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Fishes
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Genetics and Breeding in Aquaculture
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Genetics and Breeding in Aquaculture

A special issue of Fishes (ISSN 2410-3888). This special issue belongs to the section "Genetics and Biotechnology".

Deadline for manuscript submissions: closed (1 September 2024) | Viewed by 11001

Special Issue Editor

Prof. Dr. Xidong Mu

E-Mail Website
Guest Editor
Key Laboratory of Prevention and Control for Aquatic Invasive Alien Species, Ministry of Agriculture and Rural Affairs, Guangdong Modern Recreational Fisheries Engineering Technology Center, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou, China
Interests: fish genomics and genetics; molecular breeding; sex determination; population genetics; adaptive evolution

Special Issue Information

Dear Colleagues,

Aquaculture plays an essential role in addressing the world's increasing food demand. The significance of genetics and breeding in aquaculture is becoming increasingly evident as a result of population development and the depletion of marine resources. The Special Issue “Genetics and Breeding in Aquaculture” highlights the applications of genomics and molecular breeding in aquaculture. Aquaculture has benefited greatly from the extensive application of genomics technologies due to developments in high-throughput sequencing. The focus of the Special Issue is on the use of cutting-edge methods to improve the traits and quality of aquaculture species, such as marker-assisted selection, genome selection, and genome editing. This Special Issue is seeking papers that address the latest developments of genetics and breeding in aquaculture, as well as how these insights might be applied to encourage the advancement of the modern aquaculture industry.

Prof. Dr. Xidong Mu
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.

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Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2600 CHF (Swiss Francs). 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

  • genomics in aquaculture
  • molecular breeding
  • marker-assisted selection
  • genomic selection methods
  • genetic diversity
  • gene editing
  • epigenetics in aquaculture breeding

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Published Papers (9 papers)

