Genetic Breeding of Aquaculture

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

Deadline for manuscript submissions: 20 May 2024 | Viewed by 10719

Special Issue Editors


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Guest Editor
Deputy Director, Division of Aquaculture & Genetic Breeding, South China Sea Fisheries Research Institutes, Chinese Academy of Fishery Scieces, Guangzhou 510300, China
Interests: aquaculture; fish; genetic breeding; gene function; genomics; gene editing

E-Mail Website
Guest Editor
Division of Aquaculture & Genetic Breeding, South China Sea Fisheries Research Institutes, Chinese Academy of Fishery Scieces, Guangzhou 510300, China
Interests: fish; genetic breeding; gene function; genomics; gene editing

Special Issue Information

Dear Colleagues,

The rapid development of aquaculture genetic breeding has brought about huge economic benefits to the global aquaculture industry. Along with the rapid development of biotechnologies, aquaculture genetic breeding has transformed from traditional selection breeding and hybrid breeding to cell engineering breeding, sex control breeding, marker-assisted selection breeding, genome-wide genotyping-based selective breeding, molecular design breeding, and genome editing breeding. Advances in basic research and the biotechnology of aquaculture genetic breeding have promoted the formation of the aquaculture seed industry in the world.

This Special Issue aims to provide a snapshot of current aquaculture genetic breeding methods, focusing on breeding technique, gene function, genomics, population genetics, genome editing, and so on. Contributions might shed light on the theoretical basis of genetic breeding technology of aquatic organisms, explore novel breeding approaches, analyze the genetic mechanism of the formation of good traits, and so on. To progress the knowledge of such intricate issues, contributions by experts in the field in the form of research papers and critical reviews are invited.

Dr. Dianchang Zhang
Dr. Kecheng Zhu
Guest Editors

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Keywords

  • genetic breeding
  • gene function
  • genomics
  • gene editing
  • genetic mechanism
  • population genetics

Published Papers (6 papers)

