Genetic Studies of Fish

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

Deadline for manuscript submissions: 20 October 2024 | Viewed by 5057

Special Issue Editors

Yellow Sea Fisheries Research Institute Chinese Academy of Fishery Science, Qingdao, China
Interests: fish; genetic; breeding

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Guest Editor
Yellow Sea Fisheries Research Institute Chinese Academy of Fishery Science, Qingdao, China
Interests: fish; functional genomics; sexual size dimorphism; germplasm preservation and utilization

Special Issue Information

Dear Colleagues,

There are more than 32,000 species of fish in nature, making them the most diverse group of vertebrates. Fish have a variety of reproductive methods and experience genome-doubling events. The study of fish genetics is conducive to the research of fish evolution, chromosome diversity, and molecular breeding. At present, several genetic-breeding technologies are used to prevent species deterioration in fish, including hybridization, gynogenesis, androgenesis, selective breeding, transgenosis, and gene editing. Moreover, the improved offspring frequently exhibit superiority in growth rate, survival rate, disease resistance, and stress tolerance. Candidate genes and genetic markers for economic traits are detected by combining genome-wide association study, QTL-seq, and transcriptome sequencing.

This Special Issue will share the latest research trends and applications of “Genetic Studies of Fish” to shed light on fish evolution, hybridization, biological mechanisms, and novel breeding technologies. Expert contributions in the form of research papers and critical reviews are sought.

Dr. Yang Liu
Prof. Dr. Na Wang
Guest Editors

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Keywords

  • evolution in fish
  • omics analysis
  • QTLs
  • gene editing
  • functional genomics
  • germplasm preservation and utilization

Published Papers (4 papers)

