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Genetics and Molecular Breeding in Fisheries and Aquaculture
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Genetics and Molecular Breeding in Fisheries and Aquaculture

A special issue of Genes (ISSN 2073-4425). This special issue belongs to the section "Animal Genetics and Genomics".

Deadline for manuscript submissions: closed (30 September 2024) | Viewed by 12750

Special Issue Editors

Dr. Lei Liu

E-Mail Website
Guest Editor
School of Marine Sciences, Ningbo University, Ningbo 315832, China
Interests: aquaculture; genetic diversity; molecular breeding; regeneration regulation; behavioral genetics; genome; GWAS
Dr. Kai Zhang

E-Mail Website
Guest Editor Assistant
College of Marine Science and Engineering, Nanjing Normal University, Nanjing 210023, China
Interests: molecular biology; fish breeding; genetics; genome; aquatic economic animals
Special Issues, Collections and Topics in MDPI journals
Dr. Xuedi Du

E-Mail Website1 Website2
Guest Editor Assistant
College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
Interests: fish genetics; fish morphology evolution; aquatic animals; fish physiology

Special Issue Information

Dear Colleagues,

With decades of efforts, scientists have made remarkable achievements in characterizing genomic structure, genomic variations, and the genetic basis of economically important traits of aquaculture species, which is helpful to improve production efficiency in order to satisfy consumer demands and improve the commercial profits of fisheries and aquaculture. Genetic dissection of important economic traits, including growth rate, disease resistance, sexual determination, and tolerance of various environmental stressors in aquaculture animals, has become the focus of basic research. Moreover, advanced molecular biology technologies such as genome wide selective breeding, gene editing, and cell transplantation have been extensively applied to genetics and breeding in the aquaculture industry. Whereas in most fish and other aquatic animals, major genes related to economic traits have not been identified, and the understandings of regulatory mechanisms for sex determination, disease resistance, stress resistance, environmental adaptation, reproduction, and development are quite limited. In this Special Issue, we are interested in publishing research articles and reviews on genetics and molecular breeding in fisheries and aquaculture, including WGS and fine mapping, the construction of high-density genetic maps, trait-related markers, sex control, genome editing, multi-omics combinations of genome, transcriptome, proteome, metabolome, and epigenome, and other molecular breeding technologies application in aquatic genetics and breeding.

Dr. Lei Liu
Guest Editor

Dr. Kai Zhang
Dr. Xuedi Du
Guest Editor Assistants

Manuscript Submission Information

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Keywords

  • aquaculture species
  • molecular breeding
  • genomic
  • economic traits
  • sex determination
  • disease resistance
  • stress resistance
  • reproduction and development
  • genome editing
  • multi-omics

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Published Papers (10 papers)

