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Aquatic Biotechnology and Its Application in Genetic Breeding
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Aquatic Biotechnology and Its Application in Genetic Breeding

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Genetics and Genomics".

Deadline for manuscript submissions: 20 January 2025 | Viewed by 10670

Special Issue Editor

Dr. Hui Qiao

E-Mail Website
Guest Editor
Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Ministry of Agriculture and Rural Affairs, Freshwater Fisheries Research Center, Chinese Academy of Fishery Sciences, Wuxi 214081, China
Interests: aquaculture; biotechnology; germplasm improvement; genetic breeding; gene function; genomics; gene editing; population genetics
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

Recently, the aquaculture industry expands rapidly and germplasm improvement becomes a point of public attention. Along with the rapid development of aquatic biotechnology, aquaculture breeding has transformed from traditional selective breeding and hybrid breeding to advanced genetic breeding, such as sex control breeding, marker-assisted selection breeding, genome-wide genotyping-based selective breeding, and genome editing breeding. An increasing number of new aquatic organism strains have been developed with improved performance in sex, fecundity, survival rate, growth, disease resistance, etc. Although different biological methods, such as transcriptomics, proteomics, and metabolomics, have been employed, the essential mechanism of genetic changes remains unclear. A lack of this fundamental theoretical knowledge has severely hindered the progress of germplasm improvement.

This Special Issue aims to gather recent and innovative studies on aquatic biotechnology from both fundamental and applied research and provide a platform for researchers interested in aquatic biotechnology and its application in germplasm improvement and genetic breeding. Potential topics include, but are not limited to, the molecular basis of economic traits, the regulation mechanism of sex and reproduction, efficient breeding theories and methods, gene function, mechanisms of genomics and molecular breeding, and genetic structure.

Dr. Hui Qiao
Guest Editor

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Keywords

  • aquaculture
  • biotechnology
  • germplasm improvement
  • genetic breeding
  • gene function
  • genomics
  • gene editing

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Published Papers (8 papers)

