachium nipponense

by Yuefan Zhang, Hao Dong, Xiaofan Fang, Hui Qiao, Wenyi Zhang, Yiwei Xiong, Sufei Jiang and Shubo Jin

Int. J. Mol. Sci. 2026, 27(16), 7500; https://doi.org/10.3390/ijms27167500 - 21 Aug 2026

Viewed by 324

Abstract

Macrobrachium nipponense is an economically important freshwater crustacean in China, and growth-related traits are major determinants of its commercial value. Identifying single nucleotide polymorphisms (SNPs) associated with growth-related traits may provide useful molecular markers for the genetic improvement of growth performance. Previous studies have suggested that the cAMP-dependent protein kinase type I regulatory subunit-like gene (Mn-PKA-R1) is involved in the regulation of growth and molting in M. nipponense. In the present study, a cultured full-sib family comprising 120 females and 120 males was used to screen SNPs within the coding region of Mn-PKA-R1, and evaluate their associations with body weight, body length, full length, and abdominal width. Seven SNPs were identified in exon 12, including five nonsynonymous missense variants and two synonymous variants, whereas no SNPs were detected in the other exons examined. The mean effective number of alleles (N_e), observed heterozygosity (H_o), expected heterozygosity (H_e), Nei’s gene diversity (Nei), and polymorphic information content (PIC) were 1.3561, 0.3048, 0.2350, 0.2340, and 0.1962, respectively, in females, compared with 1.3118, 0.2714, 0.1868, 0.1861, and 0.1512, respectively, in males. Four SNPs were significantly associated with growth-related traits in females: C+82748G and A+82750G were associated with body weight and abdominal width, T+82810G was associated with abdominal width, and A+83324G was associated with body weight, full length, and abdominal width (p < 0.05). No significant genotype–trait associations were detected among the SNP loci that could be statistically evaluated in males. Pairwise r² values ranged from 0.001 to 0.693 in females and from 0.000 to 0.351 in males, with generally higher values observed in females within the investigated full-sib family. Females also showed slightly higher mean genetic polymorphism parameters than males, while significant SNP–trait associations were detected only in females within this family. These findings provide candidate SNPs for further validation of their potential utility in marker-assisted selection in M. nipponense. Full article

(This article belongs to the Special Issue Molecular Genetics and Genomics of Aquatic Crustaceans)

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16 pages, 8063 KB

Open AccessArticle

Identification of Potential Roles of Bestrophin 3 in the Growth Performance of Ortiental River Prawn Macrobrachium nipponense by RNA Interference

by Shubo Jin, Zijian Gao, Hongtuo Fu, Yiwei Xiong, Hui Qiao, Wenyi Zhang and Sufei Jiang

Int. J. Mol. Sci. 2026, 27(12), 5338; https://doi.org/10.3390/ijms27125338 - 13 Jun 2026

Cited by 1 | Viewed by 418

Abstract

Macrobrachium nipponense is an economically important freshwater prawn species in China, where larger individuals have higher commercial value than smaller ones. Previous studies indicated that bestrophin 3 (BEST3) may play a regulatory role in the growth performance of this species. Therefore, the present study investigated the potential functions of the BEST3 gene in the growth of M. nipponense by using quantitative real-time PCR (qPCR) and RNA interference (RNAi), and also searched for growth-related single-nucleotide polymorphisms (SNPs) within this gene. qPCR results revealed that Mn-BEST3 expression was widely detected across all tested tissues, suggesting that this gene may serve multiple functions in M. nipponense. Notably, its highest expression was observed in muscle tissue, which was significantly greater than that in all other tested tissues (p < 0.05), implicating a potential role for this gene in growth regulation. Further qPCR analysis confirmed that the synthesized dsBEST3 effectively reduced Mn-BEST3 expression. The body mass gain percentage in the dsBEST3-injected group was significantly lower than that in the dsGFP-injected control group, with differences becoming significant from Day 12 onward in both males and females (p < 0.05). These findings indicate that Mn-BEST3 plays a positive role in regulating growth in M. nipponense. Finally, three SNPs were identified in the coding region of this gene. The associations of these three SNPs with growth performance, including body weight and total length, were further validated using 50 male and 50 female prawns derived from a full-sib family at approximately 5 months post-hatching. Among them, one SNP (S31_23192836) was found to be associated with growth performance in both male prawns and female prawns. Overall, this study confirmed the positive regulatory role of BEST3 in the growth of M. nipponense and identified growth-related SNPs within this gene. These results improve our understanding of the molecular mechanisms underlying growth regulation and support the production of populations with superior growth traits through marker-assisted selection. Full article

(This article belongs to the Special Issue Molecular Genetics and Genomics of Aquatic Crustaceans)

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15 pages, 2491 KB

Open AccessArticle

Effects of Stocking Density on Growth Performance, Physiological Responses, and Transcriptomic Profile of Penaeus monodon

by Jianzhi Shi, Wenzhe Li, Song Jiang, Hongshan Diao, Jianhua Huang, Lishi Yang, Yundong Li, Yangyang Ding, Yafei Duan, Xu Chen, Qibin Yang and Falin Zhou

Int. J. Mol. Sci. 2026, 27(3), 1505; https://doi.org/10.3390/ijms27031505 - 3 Feb 2026

Cited by 1 | Viewed by 1098

Abstract

Stocking density plays an important role in P. monodon aquaculture. However, its underlying molecular mechanisms remain unknown. In this work, after a 40-day culture period, we studied the effects of different stocking densities (G1: 50, G2: 100, G3: 150 ind/m³) on P. monodon, assessing their growth performances, physiological indexes, and transcriptome profiles. It was found that increased stocking density greatly decreased the growth performance and survival rate as well as the level of immune enzymes (alkaline phosphatase, acid phosphatase) and antioxidant component (total antioxidant capacity, superoxide dismutase, reduced glutathione) activities. Transcriptomic analysis showed that there are 2284 differentially expressed genes in all groups. Enrichment analysis of WGCNA results indicated that the green module associated with G2 was enriched for amino acid metabolism, lipid metabolism and immunity-related pathway. Furthermore, the G3 associated turquoise module was dominated by stress response, detoxification and energy metabolism pathways. Together, high stocking density causes the occurrence of oxidative stress, disturbance to immune system and alteration of metabolism profiles in P. monodon, whereas medium density (G2) is favorable to maintain physiological homeostasis. The results provide theoretical support to optimize aquaculture practice and contribute valuable information for subsequent studies. Full article

(This article belongs to the Special Issue Molecular Genetics and Genomics of Aquatic Crustaceans)

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21 pages, 4068 KB

Open AccessArticle

Integrin β Regulates the Hepatopancreas Antiviral Innate Immune System by Affecting the Expression of Antimicrobial Peptides in Penaeus vannamei

by Bingbing Yang, Li Zhang, Kun Luo, Sheng Luan, Jie Kong, Qiang Fu, Jiawang Cao, Baolong Chen, Ping Dai, Xupeng Li and Xianhong Meng

Int. J. Mol. Sci. 2025, 26(17), 8478; https://doi.org/10.3390/ijms26178478 - 31 Aug 2025

Cited by 4 | Viewed by 1710

Abstract

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. Full article

(This article belongs to the Special Issue Molecular Genetics and Genomics of Aquatic Crustaceans)

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