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Research

13 pages, 1409 KiB  
Article
Assessment of Stress and Immune Gene Expression in Australasian Snapper (Chrysophrys auratus) Exposed to Chronic Temperature Change
by Kerry Bentley-Hewitt, Christina K. Flammensbeck, Duncan I. Hedderley and Maren Wellenreuther
Genes 2025, 16(4), 385; https://doi.org/10.3390/genes16040385 - 28 Mar 2025
Viewed by 485
Abstract
Background: Snapper is a significant commercial, recreational, and cultural teleost species in New Zealand, with aquaculture potential. The impact of long-term (chronic) temperature changes on immune and stress responses have not been studied in snapper, yet they have a critical importance to the [...] Read more.
Background: Snapper is a significant commercial, recreational, and cultural teleost species in New Zealand, with aquaculture potential. The impact of long-term (chronic) temperature changes on immune and stress responses have not been studied in snapper, yet they have a critical importance to the health status of the fish. Methods: We investigated a set of genes in 30 individual snapper including fin, head kidney, and liver tissue, fish (10 per group) were exposed to either warm (22 °C), cold (14 °C), or ambient temperatures (10.5–18.6 °C) for 3 months. Results: Analyses of experimental fish using NanoString technologies to assess stress- and immune-related genes in the three tissue types showed that 22 out of 25 genes changed significantly in the experiment, indicating the significant impacts of chronic temperature changes on stress and immune responses. Furthermore, using a combined dataset based on this study and a previous one testing the impact of acute temperature changes in snapper, we identified five genes in the non-lethal fin-clip samples that can predict internal organ health status. Conclusions: Taken together, our experiments demonstrate the potential of the NanoString gene expression assessment tool for the rapid monitoring of stress responses in snapper, which can aid in the selection of stress-resilient wild stocks, monitor species in aquaculture environments, and inform the selection of locations for aquaculture. Full article
(This article belongs to the Special Issue Genetics and Molecular Breeding in Fisheries and Aquaculture)
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13 pages, 2311 KiB  
Article
Assessment of a Novel Stress and Immune Gene Panel on the Development of Australasian Snapper (Chrysophrys auratus) Larvae
by Kerry L. Bentley-Hewitt and Duncan I. Hedderley
Genes 2024, 15(12), 1520; https://doi.org/10.3390/genes15121520 - 27 Nov 2024
Viewed by 618
Abstract
Background: Larvae development is a critical step in aquaculture, yet the development of immune and stress responses during this early phase of life is not well understood. Snapper is a species that has been selected as a candidate for aquaculture in New Zealand. [...] Read more.
Background: Larvae development is a critical step in aquaculture, yet the development of immune and stress responses during this early phase of life is not well understood. Snapper is a species that has been selected as a candidate for aquaculture in New Zealand. Methods: In this study we explore a set of 18 genes identified as potentially being involved in the stress and immune responses of snapper larvae during the first 30 days of development. Larvae were collected between 11:45 a.m. and 16:10 p.m. each day. Results: Most genes did not deviate from baseline expression throughout the 30 days, with some exceptions between Days 0 and 6 with glyceraldehyde-3-phosphate dehydrogenase and superoxide dismutase, mitochondrial uncoupling protein 2-like, peroxiredoxin-5 mitochondrial, and hepcidin, which predominantly increased and then stabilized by Day 6 until Day 30. Some genes were affected by the time of day, such as actin cytoplasmic 1 and catalase isoform X2. Conclusions: This exploratory study is the first to look at a panel of stress- and immune-related marker gene expression during early snapper development. It sets methods in place to explore the expression of these markers and determine the impact of different potential stressors, such as alternative food sources and other environmental changes. It also highlights the importance of same time of day collections for gene expression studies. Full article
(This article belongs to the Special Issue Genetics and Molecular Breeding in Fisheries and Aquaculture)
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17 pages, 5992 KiB  
Article
Characterization of HSP70 and HSP90 Gene Family in Takifugu fasciatus and Their Expression Profiles on Biotic and Abiotic Stresses Response