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Research

25 pages, 7178 KiB  
Article
Effects of Long-Term Cryopreservation on the Transcriptomes of Giant Grouper Sperm
by Xiaoyu Ding, Yongsheng Tian, Yishu Qiu, Pengfei Duan, Xinyi Wang, Zhentong Li, Linlin Li, Yang Liu and Linna Wang
Genes 2024, 15(4), 523; https://doi.org/10.3390/genes15040523 - 22 Apr 2024
Cited by 1 | Viewed by 688
Abstract
The giant grouper fish (Epinephelus lanceolatus), one of the largest and rarest groupers, is a fast-growing economic fish. Grouper sperm is often used for cross-breeding with other fish and therefore sperm cryopreservation is important. However, freezing damage cannot be avoided. Herein, [...] Read more.
The giant grouper fish (Epinephelus lanceolatus), one of the largest and rarest groupers, is a fast-growing economic fish. Grouper sperm is often used for cross-breeding with other fish and therefore sperm cryopreservation is important. However, freezing damage cannot be avoided. Herein, we performed a transcriptome analysis to compare fresh and frozen sperm of the giant grouper with frozen storage times of 0, 23, 49, and 61 months. In total, 1911 differentially expressed genes (DEGs), including 91 in El-0-vs-El-23 (40 upregulated and 51 downregulated), 251 in El-0-vs-El-49 (152 upregulated and 69 downregulated), and 1569 in El-0-vs-El-61 (984 upregulated and 585 downregulated), were obtained in the giant grouper sperm. DEGs were significantly increased at 61 months of cryopreservation (p < 0.05). GO and KEGG enrichment analyses of the DEGs revealed significant enrichment in the pilus assembly, metabolic process, MAPK signaling pathway, apoptosis, and P53 signaling pathway. Time-series expression profiling of the DEGs showed that consistently upregulated modules were also significantly enriched in signaling pathways associated with apoptosis. Four genes, scarb1, odf3, exoc8, and atp5f1d, were associated with mitochondria and flagella in a weighted correlation network analysis. These genes may play an important role in the response to sperm freezing. The experimental results show that long-term cryopreservation results in freezing damage to the giant grouper sperm. This study provides rich data for studies of the mechanism underlying frozen fish sperm damage as well as a technical reference and evaluation index for the long-term cryopreservation of fish sperm. Full article
(This article belongs to the Special Issue Genetic Studies of Fish)
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14 pages, 2554 KiB  
Article
Assessment of the Genetic Diversity and Structure of the Korean Endemic Freshwater Fish Microphysogobio longidorsalis (Gobioninae) Using Microsatellite Markers: A First Glance from Population Genetics
by Kang-Rae Kim, Mu-Sung Sung, Yujin Hwang, Ju Hui Jeong and Jeong-Nam Yu
Genes 2024, 15(1), 69; https://doi.org/10.3390/genes15010069 - 4 Jan 2024
Viewed by 1236
Abstract
Microphysogobio longidorsalis is endemic to South Korea and inhabits small areas of the Namhangang, Bukhangang, and Imjingang Rivers in the Hangang River water system. Endemic species usually are more vulnerable than species with a wide distribution. Notably, there is a lack of basic [...] Read more.
Microphysogobio longidorsalis is endemic to South Korea and inhabits small areas of the Namhangang, Bukhangang, and Imjingang Rivers in the Hangang River water system. Endemic species usually are more vulnerable than species with a wide distribution. Notably, there is a lack of basic conservation data for M. longidorsalis. We analyzed 19 microsatellite loci in six populations of M. longidorsalis in South Korea to characterize their population structure and genetic diversity. The genetic diversity of the microsatellites was 0.741–0.779, which is lower than that of other freshwater fishes. The pairwise genetic differentiation of microsatellite (FST) values ranged from 0.007 to 0.041, suggesting low genetic differentiation between the populations. The Jojongicheon stream population (CP) had an effective population size of <100. Therefore, conservation efforts are required to prevent inbreeding depression in M. longidorsalis. Discriminant analysis of principal components showed that the Hangang River water system would be a single management unit (MU). Our findings provide fundamental genetic insights for the formulation of conservation strategies for M. longidorsalis. Full article
(This article belongs to the Special Issue Genetic Studies of Fish)
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15 pages, 2759 KiB  
Article
The Impact of Weir Construction in Korea’s Nakdong River on the Population Genetic Variability of the Endangered Fish Species, Rapid Small Gudgeon (Microphysogobio rapidus)
by Yang-Ki Hong, Kang-Rae Kim, Keun-Sik Kim and In-Chul Bang
Genes 2023, 14(8), 1611; https://doi.org/10.3390/genes14081611 - 11 Aug 2023
Cited by 2 | Viewed by 993
Abstract
Microphysogobio rapidus, an endemic cyprinid fish species found exclusively in Korea, has been identified in only two tributaries of the Nakdong River. The species predominantly occupies the near-gravel bottom waters within shallow sections of the middle and lower reaches of the river, [...] Read more.
Microphysogobio rapidus, an endemic cyprinid fish species found exclusively in Korea, has been identified in only two tributaries of the Nakdong River. The species predominantly occupies the near-gravel bottom waters within shallow sections of the middle and lower reaches of the river, characterized by swift currents. M. rapidus is currently recognized as a critically endangered species due to its distinct habitat preference, as well as the negative impacts of stream dam development and water environment pollution. In this study, we used 10 microsatellite markers to examine the genetic diversity of M. rapidus in the upper Nam (UN), lower Nam (LN), and Deokcheon Rivers (DC) in Korea, with a specific focus on assessment of the impact of dam development. Fish sampled from the UN and LN showed a greater average number of alleles and allelic richness (A = 18.3–18.4, AR = 13.8) compared to those from DC (A = 11.8, AR = 11.5). The observed heterozygosity among the fish examined ranged from HO = 0.748 (LN) to 0.766 (DC). All three fish groups exhibited a significant departure from Hardy–Weinberg equilibrium (HWE) (p < 0.05). Despite having the largest effective population size (Ne = 175 and 157, respectively), the fish sampled from UN and LN showed the highest inbreeding coefficients (FIS = 0.056–0.053, respectively), which were highly significant (p < 0.01). In contrast, the fish sampled from DC exhibited the smallest effective population size (Ne = 61) and showed an inbreeding coefficient close to zero (p > 0.05). BOTTLENECK analysis and estimated M-ratio values (0.341–0.372) revealed indications of past population size reduction in all fish groups examined. No significant genetic differentiation (FST < 0.05) was detected using the DAPC, STRUCTURE, and AMOVA among the fish studied. However, pairwise comparisons of FST between fish sampled from the Nam and Deokcheon Rivers revealed significant values (p < 0.001) ranging from 0.013 to 0.014. In addition, the closest genetic distance (0.026) was observed between UN and LN, while the greatest distance (0.087) was found between UN and DC. Analysis of gene flow rates among the fish examined indicated asymmetrical gene exchange within the Nam River, which was 31.51% in the downstream direction (from UN to LN), with a minimal gene flow rate (0.41%) in the upstream (from LN to UN) direction. The opposite trend was recorded between DC and LN, with a higher gene flow rate (29.74%) in the upstream direction compared to the downstream direction (0.12%). Our study highlighted the importance of implementing long-term conservation efforts focused on maintaining river integrity by removing water barriers such as weirs that impede fish migration and implementing active protection measures, such as aquaculture breeding and reasonable stocking practices, to preserve M. rapidus in the study area. Full article
(This article belongs to the Special Issue Genetic Studies of Fish)
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17 pages, 2991 KiB  
Article
An Attempt to Identify the Medaka Receptor for Somatolactin Alpha Using a Reverse Genetics Approach
by Yuko Moroki, Mamiko Komori, Yuko Ogawa, Erina Nagumo, Haruna Ohno and Shoji Fukamachi
Genes 2023, 14(4), 796; https://doi.org/10.3390/genes14040796 - 26 Mar 2023
Viewed by 1634
Abstract
Somatolactin alpha (SLα) is a fish-specific hormone involved in body color regulation. The growth hormone (GH) is another hormone that is expressed in all vertebrates and promotes growth. These peptide hormones act by binding to receptors (SLα receptor (SLR) and GH receptor (GHR)); [...] Read more.
Somatolactin alpha (SLα) is a fish-specific hormone involved in body color regulation. The growth hormone (GH) is another hormone that is expressed in all vertebrates and promotes growth. These peptide hormones act by binding to receptors (SLα receptor (SLR) and GH receptor (GHR)); however, the relationships between these ligands and their receptors vary among species. Here, we first performed phylogenetic tree reconstruction by collecting the amino-acid sequences classified as SLR, GHR, or GHR-like from bony fish. Second, we impaired SLR or GHR functions in medaka (Oryzias sakaizumii) using CRISPR/Cas9. Lastly, we analyzed SLR and GHR mutants for phenotypes to deduce their functions. Phylogenetic tree reconstruction was performed using a total of 222 amino-acid sequences from 136 species, which revealed that many GHRa and GHRb are vaguely termed as GHR or GHR-like, while showing no orthologous/paralogous relationships. SLR and GHR mutants were successfully established for phenotyping. SLR mutants exhibited premature lethality after hatching, indicating an essential role for SLR in normal growth. GHR mutations did not affect viability, body length, or body color. These results provide no evidence that either SLR or GHR functions as a receptor for SLα; rather, phylogenetically and functionally, they seem to be receptors for GH, although their (subfunctionalized) roles warrant further investigation. Full article
(This article belongs to the Special Issue Genetic Studies of Fish)
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