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21 pages, 4143 KiB  
Article
Roadmap and Considerations for Genome Editing in a Non-Model Organism: Genetic Variations and Off-Target Profiling
by Hanin Wattad, Jonathan Molcho, Rivka Manor, Simy Weil, Eliahu D. Aflalo, Vered Chalifa-Caspi and Amir Sagi
Int. J. Mol. Sci. 2024, 25(23), 12530; https://doi.org/10.3390/ijms252312530 - 22 Nov 2024
Viewed by 120
Abstract
The CRISPR/Cas genome editing approach in non-model organisms poses challenges that remain to be resolved. Here, we demonstrated a generalized roadmap for a de novo genome annotation approach applied to the non-model organism Macrobrachium rosenbergii. We also addressed the typical genome editing [...] Read more.
The CRISPR/Cas genome editing approach in non-model organisms poses challenges that remain to be resolved. Here, we demonstrated a generalized roadmap for a de novo genome annotation approach applied to the non-model organism Macrobrachium rosenbergii. We also addressed the typical genome editing challenges arising from genetic variations, such as a high frequency of single nucleotide polymorphisms, differences in sex chromosomes, and repetitive sequences that can lead to off-target events. For the genome editing of M. rosenbergii, our laboratory recently adapted the CRISPR/Cas genome editing approach to embryos and the embryonic primary cell culture. In this continuation study, an annotation pipeline was trained to predict the gene models by leveraging the available genomic, transcriptomic, and proteomic data, and enabling accurate gene prediction and guide design for knock-outs. A next-generation sequencing analysis demonstrated a high frequency of genetic variations in genes on both autosomal and sex chromosomes, which have been shown to affect the accuracy of editing analyses. To enable future applications based on the CRISPR/Cas tool in non-model organisms, we also verified the reliability of editing efficiency and tracked off-target frequencies. Despite the lack of comprehensive information on non-model organisms, this study provides an example of the feasibility of selecting and editing specific genes with a high degree of certainty. Full article
(This article belongs to the Special Issue Aquatic Biotechnology and Its Application in Genetic Breeding)
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21 pages, 9778 KiB  
Article
Gonadal Development and Differentiation of Hybrid F1 Line of Ctenopharyngodon idella (♀) × Squaliobarbus curriculus (♂)
by Qiaolin Liu, Shitao Hu, Xiangbei Tang, Chong Wang, Le Yang, Tiaoyi Xiao and Baohong Xu
Int. J. Mol. Sci. 2024, 25(19), 10566; https://doi.org/10.3390/ijms251910566 - 30 Sep 2024
Viewed by 604
Abstract
The hybrid F1 offspring of Ctenopharyngodon idella (♂) and Squaliobarbus curriculus (♀) exhibit heterosis in disease resistance and also show abnormal sex differentiation. To understand the mechanism behind gonadal differentiation in the hybrid F1, we analyzed the transcriptomes of C. [...] Read more.
The hybrid F1 offspring of Ctenopharyngodon idella (♂) and Squaliobarbus curriculus (♀) exhibit heterosis in disease resistance and also show abnormal sex differentiation. To understand the mechanism behind gonadal differentiation in the hybrid F1, we analyzed the transcriptomes of C. idella, S. curriculus, and the hybrid F1; screened for genes related to gonad development in these samples; and measured their expression levels. Our results revealed that compared to either C. idella or S. curriculus, the gene expressions in most sub-pathways of the SNARE interactions in the vesicular transport pathway in the hypothalamus, pituitary, and gonadal tissues of their hybrid F1 offspring were significantly up-regulated. Furthermore, insufficient transcription of genes involved in oocyte meiosis may be the main reason for the insufficient reproductive ability of the hybrid F1 offspring. Through transcriptome screening, we identified key molecules involved in gonad development, including HSD3B7, HSD17B1, HSD17B3, HSD20B2, CYP17A2, CYP1B1, CYP2AA12, UGT2A1, UGT1A1, and FSHR, which showed significant differences in expression levels in the hypothalamus, pituitary, and gonads of these fish. Notably, the expression levels of UGT1A1 in the gonads of the hybrid F1 were significantly higher than those in C. idella and S. curriculus. These results provide a scientific basis for further research on the gonadal differentiation mechanism of hybrid F1 offspring. Full article
(This article belongs to the Special Issue Aquatic Biotechnology and Its Application in Genetic Breeding)
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13 pages, 10262 KiB  