by Wenwen Zhang, Ziang Qian, Jie Ji, Tao Wang, Shaowu Yin and Kai Zhang
Genes 2024, 15(11), 1445; https://doi.org/10.3390/genes15111445 - 8 Nov 2024
Viewed by 1219
Abstract
Background: Heat shock proteins (HSPs) play crucial roles in response to temperature changes and biotic stresses. However, the HSP gene family in the pufferfish (Takifugu fasciatus) herring has not been comprehensively investigated. Methods and Results: This study presents a systematic analysis [...] Read more.
Background: Heat shock proteins (HSPs) play crucial roles in response to temperature changes and biotic stresses. However, the HSP gene family in the pufferfish (Takifugu fasciatus) herring has not been comprehensively investigated. Methods and Results: This study presents a systematic analysis of the HSP70 and HSP90 gene families in T. fasciatus, focusing on gene characterization, conserved structural domains, molecular evolutionary history, and expression patterns of the HSP gene family under stress conditions. The findings reveal that 16 HSP genes are evolutionarily conserved, while hspa4 and hsp90aa appear specific to teleost fish. HSP genes exhibit widespread expression across 11 examined tissues, with most demonstrating high expression levels in the heart, brain, and liver. Furthermore, T. fasciatus was subjected to cryogenic and biotic stresses, revealing distinct expression patterns of HSPs under various stress conditions. The response of HSPs to cold stress and Aeromonas hydrophila infection was sustained. In contrast, gene expression of HSPs significantly changed only in the pre-infection period following Ichthyophthirius multifiliis infection, gradually returning to normal levels in the later stages. Conclusions: These experimental results provide a foundation for further in-depth investigations into the characteristics and functions of HSPs in T. fasciatus. Full article
(This article belongs to the Special Issue Genetics and Molecular Breeding in Fisheries and Aquaculture)
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12 pages, 2018 KiB  
Article
Genome-Wide Genetic Diversity and Population Structure of Charybdis feriata (Crustacea, Decapoda, and Portunidae) Along the Southeast Coast of China Inferred from Genotyping-by-Sequencing (GBS) Approach
by Jie He, Jialin Wu, Litao Wan, Wenjun Xu and Tianyan Yang
Genes 2024, 15(11), 1421; https://doi.org/10.3390/genes15111421 - 31 Oct 2024
Viewed by 983
Abstract
Background/Objectives: The swimming crab Charybdis feriata is an important commercial fishery species and a major economic contributor to the southeast coastal fishing communities in China. Under the scenario of resource decline and shortage in the market over recent years, it has become more [...] Read more.
Background/Objectives: The swimming crab Charybdis feriata is an important commercial fishery species and a major economic contributor to the southeast coastal fishing communities in China. Under the scenario of resource decline and shortage in the market over recent years, it has become more urgent and necessary to explore the fine-scale population genetic characteristics of C. feriata. Methods: In this study, the genotyping-by-sequencing (GBS) method was used to estimate the genome-wide genetic variation in and population differentiation pattern of C. feriata collected from four geographical locations (Zhoushan, Quanzhou, Yangjiang, and Qinzhou) along the southeast coast of China. Results: A total of 18,815 high-quality single-nucleotide polymorphisms (SNPs) were identified and the results revealed the existence of high genetic diversity and low genetic divergence among the populations of C. feriata. Floating eggs and larvae transported by alongshore currents during the reproductive season might enhance the interpopulation genetic exchange. Principal component analysis (PCA) and a phylogenetic tree showed a high genetic connectivity of C. feriata across the southeast coast of China, but C. feriata distributed in the Zhoushan Archipelago might possess some genetic distinctiveness and diversification. Conclusions: The results supplemented basic genetic information of C. feriata at the genome level and also provided specific knowledge that could lead to the improved spatial management of fishery resources. Full article
(This article belongs to the Special Issue Genetics and Molecular Breeding in Fisheries and Aquaculture)
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24 pages, 2839 KiB  
Article
Development of a Novel Stress and Immune Gene Panel for the Australasian Snapper (Chrysophrys auratus)
by Kerry L. Bentley-Hewitt, Christina K. Flammensbeck, Ross N. Crowhurst, Duncan I. Hedderley and Maren Wellenreuther
Genes 2024, 15(11), 1390; https://doi.org/10.3390/genes15111390 - 29 Oct 2024