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Research

13 pages, 2805 KiB  
Article
A New Mutagenesis Tool for Songpu Mirror Carp (Cyprinus carpio L.) for Selective Breeding: Atmospheric-Pressure Room-Temperature Plasma Mutagenesis Technology
by Xiaona Jiang, Chitao Li, Mei Shang, Xuesong Hu, Yanlong Ge and Zhiying Jia
Fishes 2024, 9(11), 448; https://doi.org/10.3390/fishes9110448 - 1 Nov 2024
Viewed by 532
Abstract
As a new, safe, and efficient method, Atmospheric-Pressure Room-Temperature Plasma (ARTP) mutagenesis has been widely applied in the field of microbial breeding and industrial applications, but it is rarely used in fish. In this study, ARTP mutagenesis technology was applied for the first [...] Read more.
As a new, safe, and efficient method, Atmospheric-Pressure Room-Temperature Plasma (ARTP) mutagenesis has been widely applied in the field of microbial breeding and industrial applications, but it is rarely used in fish. In this study, ARTP mutagenesis technology was applied for the first time to a common carp strain, Songpu mirror carp (Cyprinus carpio L.), to increase genetic variation in this species. The appropriate experimental conditions were determined to include a radio frequency output power of 160 W and the processing of fertilized eggs for 360 s. The ARTP treatment group had a lower survival rate than the control group. The CV of morphological characters in the ARTP treatment group was significantly higher than that in the control group, and the CV of body weight was the highest (p < 0.05). In addition, the deformity rate in the ARTP treatment group was significantly higher than in the control group (p < 0.05). Individuals with high weight and no deformities were screened within the selection pressure of 1:15 of ARTP treatment group and fed in the same pool with the control group of the same age. The measurement of serum indices showed that, in the ARTP treatment group, TP, ALP, ALB, T-CHO, LDL levels were significantly higher than those in the control group (p < 0.05). Furthermore, the relative expressions of SOD, growth-related genes GH, IGF-I, protein synthesis-related genes TOR and 4EBP1 were significantly higher in the ARTP treatment group than in the control group (p < 0.05). In summary, Songpu mirror carp subjected to ARTP treatment showed a higher growth potential and antioxidant capacity. Full article
(This article belongs to the Special Issue Genetics and Breeding in Aquaculture)
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23 pages, 8471 KiB  
Article
Construction of a Growth Model and Screening of Growth-Related Genes for a Hybrid Puffer (Takifugu obscurus ♀ × Takifugu rubripes ♂)
by Chaoyu Wang, Yan Shi, Yuanye Gao, Shuo Shi, Mengmeng Wang, Yunlong Yao, Zhenlong Sun, Yaohui Wang and Zhe Zhao
Fishes 2024, 9(10), 404; https://doi.org/10.3390/fishes9100404 - 6 Oct 2024
Viewed by 946
Abstract
The obscure puffer (Takifugu obscurus) is a popular cultured species and accounts for around 50% of the total pufferfish production in China. A hybrid puffer was generated by crossing a female obscure puffer with a male tiger puffer (T. rubripes [...] Read more.
The obscure puffer (Takifugu obscurus) is a popular cultured species and accounts for around 50% of the total pufferfish production in China. A hybrid puffer was generated by crossing a female obscure puffer with a male tiger puffer (T. rubripes). Its growth model has not been developed and the genetic basis underlying its growth superiority has not yet been fully investigated. In this study, the growth model and morphological traits of the hybrid puffer were explored. The results indicated that the hybrid puffer exhibited a significant growth advantage compared to the obscure puffer. There were also significant differences in their morphological traits. We conducted genotyping-by-sequencing (GBS) on hybrid and obscure puffer groups, identifying 215,288 high-quality single nucleotide polymorphisms (SNPs) on 22 chromosomes. Subsequently, a total of 13 growth-related selection regions were identified via a combination of selection signatures and a genome-wide association study (GWAS); these regions were mainly located on chromosomes 10 and 22. Ultimately, the screened regions contained 13 growth-related genes, including itgav, ighv3-43, ighm, atp6v1b2, pld1, xmrk, inhba, dsp, dsg2, and dsc2, which regulate growth through a variety of pathways. Taken together, the growth models and candidate genes used in this study will aid our understanding of production characteristics and the genetic basis of growth rates. The hybrid will also be of great significance for the genome-assisted breeding of pufferfish in the future. Full article
(This article belongs to the Special Issue Genetics and Breeding in Aquaculture)
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19 pages, 7799 KiB  
Article
Molecular Cloning and Characterization of Scavenger Receptor Class B Type 1 in Grass Carp (Ctenopharyngodon idellus) and Its Expression Profile following Grass Carp Reovirus Challenge
by Yang Zhang, Jiayuan Shi, Yuntao Lu, Qing Luo, Pengfei Chu, Rong Huang, Kunci Chen, Jian Zhao, Yaping Wang and Mi Ou
Fishes 2024, 9(7), 276; https://doi.org/10.3390/fishes9070276 - 12 Jul 2024
Viewed by 879
Abstract
As a member of the pattern recognition receptor (PRR) class, scavenger receptor class B type 1 (SRB1) plays a key role in innate immunity. Grass carp (Ctenopharyngodon idellus) ranks among the most extensively cultivated freshwater aquaculture species in China. However, little [...] Read more.