Article
Enhancing Cryopreserved Sperm Quality in Chinese Rare Minnow Gobiocypris rarus: The Impact of Antifreeze Proteins
by Huan Ye, Xin Li, Li Shen, Hao Du, Qing Zhang, Yongfeng He and Jinming Wu
Int. J. Mol. Sci. 2024, 25(19), 10364; https://doi.org/10.3390/ijms251910364 - 26 Sep 2024
Viewed by 463
Abstract
The Chinese rare minnow (Gobiocypris rarus), an important model fish in China, faces endangerment in the wild. Sperm cryopreservation facilitates the development of new strains and germplasm conservation, but the quality of its cryopreserved sperm remains low. This study evaluates the [...] Read more.
The Chinese rare minnow (Gobiocypris rarus), an important model fish in China, faces endangerment in the wild. Sperm cryopreservation facilitates the development of new strains and germplasm conservation, but the quality of its cryopreserved sperm remains low. This study evaluates the protective effects of different concentrations of antifreeze proteins (AFP I and AFP III) on the cryopreservation of Chinese rare minnow sperm. Cryopreserved sperm showed significant declines in progressive motility, curvilinear velocity (VCL), average path velocity (VAP), and lifespan compared to fresh sperm, except for straight-line velocity (VSL). The cryomedium containing 10 μg/mL AFP I improved these parameters to their highest levels. However, no significant difference was found in progressive motility and kinetic parameters between cryopreserved sperm with and without AFPs. Cryopreserved sperm with 10 μg/mL AFP I showed the highest plasma membrane integrity, mitochondrial activity, and DNA integrity, significantly better than without AFPs; importantly, the fertilization rate of cryopreserved sperm with 10 μg/mL AFP I was not significantly different from that of fresh sperm. These results indicate that the addition of 10 μg/mL AFP I to the cryomedium for Chinese rare minnow sperm does not improve kinetic parameters but significantly enhances sperm quality, aiding in its new strain development and germplasm conservation. Full article
(This article belongs to the Special Issue Aquatic Biotechnology and Its Application in Genetic Breeding)
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17 pages, 4019 KiB  
Article
Comparative Transcriptomic Analysis of WSSV-Challenged Penaeus vannamei with Variable Resistance Levels
by Xupeng Li, Qian Xue, Sheng Luan, Kun Luo, Jie Kong and Xianhong Meng
Int. J. Mol. Sci. 2024, 25(9), 4961; https://doi.org/10.3390/ijms25094961 - 2 May 2024
Viewed by 1099
Abstract
The Pacific white shrimp, Penaeus vannamei, is highly susceptible to white spot syndrome virus (WSSV). Our study explored the transcriptomic responses of P. vannamei from resistant and susceptible families, uncovering distinct expression patterns after WSSV infection. The analysis revealed a higher [...] Read more.
The Pacific white shrimp, Penaeus vannamei, is highly susceptible to white spot syndrome virus (WSSV). Our study explored the transcriptomic responses of P. vannamei from resistant and susceptible families, uncovering distinct expression patterns after WSSV infection. The analysis revealed a higher number of differentially expressed genes (DEGs) in the susceptible family following WSSV infection compared to the resistant family, when both were evaluated against their respective control groups, indicating that the host resistance of the family line influences the transcriptome. The results also showed that subsequent to an identical duration following WSSV infection, there were more DEGs in P. vannamei with a high viral load than in those with a low viral load. To identify common transcriptomic responses, we profiled DEGs across families at 96 and 228 h post-infection (hpi). The analysis yielded 64 up-regulated and 37 down-regulated DEGs at 96 hpi, with 33 up-regulated and 34 down-regulated DEGs at 228 hpi, showcasing the dynamics of the transcriptomic response over time. Real-time RT-PCR assays confirmed significant DEG expression changes post-infection. Our results offer new insights into shrimp’s molecular defense mechanisms against WSSV. Full article
(This article belongs to the Special Issue Aquatic Biotechnology and Its Application in Genetic Breeding)
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12 pages, 3049 KiB  
Article
Functional Analysis of β-Carotene Oxygenase 2 (BCO2) Gene in Yesso Scallop (Patinopecten yessoensis)
by Shiqi Liu, Shuyue Wang, Liang Zhao, Tingting Li, Yihan Zhang, Huizhen Wang, Zhenmin Bao and Xiaoli Hu
Int. J. Mol. Sci. 2024, 25(7), 3947; https://doi.org/10.3390/ijms25073947 - 2 Apr 2024
Viewed by 1173
Abstract