Cited by 2 | Viewed by 1492
Abstract
Background: Snapper (Chrysophrys auratus) is a commercially, recreationally and culturally important teleost species in New Zealand and has been selected as a potential new species for aquaculture. Selective breeding to enhance stress tolerance, survival and growth are major breeding targets, yet [...] Read more.
Background: Snapper (Chrysophrys auratus) is a commercially, recreationally and culturally important teleost species in New Zealand and has been selected as a potential new species for aquaculture. Selective breeding to enhance stress tolerance, survival and growth are major breeding targets, yet research into snapper immune and stress responses has been limited. Methods: We explored a set of candidate genes in the fin, head kidney and liver tissues of 50 individuals by exposing 20 fish to increasing temperature (up to 31 °C) and 20 fish to decreasing temperature (down to 7 °C) for up to 37 h. Of these, we analysed 10 temperature-sensitive and 10 temperature-tolerant fish, along with 10 fish kept at 18 °C (acclimation temperature) as a control group. Results: Expression analyses of candidate stress genes in the three tissue types via NanoString Technologies, Inc., Seattle, WA, USA. showed that 20 out of 25 genes significantly changed in each experiment, demonstrating the significant impact of temperature on stress and immune responses. We further document that 10 key gene biomarkers can be used to predict genotypes that are tolerant to extreme temperatures. Conclusions: Taken together, our novel NanoString method can be used to monitor stress in snapper rapidly, and applications of this tool in this and potentially closely related teleost species can provide insights into stress resilience of wild stocks and inform the selection of grow-out locations for aquaculture. Full article
(This article belongs to the Special Issue Genetics and Molecular Breeding in Fisheries and Aquaculture)
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14 pages, 2760 KiB  
Article
Genomic and Transcriptional Analysis of the Necroptosis Pathway Elements RIPK and MLKL in Sea Cucumber, Holothuria leucospilota
by Rong Chen, Qianying Huang, Yingzhu Rao, Junyan Wang, Ruiming Yu, Shuangxin Peng, Kaiyi Huang, Yihang Huang, Xiangxing Zhu, Dongsheng Tang, Xiaoli Zhang, Tiehao Lin, Ting Chen and Aifen Yan
Genes 2024, 15(10), 1297; https://doi.org/10.3390/genes15101297 - 3 Oct 2024
Cited by 1 | Viewed by 1550
Abstract
Background: Receptor-interacting protein kinases (RIPKs) and mixed-lineage kinase domain-like protein (MLKL) are crucial in regulating innate immune responses and cell death signaling (necroptosis and apoptosis), and are potential candidates for genetic improvement in breeding programs. Knowledge about the RIPK family and MLKL in [...] Read more.
Background: Receptor-interacting protein kinases (RIPKs) and mixed-lineage kinase domain-like protein (MLKL) are crucial in regulating innate immune responses and cell death signaling (necroptosis and apoptosis), and are potential candidates for genetic improvement in breeding programs. Knowledge about the RIPK family and MLKL in sea cucumber remains limited. Methods: We searched the genomes of sea cucumber Holothuria leucospilota for genes encoding RIPKs and MLKL, performed phylogenetic tree, motif and functional domain analyses, and examined tissue distribution and embryonic development patterns using qPCR. Results: RIPK5 (Hl-RIPK5), RIPK7 (Hl-RIPK7) and MLKL (Hl-MLKL) were identified in sea cucumber H. leucospilota. Hl-RIPK5 and Hl-RIPK7 were mainly expressed in coelomocytes, suggesting that they play a role in innate immunity, whereas Hl-MLKL exhibited relatively low expression across tissues. During embryonic development, Hl-MLKL was highly expressed from the 2-cell stage to the morula stage, while Hl-RIPK5 and Hl-RIPK7 were primarily expressed after the morula stage, indicating different roles in embryonic development. In primary coelomocytes, Hl-RIPK5 transcriptional activity was significantly depressed by LPS, poly(I:C), or pathogen Vibrio harveyi. Hl-RIPK7 expression levels were unchanged following the same challenges. Hl-MLKL mRNA levels were significantly decreased with poly(I:C) or V. harveyi, but did not change with LPS. Conclusions: These findings provide valuable insights into the evolutionary tree and characterization of RIPK and MLKL genes in sea cucumber, contributing to the broader understanding of the RIPK gene family and MLKL in ancient echinoderms. Full article
(This article belongs to the Special Issue Genetics and Molecular Breeding in Fisheries and Aquaculture)
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16 pages, 14888 KiB  