As a member of the pattern recognition receptor (PRR) class, scavenger receptor class B type 1 (SRB1) plays a key role in innate immunity. Grass carp (Ctenopharyngodon idellus) ranks among the most extensively cultivated freshwater aquaculture species in China. However, little is known about the function of SRB1 in C. idellus. In this research study, a SRB1 gene was identified in C. idellus, named CiSRB1. The full-length cDNA of CiSRB1 is 2486 bp long, with an open reading frame (ORF) of 2486 bp encoding a 497 amino acid (aa) protein containing a conserved CD36 domain. The identified genomic DNA length of CiSRB1 is 20,042 bp, including 12 exons and 11 introns. The predictive analysis of protein interactions revealed that CiSRB1 could interact with the outer capsid proteins of typical GCRV strains. The tissue distribution of CiSRB1 exhibited age-dependent characteristics. CiSRB1 displayed the highest expression in the intestines and moderate levels in muscle, spleen, liver, and brain of one-year-old grass carp while maintaining relatively low levels in three-year-old grass carp. Following grass carp reovirus (GCRV) infection, notable upregulation of CiSRB1 transcripts was observed in major immune tissues (gills, intestines, spleen, and liver). Furthermore, significant differences were found between one-year-old and three-year-old grass carp, with lower CiSRB1 expression levels being detected in the older group. Additionally, a distinct response to GCRV infection was observed in one-year-old and three-year-old grass carp. It was found that one-year-old individuals had a mortality rate of up to 84% 6 days post-infection (dpi), whereas all three-year-old counterparts survived after GCRV infection. The analysis of GCRV copy numbers across tissues revealed substantially higher levels in one-year-old grass carp compared with their older counterparts, confirming the existence of age-dependent susceptibility to GCRV infection in grass carp. Combined with these results, it was speculated that the decline in cell-surface CiSRB1 expression with age may impede reovirus binding to host cells, potentially explaining why older grass carp demonstrated enhanced resistance to GCRV infection. This observation accentuates the importance of CiSRB1 in the context of GCRV infection and provides insights into age-dependent susceptibility to reovirus. Full article
(This article belongs to the Special Issue Genetics and Breeding in Aquaculture)
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18 pages, 6109 KiB  
Article
Identification and Characterization of microRNAs in Morphological Color Change of Polychromatic Midas Cichlids (Amphilophus citrinellus)
by Guoqiang Wu, Xidong Mu, Yi Liu, Chao Liu, Xuejie Wang, Yexin Yang and Hongmei Song
Fishes 2024, 9(6), 194; https://doi.org/10.3390/fishes9060194 - 24 May 2024
Viewed by 1066
Abstract
As a representative genetic and economic trait, pigmentation has a strong impact on speciation and adaptation. However, information and reports on microRNAs (miRNAs) associated with pigmentation remain limited. The Midas cichlid fish, with three typical distinct stages of body color pattern, “black-gray-gold”, is [...] Read more.
As a representative genetic and economic trait, pigmentation has a strong impact on speciation and adaptation. However, information and reports on microRNAs (miRNAs) associated with pigmentation remain limited. The Midas cichlid fish, with three typical distinct stages of body color pattern, “black-gray-gold”, is an ideal model system for investigating pigmentation traits. In this study, miRNA libraries from scale tissues with the attached epidermis of Midas cichlids at three distinct stages of color transformation, black (B), transition (T), and gold (G), were sequenced using Illumina sequencing technology. In total, 53 (B vs. G), 88 (B vs. T), and 57 (T vs. G) miRNAs were differentially expressed between the respective groups. Target genes of the identified miRNAs were predicted, and the results showed that multiple target genes were related to pigmentation and pigment–cell differentiation. The miRNA–mRNA regulatory network suggests that miR-183-x and miR-133-x were predicted to be involved in regulating morphological color changes in Midas cichlids. The results advance our understanding of potential functions of miRNAs in skin pigment differentiation and early skin color fading of fishes. Full article
(This article belongs to the Special Issue Genetics and Breeding in Aquaculture)
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16 pages, 5922 KiB  
Article
Comparative Analysis of Enzymatic Activities and Transcriptional Profiles of Various Hepatic Enzymes between Male and Female Yellowfin Tuna (Thunnus albacares)
by Dongge Liu, Hao Yang, Shuisheng Li, Hai Huang, Guangli Li and Huapu Chen
Fishes 2024, 9(5), 184; https://doi.org/10.3390/fishes9050184 - 17 May 2024
Cited by 2 | Viewed by 1247
Abstract
Yellowfin tuna (Thunnus albacares) is a valuable pelagic migratory fish with potential for aquaculture. Despite this, there is limited understanding of the biological and physiological characteristics of this species, particularly regarding sex differences in growth performance. The liver, a crucial organ [...] Read more.
