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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: closed (30 April 2024) | Viewed by 5994

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

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. International Journal of Molecular Sciences is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. There is an Article Processing Charge (APC) for publication in this open access journal. For details about the APC please see here. Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

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

Published Papers (5 papers)

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Research

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 423
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 584
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 3 | Viewed by 1688
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 1163
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 1 | Viewed by 1329
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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