Article
Molecular Cloning of the scd1 Gene and Its Expression in Response to Feeding Artificial Diets to Mandarin Fish (Siniperca chuatsi)
by Jiangjiang Wang, Lihan Zhang, Xiaowei Gao, Yanfeng Sun, Chunlong Zhao, Xiaotian Gao and Chengbin Wu
Genes 2024, 15(9), 1211; https://doi.org/10.3390/genes15091211 - 16 Sep 2024
Cited by 1 | Viewed by 1475
Abstract
Background/Objectives: Stearoyl-coenzyme A desaturase 1 (SCD1) plays a crucial role in fatty acid metabolism. However, its roles in the feeding habit transformation of mandarin fish (Siniperca chuatsi) remain largely unknown. Methods: Juvenile mandarin fish (10.37 ± 0.54)g were trained to [...] Read more.
Background/Objectives: Stearoyl-coenzyme A desaturase 1 (SCD1) plays a crucial role in fatty acid metabolism. However, its roles in the feeding habit transformation of mandarin fish (Siniperca chuatsi) remain largely unknown. Methods: Juvenile mandarin fish (10.37 ± 0.54)g were trained to feed on an artificial diet and then divided into artificial diet feeders and nonfeeders according to their feed preference. Afterwards, the scd1 gene of mandarin fish (Sc-scd1) was identified and characterized, and its transcription difference was determined between S. chuatsi fed live artificial diets and those fed prey fish. Results: Our results show that Sc-scd1 coding sequence is 1002 bp long, encoding 333 amino acids. The assumed Sc-SCD1 protein lacks a signal peptide, and it contains 1 N-linked glycosylation site, 24 phosphorylation sites, 4 transmembrane structures, and 3 conserved histidine elements. We found that Sc-SCD1 exhibits a high similarity with its counterparts in other fish by multiple alignments and phylogenetic analysis. The expression level of Sc-scd1 was detected with different expression levels in all tested tissues between male and female individuals fed either live prey fish or artificial diets. Conclusions: In particular, the Sc-scd1 expression level was the highest in the liver of both male and female mandarin fish fed artificial diets, indicating that scd1 genes may be associated with feed adaption of mandarin fish. Taken together, our findings offer novel perspectives on the potential roles of scd1 in specific domestication, and they provide valuable genetic information on feeding habits for the domestication of mandarin fish. Full article
(This article belongs to the Special Issue Genetics and Molecular Breeding in Fisheries and Aquaculture)
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14 pages, 2145 KiB  
Article
Expression Patterns of TGF-β1, TβR-I, TβR-II, and Smad2 Reveal Insights into Heterosis for Growth of Hybrid Offspring between Acanthopagrus schlegelii and Pagrus major
by Xinran Du, Yue Zhao, Jingbo Li, Wenli Xie, Linna Lyu, Shuyin Chen, Chaofeng Jia, Jie Yan and Peng Li
Genes 2024, 15(7), 945; https://doi.org/10.3390/genes15070945 - 19 Jul 2024
Viewed by 1368
Abstract
TGF-β1/Smads is a classic signaling pathway, which plays important roles in the development process of organisms. Black porgy Acanthopagrus schlegelii and red porgy Pagrus major are valuable economic fishes, and their hybrid offspring show excellent heterosis traits. Yet the molecular regulation mechanism of [...] Read more.
TGF-β1/Smads is a classic signaling pathway, which plays important roles in the development process of organisms. Black porgy Acanthopagrus schlegelii and red porgy Pagrus major are valuable economic fishes, and their hybrid offspring show excellent heterosis traits. Yet the molecular regulation mechanism of the heterosis traits is less clear. Here, we explored the TGF-β1/Smads pathway’s molecular genetic information for heterosis in A. schlegelii ♂ × P. major ♀ (AP) and A. schlegelii ♀ × P. major ♂ (PA) in terms of growth and development. The mRNA expression levels of TGF-β1, TβR-I, TβR-II, and Smad2 genes in different developmental stages of A. schlegelii were detected. Furthermore, the expression levels of TGF-β1, TβR-I, TβR-II, and Smad2 genes in different tissues of adult (mRNA level) and larva (mRNA and protein level) of A. schlegelii, P. major, and their hybrids were determined by both real-time quantitative PCR and Western blot techniques. The results indicated the ubiquitous expression of these genes in all developmental stages of A. schlegelii and in all tested tissues of A. schlegelii, P. major, and its hybrids. Among them, the mRNA of TGF-β1, TβR-I, and TβR-II genes is highly expressed in the liver, gill, kidney, and muscle of black porgy, red porgy, and their hybrid offspring. There are significant changes in gene and protein expression levels in hybrid offspring, which indirectly reflect hybrid advantage. In addition, there was no correlation between protein and mRNA expression levels of Smad2 protein. The results provide novel data for the differential expression of growth and development genes between the reciprocal hybridization generation of black porgy and red porgy and its parents, which is conducive to further explaining the molecular regulation mechanism of heterosis in the growth and development of hybrid porgy. Full article