Yellowfin tuna (Thunnus albacares) is a valuable pelagic migratory fish with potential for aquaculture. Despite this, there is limited understanding of the biological and physiological characteristics of this species, particularly regarding sex differences in growth performance. The liver, a crucial organ for digestion and metabolism, plays a significant role in regulating fish growth. This study aimed to compare liver enzyme activities and transcriptome profiles between female and male yellowfin tuna to uncover the molecular mechanisms underlying difference between the sexes. The results revealed that female yellowfin tuna exhibited higher amylase and lipid metabolism enzyme activities, while male yellowfin tuna showed higher glucose-6-phosphate dehydrogenase and antioxidant enzyme activities. Additionally, through Illumina sequencing technology, the study generated 37.74 Gb of clean data and identified 36,482 unique genes (UniGenes) in the liver transcriptome. A total of 2542 differentially expressed genes were found, with enriched Gene Ontology terms and pathways related to metabolic processes, particularly lipid metabolism and transport. These findings suggest that female yellowfin tuna have superior digestive enzyme activities and lipid metabolism, while male yellowfin tuna excel in sugar metabolism, ATP production, and antioxidant defense. This study provides valuable insights into sex differences in yellowfin tuna and could aid in advancing full-cycle aquaculture practices for this species. Full article
(This article belongs to the Special Issue Genetics and Breeding in Aquaculture)
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21 pages, 6989 KiB  
Article
Mechanistic Insights into Nonylphenol Stress on BMP2 and BMP4 Gene Expression in Red Crucian Carp (Carassius auratus Red var.)
by Die Li, Xiaojuan Cui, Shuailin Chen, Jia Xu, Yujing Li, Qiongyu Zhang and Yuandong Sun
Fishes 2024, 9(5), 159; https://doi.org/10.3390/fishes9050159 - 28 Apr 2024
Viewed by 972
Abstract
Nonylphenol (NP) is a known endocrine-disrupting chemical (EDC) that has been shown to affect bone development in mammals. However, the detrimental impacts of NP on the skeletal growth and development of aquatic species, especially bony fish, remain poorly understood. Bone morphogenic proteins (BMPs), [...] Read more.
Nonylphenol (NP) is a known endocrine-disrupting chemical (EDC) that has been shown to affect bone development in mammals. However, the detrimental impacts of NP on the skeletal growth and development of aquatic species, especially bony fish, remain poorly understood. Bone morphogenic proteins (BMPs), essential for bone formation and osteoblast differentiation, act through the BMP-Smad signaling pathway. In this study, two BMP genes, BMP2 and BMP4, were cloned and characterized in the red crucian carp (Carassius auratus red var.). The full-length cDNAs of BMP2 and BMP4 were 2029 bp and 2095 bp, respectively, encoding polypeptides of 411 and 433 amino acids, and share a typical TGF-β domain with other BMPs. The tissue expression patterns of both genes were identified, showing ubiquitous expression across all studied tissues. Additionally, the exposure of embryos or adult fish to NP stress resulted in a downregulation of BMP2, BMP4, and other genes associated with the BMP-Smad signaling pathway. Moreover, the combined treatment of adult fish with NP and the specific BMP receptor inhibitor significantly reduced these genes’ expression. These findings elucidate the mechanism of NP stress on BMP2 and BMP4, suggesting a role for the BMP-Smad signaling pathway in the response to endocrine-disrupting chemicals in fish. Full article
(This article belongs to the Special Issue Genetics and Breeding in Aquaculture)
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21 pages, 5600 KiB  
Article
Molecular Characteristics, Expression Patterns, and Response of Insulin-like Growth Factors Gene Induced by Sex Steroid Hormones in Blotched Snakehead (Channa maculata)
by Xiaotian Zhang, Yuxia Wu, Yang Zhang, Jin Zhang, Kunci Chen, Haiyang Liu, Qing Luo, Shuzhan Fei, Jian Zhao and Mi Ou
Fishes 2024, 9(4), 120; https://doi.org/10.3390/fishes9040120 - 28 Mar 2024
Viewed by 1302
Abstract
Insulin-like growth factors (IGFs) play central roles in the growth and development of vertebrates. Blotched snakehead (Channa maculata), an economically significant fish, exhibits obvious sexual dimorphism and achieves sexual maturity in one year. However, the role of IGFs in C. maculata [...] Read more.
Insulin-like growth factors (IGFs) play central roles in the growth and development of vertebrates. Blotched snakehead (Channa maculata), an economically significant fish, exhibits obvious sexual dimorphism and achieves sexual maturity in one year. However, the role of IGFs in C. maculata remains unknown. Three IGF genes were identified in C. maculata, designated as CmIGF1-1, CmIGF1-2, and CmIGF2. The cDNA sequences of these genes are 1184, 655, and 695 bp, encoding putative proteins of 168, 131, and 215 amino acids, respectively, and all three proteins contain a conserved IGF domain. Quantitative real-time PCR (qPCR) revealed the predominant expression of CmIGFs in the liver of adult fish, with higher expression levels observed in males. Notably, CmIGF1-1, CmIGF1-2, and CmIGF2 displayed analogous expression profiles in the liver across various developmental stages, peaking at 365 days after hatching (dah). Subsequently, 600 individuals at 75 dah, at an early developmental stage, were randomly divided equally into six groups and reared in aerated 2 m × 2 m × 2 m cement ponds at 26.0 ± 1.0 °C. Following a one-week acclimatization period, fish without observed abnormalities were intraperitoneally injected with either 17α-ethynylestradiol (EE2) or 17α-methyltestosterone (MT) at a dose of 10 μg/g body weight. Three groups underwent short-term hormone treatment, and the remaining three groups underwent long-term hormone treatment, which included five injections at two-week intervals over ten weeks. The analysis of CmIGFs expression levels in the liver under different hormone treatments revealed