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Research

12 pages, 7126 KiB  
Article
Characterization of the MMP9 Gene and Its Association with Cryptocaryon irritans Resistance Traits in Trachinotus ovatus (Linnaeus, 1758)
by Jun Liu, Ke-Cheng Zhu, Jin-Min Pan, Hua-Yang Guo, Bao-Suo Liu, Nan Zhang, Jing-Wen Yang and Dian-Chang Zhang
Genes 2023, 14(2), 475; https://doi.org/10.3390/genes14020475 - 13 Feb 2023
Cited by 4 | Viewed by 1815
Abstract
The MMPs are endogenous proteolytic enzymes that require zinc and calcium as cofactors. MMP9 is one of the most complex matrix metalloproteinases in the gelatinase family and has many biological functions. In mammals, mmp9 is thought to be closely associated with cancer. However, [...] Read more.
The MMPs are endogenous proteolytic enzymes that require zinc and calcium as cofactors. MMP9 is one of the most complex matrix metalloproteinases in the gelatinase family and has many biological functions. In mammals, mmp9 is thought to be closely associated with cancer. However, studies in fish have rarely been reported. In this study, to understand the expression pattern of the ToMMP9 gene and its association with the resistance of Trachinotus ovatus to Cryptocaryon irritans, the sequence of the MMP9 gene was obtained from the genome database. The expression profiles were measured by qRT–PCR, the SNPs were screened by direct sequencing, and genotyping was performed. The ToMMP9 gene contained a 2058 bp ORF encoding a putative amino acid sequence of 685 residues. The homology of the ToMMP9 in teleosts was more than 85%, and the genome structure of ToMMP9 was conserved in chordates. The ToMMP9 gene was expressed in different tissues of healthy individuals and was highly expressed in the fin, the gill, the liver and the skin tissues. The ToMMP9 expression in the skin of the infected site and its adjacent sites increased significantly after C. irritans infection. Two SNPs were identified in the ToMMP9 gene, and the SNP (+400A/G) located in the first intron was found to be significantly associated with the susceptibility/resistance to C. irritans. These findings suggest that ToMMP9 may play an important role in the immune response of T. ovatus against C. irritans. Full article
(This article belongs to the Special Issue Genetic Breeding of Aquaculture)
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17 pages, 3733 KiB  
Article
Characterization of the Complete Mitochondrial Genome of the Spotted Catfish Arius maculatus (Thunberg, 1792) and Its Phylogenetic Implications
by Min Yang, Zimin Yang, Cuiyu Liu, Xuezhu Lee and Kecheng Zhu
Genes 2022, 13(11), 2128; https://doi.org/10.3390/genes13112128 - 16 Nov 2022
Cited by 2 | Viewed by 1552
Abstract
The spotted catfish, Arius maculatus (Siluriformes), is an important economical aquaculture species inhabiting the Indian Ocean, as well as the western Pacific Ocean. The bioinformatics data in previous studies about the phylogenetic reconstruction of Siluriformes were insufficient and incomplete. In the present study, [...] Read more.
The spotted catfish, Arius maculatus (Siluriformes), is an important economical aquaculture species inhabiting the Indian Ocean, as well as the western Pacific Ocean. The bioinformatics data in previous studies about the phylogenetic reconstruction of Siluriformes were insufficient and incomplete. In the present study, we presented a newly sequenced A. maculatus mitochondrial genome (mtDNA). The A. maculatus mtDNA was 16,710 bp in length and contained two ribosomal RNA (rRNA) genes, thirteen protein-coding genes (PCGs), twenty-two transfer RNA (tRNA) genes, and one D-loop region. The composition and order of these above genes were similar to those found in most other vertebrates. The relative synonymous codon usage (RSCU) of the 13 PCGs in A. maculatus mtDNA was consistent with that of PCGs in other published Siluriformes mtDNA. Furthermore, the average non-synonymous/synonymous mutation ratio (Ka/Ks) analysis, based on the 13 PCGs of the four Ariidae species, showed a strong purifying selection. Additionally, phylogenetic analysis, according to 13 concatenated PCG nucleotide and amino acid datasets, showed that A. maculatus and Netuma thalassina (Netuma), Occidentarius platypogon (Occidentarius), and Bagre panamensis (Bagre) were clustered as sister clade. The complete mtDNA of A. maculatus provides a helpful dataset for research on the population structure and genetic diversity of Ariidae species. Full article
(This article belongs to the Special Issue Genetic Breeding of Aquaculture)
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14 pages, 5453 KiB  
Article
RNA Interference Analysis of the Functions of Cyclin B in Male Reproductive Development of the Oriental River Prawn (Macrobrachium nipponense)
by Wenyi Zhang, Pengchao Wang, Yiwei Xiong, Tianyong Chen, Sufei Jiang, Hui Qiao, Yongsheng Gong, Yan Wu, Shubo Jin and Hongtuo Fu
Genes 2022, 13(11), 2079; https://doi.org/10.3390/genes13112079 - 9 Nov 2022
Cited by 6 | Viewed by 1302
Abstract
Cyclin B (CycB) plays essential roles in cell proliferation and promotes gonad development in many crustaceans. The goal of this study was to investigate the regulatory roles of this gene in the reproductive development of male oriental river prawns (Macrobrachium [...] Read more.