Carotenoids are essential nutrients for humans and animals, and carotenoid coloration represents an important meat quality parameter for many farmed animals. Increasingly, studies have demonstrated that vertebrate carotenoid cleavage oxygenases (CCOs) are essential enzymes in carotenoid metabolism and are therefore potential [...] Read more.
Carotenoids are essential nutrients for humans and animals, and carotenoid coloration represents an important meat quality parameter for many farmed animals. Increasingly, studies have demonstrated that vertebrate carotenoid cleavage oxygenases (CCOs) are essential enzymes in carotenoid metabolism and are therefore potential candidate genes for improving carotenoid deposition. However, our understanding of carotenoid bioavailability and CCOs functions in invertebrates, particularly marine species, is currently quite limited. We previously identified that a CCO homolog, PyBCO-like 1, was the causal gene for carotenoid coloration in the ‘Haida golden scallop’, a variety of Yesso scallop (Patinopecten yessoensis) characterized by carotenoid enrichment. Here, we found that another CCO-encoding gene named PyBCO2 (β-carotene oxygenase 2) was widely expressed in P. yessoensis organs/tissues, with the highest expression in striated muscle. Inhibiting BCO2 expression in P. yessoensis through RNA interference led to increased carotenoid (pectenolone and pectenoxanthin) deposition in the striated muscle, and the color of the striated muscle changed from white to light orange. Our results indicate that PyBCO2 might be a candidate gene used for improving carotenoid content in normal Yesso scallops, and also in ‘Haida golden scallops’. Full article
(This article belongs to the Special Issue Aquatic Biotechnology and Its Application in Genetic Breeding)
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19 pages, 3868 KiB  
Article
Genetic Diversity, Population Structure, and Environmental Adaptation Signatures of Chinese Coastal Hard-Shell Mussel Mytilus coruscus Revealed by Whole-Genome Sequencing
by Feng Guo, Yingying Ye, Kecheng Zhu, Shuangrui Lin, Yuxia Wang, Zhenyu Dong, Ronghui Yao, Hongfei Li, Weifeng Wang, Zhi Liao, Baoying Guo and Xiaojun Yan
Int. J. Mol. Sci. 2023, 24(17), 13641; https://doi.org/10.3390/ijms241713641 - 4 Sep 2023
Cited by 6 | Viewed by 2448
Abstract
The hard-shell mussel (Mytilus coruscus) is widespread in the temperate coastal areas of the northwest Pacific and holds a significant position in the shellfish aquaculture market in China. However, the natural resources of this species have been declining, and population genetic [...] Read more.
The hard-shell mussel (Mytilus coruscus) is widespread in the temperate coastal areas of the northwest Pacific and holds a significant position in the shellfish aquaculture market in China. However, the natural resources of this species have been declining, and population genetic studies of M. coruscus are also lacking. In this study, we conducted whole-genome resequencing (WGR) of M. coruscus from eight different latitudes along the Chinese coast and identified a total of 25,859,986 single nucleotide polymorphism (SNP) markers. Our findings indicated that the genetic diversity of M. coruscus from the Zhoushan region was lower compared with populations from other regions. Furthermore, we observed that the evolutionary tree clustered into two primary branches, and the Zhangzhou (ZZ) population was in a separate branch. The ZZ population was partly isolated from populations in other regions, but the distribution of branches was not geographically homogeneous, and a nested pattern emerged, consistent with the population differentiation index (FST) results. To investigate the selection characteristics, we utilized the northern M. coruscus populations (Dalian and Qingdao) and the central populations (Zhoushan and Xiangshan) as reference populations and the southern ZZ population as the target population. Our selection scan analysis identified several genes associated with thermal responses, including Hsp70 and CYP450. These genes may play important roles in the adaptation of M. coruscus to different living environments. Overall, our study provides a comprehensive understanding of the genomic diversity of coastal M. coruscus in China and is a valuable resource for future studies on genetic breeding and the evolutionary adaptation of this species. Full article
(This article belongs to the Special Issue Aquatic Biotechnology and Its Application in Genetic Breeding)
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13 pages, 4434 KiB  
Article