that EE2 suppressed the expression of CmIGF1-1 and CmIGF1-2 while promoting CmIGF2 expression. In females, MT up-regulated the expression of CmIGF1-1 and CmIGF2 in a time-dependent manner, but consistently inhibited CmIGF2 expression. In males, MT promoted the expression of CmIGFs in a time-dependent manner, reaching peak levels for CmIGF1-1, CmIGF1-2, and CmIGF2 after 8, 10, and 2 weeks of injection, respectively. Additionally, CmIGF1 and CmIGF2 might exhibit a complementary relationship, with a compensatory increase in CmIGF2 expression in response to low CmIGF1 concentration. These findings highlight the potential key role of IGFs upon growth and their regulation by sex steroid hormones in C. maculata, providing a crucial foundation for future research aimed at elucidating the molecular mechanisms underlying the growth dimorphism between female and male blotched snakeheads. Full article
(This article belongs to the Special Issue Genetics and Breeding in Aquaculture)
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13 pages, 3760 KiB  
Article
Heritability Estimates for Growth Traits and Correlation Analysis between Weight and Metamorphosis Rate in the Bullfrog Rana (Aquarana) catesbeiana
by Wencheng Xu, Yanzhe Wang, Guodong Wang, Lili Zhang, Guiling Zhang, Zhipeng Huo and Hui Ge
Fishes 2024, 9(3), 105; https://doi.org/10.3390/fishes9030105 - 9 Mar 2024
Viewed by 1475
Abstract
Metamorphosis is a crucial process in the life cycle of Rana (Aquarana) catesbeiana. R. catesbeiana tadpoles, in their short larval period, possess a high survival rate and also a highly competitive ability in the amphibious stage. In actual seed production, [...] Read more.
Metamorphosis is a crucial process in the life cycle of Rana (Aquarana) catesbeiana. R. catesbeiana tadpoles, in their short larval period, possess a high survival rate and also a highly competitive ability in the amphibious stage. In actual seed production, the economic traits of larval period and metamorphosis rate are used as quantifiable indicators of quality for individuals and populations, respectively. However, studies of these economic traits in larval cultivation and production are still lacking. In this study, we constructed 40 full-sib families of R. catesbeiana and measured the weight and metamorphosis rate of tadpoles at different developmental stages. Subsequently, we calculated the phenotypic and genetic association between weight and metamorphosis rate in tadpoles and assessed the heritability of these two traits. The heritabilities of weight at three developmental stages were all higher than 0.40 and decreased with advancement of the developmental stage; the heritability of the metamorphosis rate was 0.18 ± 0.20, a moderate level. Correlation analysis of weight and metamorphosis rate at each developmental stage in each tadpole family showed that weight at stages 25-I, 25-II, and 25-III was significantly correlated at the phenotypic level but non-significantly at the genetic level. The metamorphosis rate was only moderately associated with stage 25-III weight (0.38, p < 0.05). The results of this study confirm the importance and transportability of tadpole weight in actual seed production and provide basic data and a potentially optimized direction for the selective breeding of high-metamorphosis-rate bullfrogs. Full article
(This article belongs to the Special Issue Genetics and Breeding in Aquaculture)
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15 pages, 3215 KiB  
Article
Does Size Matter? Small and Large Larvae of Pikeperch (Sander lucioperca) in a Comparative Gene Expression Analysis
by Katrin Tönißen, George Philipp Franz, Alexander Rebl, Philipp Lutze and Bianka Grunow
Fishes 2024, 9(1), 33; https://doi.org/10.3390/fishes9010033 - 12 Jan 2024
Viewed by 1685
Abstract
Size differences are common in the aquaculture of fishes. In the larviculture of cannibalistic species such as pikeperch, they majorly influence mortality rates and consequently provoke losses in the aquaculture industry. With this study, we aim to reveal molecular differences between small and [...] Read more.
Size differences are common in the aquaculture of fishes. In the larviculture of cannibalistic species such as pikeperch, they majorly influence mortality rates and consequently provoke losses in the aquaculture industry. With this study, we aim to reveal molecular differences between small and large pikeperch of the same age using a set of 20 genes associated with essential developmental processes. Hereby, we applied a general study design to early and late larval pikeperch before the onset of piscivory to explore the causes of growth differences in these developmental groups. The analysis of the expression levels showed developmental but not size-related differences in PGC1A, TGFB1, MYOD1, MRF4, and the collagens COL1A1 and COL1A2. Furthermore, increased head lengths were found in larger late larvae compared to their smaller conspecifics. While no uniquely size-related expression differences were found, the expression patterns of PGC1A in combination with TGFB1 as regulators of the citric acid cycle indicate a possible influence of mitochondrial energy metabolism. Furthermore, expression differences of MYOD1 and MRF4 point out possible temporal advantages of myogenetic processes in the larger late larval group and hypothesise growth advantages of the larger late larvae resulting from various influences, which provide a promising target for future research. Full article
(This article belongs to the Special Issue Genetics and Breeding in Aquaculture)
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