(This article belongs to the Special Issue Genetics and Molecular Breeding in Fisheries and Aquaculture)
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13 pages, 4458 KiB  
Article
Fine Mapping of QTLs for Alkaline Tolerance in Crucian Carp (Carassius auratus) Using Genome-Wide SNP Markers
by Liang Zhang, Baofeng Su, Jing Huang, Limin Zhang, Yumei Chang and Guo Hu
Genes 2024, 15(6), 751; https://doi.org/10.3390/genes15060751 - 7 Jun 2024
Cited by 2 | Viewed by 1101
Abstract
Crucian carp (Carassius auratus) is widely distributed in the world and has become an economically freshwater fish. The population in Lake Dali Nur can tolerate the extreme alkaline environment with alkalinity over 50 mmol/L (pH 9.6), thus providing a special model for [...] Read more.
Crucian carp (Carassius auratus) is widely distributed in the world and has become an economically freshwater fish. The population in Lake Dali Nur can tolerate the extreme alkaline environment with alkalinity over 50 mmol/L (pH 9.6), thus providing a special model for exploring alkali-tolerant molecular markers in an extremely alkaline environment. In this study, we constructed a high-density and high-resolution linkage map with 16,224 SNP markers based on genotyping-by-sequencing (GBS) consisting of 152 progenies and conducted QTL studies for alkali-tolerant traits. The total length of the linkage map was 3918.893 cM, with an average distance of 0.241 cM. Two QTLs for the ammonia-N-tolerant trait were detected on LG27 and LG45. A QTL for the urea-N-tolerant trait was detected on LG27. Interestingly, mapping the two QTLs on LG27 revealed that the mapped genes were both located in the intron of CDC42. GO functional annotation and KEGG enrichment analysis results indicated that the biological functions might be involved in the cell cycle, cellular senescence, MAPK, and Ras signaling pathways. These findings suggest that CDC42 may play an important role in the process of dealing with extremely alkaline environments. Full article
(This article belongs to the Special Issue Genetics and Molecular Breeding in Fisheries and Aquaculture)
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15 pages, 4078 KiB  
Article
Establishment of Parentage Identification Method for Sea Urchin Strongylocentrotus intermedius Based on SSR-seq Technology
by Xuechun Jiang, Lei Liu, Hao Guo, Peng Liu, Wenzhuo Tian, Fanjiang Ou, Jun Ding, Weijie Zhang and Yaqing Chang
Genes 2024, 15(5), 630; https://doi.org/10.3390/genes15050630 - 16 May 2024
Cited by 1 | Viewed by 1304
Abstract
To establish a parentage identification method for Strongylocentrotus intermedius, 15 microsatellite loci and simple sequence repeat sequencing (SSR-seq) technology were used to perform SSR sequencing and typing of the validation population with known pedigree information and the simulation population. Cervus v3.0 was [...] Read more.
To establish a parentage identification method for Strongylocentrotus intermedius, 15 microsatellite loci and simple sequence repeat sequencing (SSR-seq) technology were used to perform SSR sequencing and typing of the validation population with known pedigree information and the simulation population. Cervus v3.0 was used for gene frequency statistics, simulated analysis, and parentage identification analysis. The results showed that, in validation population, using 15 microsatellite loci, the highest success rate of parent pairs identification was 86%, the highest success rate of female parent identification was 93%, and the highest success rate of male parent identification was 90%. The simulated population was analyzed using 12–15 loci, and the identification rate was up to 90%. In cases where accurate parentage was not achieved, individuals could exhibit genetic similarities with 1–3 male or female parents. Individuals identified as lacking a genetic relationship can be selected as parents to prevent inbreeding. This study shows that parent pairs or single parents of most offspring can be identified successfully using these 15 selected loci. The results lay a foundation for the establishment of a parentage identification method for S. intermedius. Full article
(This article belongs to the Special Issue Genetics and Molecular Breeding in Fisheries and Aquaculture)
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