Deciphering Molecular Mechanisms Governing the Reproductive Molt of Macrobrachium nipponense: A Transcriptome Analysis of Ovaries across Various Molting Stages
by Huwei Yuan, Zijian Gao, Pengfei Cai, Wenyi Zhang, Shubo Jin, Sufei Jiang, Yiwei Xiong, Yongsheng Gong, Hui Qiao and Hongtuo Fu
Int. J. Mol. Sci. 2023, 24(13), 11056; https://doi.org/10.3390/ijms241311056 - 4 Jul 2023
Cited by 1 | Viewed by 1717
Abstract
The relationship between molting and reproduction has received more attention in economically important crustacean decapods. Molting and reproduction are synergistic events in Macrobrachium nipponense, but the molecular regulatory mechanisms behind them are unclear. In the current study, we performed Illumina sequencing for [...] Read more.
The relationship between molting and reproduction has received more attention in economically important crustacean decapods. Molting and reproduction are synergistic events in Macrobrachium nipponense, but the molecular regulatory mechanisms behind them are unclear. In the current study, we performed Illumina sequencing for the ovaries of M. nipponense during the molt cycle (pre-molting, Prm; mid-molting, Mm; and post-molting, Pom). A total of 66.57 Gb of transcriptome data were generated through sequencing, resulting in the identification of 105,149 unigenes whose alignment ratio with the reference genome exceeded 87.57%. Differentially expressed genes (DEGs) were annotated through the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases for gene classification and pathway analysis. A total of twenty-six molt-related DEGs were found, and their expression patterns were examined across various molting stages. The KEGG enrichment analysis revealed that the key pathways involved in regulating the molting process of M. nipponense primarily include the mTOR, insect hormone biosynthesis, TGF-beta, and Wnt signaling pathways. Our transcriptomic data suggest that these pathways crosstalk with each other to regulate the synthesis and degradation of ecdysone throughout the molt cycle. The current study has deepened our understanding of the molecular mechanisms of crustacean molting and will serve as a basis for future studies of crustaceans and other molting animals. Full article
(This article belongs to the Special Issue Aquatic Biotechnology and Its Application in Genetic Breeding)
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17 pages, 9010 KiB  
Article
Function Analysis of Cholesterol 7-Desaturase in Ovarian Maturation and Molting in Macrobrachium nipponense: Providing Evidence for Reproductive Molting Progress
by Jisheng Wang, Sufei Jiang, Wenyi Zhang, Yiwei Xiong, Shubo Jin, Dan Cheng, Yalu Zheng, Hui Qiao and Hongtuo Fu
Int. J. Mol. Sci. 2023, 24(8), 6940; https://doi.org/10.3390/ijms24086940 - 8 Apr 2023
Cited by 3 | Viewed by 1768
Abstract
The Cholesterol 7-desaturase gene plays an important role in insect ecdysone synthesis, but its role in ovarian development has not been reported. In this study, characteristics and the phylogenetic relationship of Cholesterol 7-desaturase were identified by bioinformatics. qPCR showed that the Mn-CH7D gene [...] Read more.
The Cholesterol 7-desaturase gene plays an important role in insect ecdysone synthesis, but its role in ovarian development has not been reported. In this study, characteristics and the phylogenetic relationship of Cholesterol 7-desaturase were identified by bioinformatics. qPCR showed that the Mn-CH7D gene was highly expressed in the ovary, which was much higher than that in other tissues, and the expression level of Mn-CH7D reached the highest level at the third stage of the ovarian development stage (O-III). During embryonic development, the Mn-CH7D gene expression was highest in the zoea stage. The function of the Mn-CH7D gene was explored by RNA interference. The experimental group was injected with Mn-CH7D dsRNA through the pericardial cavity of M. nipponense, while the control group was injected with the same volume of dsGFP. Statistical analysis of gonadal development and GSI calculation showed that the silencing of Mn-CH7D resulted in the suppression of gonadal development. In addition, the molting frequency of the experimental group was significantly lower than that of the control group during the second molting cycle after silencing Mn-CH7D. On the seventh day after silencing, ecdysone content in the experimental group was significantly reduced. These results demonstrated that the Mn-CH7D gene played a dual role in ovarian maturation and molting of M. nipponense. Full article
(This article belongs to the Special Issue Aquatic Biotechnology and Its Application in Genetic Breeding)
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