Cyclin B (CycB) plays essential roles in cell proliferation and promotes gonad development in many crustaceans. The goal of this study was to investigate the regulatory roles of this gene in the reproductive development of male oriental river prawns (Macrobrachium nipponense). A phylo-genetic tree analysis revealed that the protein sequence of Mn-CycB was most closely related to those of freshwater prawns, whereas the evolutionary distance from crabs was much longer. A quantitative PCR analysis showed that the expression of Mn-CycB was highest in the gonad of both male and female prawns compared to that in other tissues (p < 0.05), indicating that this gene may play essential roles in the regulation of both testis and ovary development in M. nipponense. In males, Mn-CycB expression in the testis and androgenic gland was higher during the reproductive season than during the non-reproductive season (p < 0.05), implying that CycB plays essential roles in the reproductive development of male M. nipponense. An RNA interference analysis revealed that the Mn-insulin-like androgenic gland hormone expression decreased as the Mn-CycB expression decreased, and that few sperm were detected 14 days after the dsCycB treatment, indicating that CycB positively affects testis development in M. nipponense. The results of this study highlight the functions of CycB in M. nipponense, and they can be applied to studies of male reproductive development in other crustacean species. Full article
(This article belongs to the Special Issue Genetic Breeding of Aquaculture)
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15 pages, 3248 KiB  
Article
Development of Single Nucleotide Polymorphism and Association Analysis with Growth Traits for Black Porgy (Acanthopagrus schlegelii)
by Zhiwei Zhang, Zhijie Lin, Mingliang Wei, Ziqiang Chen, Mingjun Shen, Guangyong Cao, Yue Wang, Zhiyong Zhang and Dianchang Zhang
Genes 2022, 13(11), 1992; https://doi.org/10.3390/genes13111992 - 31 Oct 2022
Cited by 3 | Viewed by 1601
Abstract
Black porgy is an important marine aquaculture fish species whose production is at the fifth position in all kinds of marine-cultured fishes in China. In this study, Illumina high-throughput sequencing technology was used to sequence the total RNA of black porgy. Sixty-one candidate [...] Read more.
Black porgy is an important marine aquaculture fish species whose production is at the fifth position in all kinds of marine-cultured fishes in China. In this study, Illumina high-throughput sequencing technology was used to sequence the total RNA of black porgy. Sixty-one candidate SNPs (Single Nucleotide Polymorphism) were screened out and genotyped through GATK4 (Genome Analysis ToolKit) software and MALDI-TOF MS (Matrix-Assisted Laser Desorption/ Ionization Time of Flight Mass Spectrometry). The experimental results showed that a total of sixty SNPs were successfully genotyped, with a success rate of 98.36%. The results of principal component analysis and correlation analysis of growth traits showed that body weight was the first principal component, with a cumulative contribution rate of 74%. There were significant correlations (p < 0.05) or extremely significant correlations (p < 0.01) between different growth traits. The results of genetic parameter analysis and association analysis showed that scaffold12-12716321, scaffold13-4787950, scaffold2-13687576 and scaffold290-11890 were four SNPs that met the requirement of polymorphic information content and conformed to the Hardy–Weinberg equilibrium. There were significant differences between their genotype and the phenotype of growth traits. The four SNP molecular markers developed in this research will lay a foundation for further exploration of molecular markers related to the growth traits of black porgy and will provide a scientific reference for the further study of its growth mechanisms. At the same time, these molecular markers can be applied to the production practices of black porgy, so as to realize selective breeding at the molecular level and speed up the breeding process. Full article
(This article belongs to the Special Issue Genetic Breeding of Aquaculture)
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13 pages, 3415 KiB  
Article
Cathepsin D Plays a Vital Role in Macrobrachium nipponense of Ovary Maturation: Identification, Characterization, and Function Analysis
by Dan Cheng, Wenyi Zhang, Sufei Jiang, Yiwei Xiong, Shubo Jin, Fangyan Pan, Junpeng Zhu, Yongsheng Gong, Yan Wu, Hui Qiao and Hongtuo Fu
Genes 2022, 13(8), 1495; https://doi.org/10.3390/genes13081495 - 21 Aug 2022
Cited by 3 | Viewed by 1699
Abstract
The oriental river prawn Macrobrachium nipponense is an economically important aquacultural species. However, its aquaculture is negatively impacted by the rapid sexual maturation of female M. nipponense. The fast sexual maturation produces a large number of offspring which leads to a reduction [...] Read more.
The oriental river prawn Macrobrachium nipponense is an economically important aquacultural species. However, its aquaculture is negatively impacted by the rapid sexual maturation of female M. nipponense. The fast sexual maturation produces a large number of offspring which leads to a reduction in resilience, a low survival rate, and an increased risk of hypoxia, this in turn, seriously affects the economic benefits of prawn farming. Cathepsin D is a lysosomal protease involved in the ovarian maturation of M. nipponense. In the current study, the cDNA of the gene encoding cathepsin D (Mn-CTSD) was cloned from M. nipponense. The total length was 2391 bp and consisted of an open reading frame (ORF) of 1158 bp encoding 385 amino acids. Sequence analysis confirmed the presence of conserved N-glycosylation sites and characteristic sequences of nondigestive cathepsin D. The qPCR analysis indicated that Mn-CTSD was highly expressed in all tissues tested, most significantly in the ovaries, whereas in situ hybridization showed that expression occurred mainly in oocyte nuclei. Analysis of its expression during development showed that Mn-CTSD peaked during the O-IV stage of ovarian maturation. For the RNAi interference experiment, female M. nipponense specimens in the ovary stage I were selected. Injection of Mn-CTSD double-stranded (ds)RNA into female M. nipponense decreased the expression of Mn-CTSD in the ovaries, such that the Gonad Somatic Index (GSI) of the experimental group was significantly lower than that of the control group (1.79% versus 4.57%; p < 0.05). Ovary development reached the O-III stage in 80% of the control group, compared with 0% in the experimental group. These results suggest that Mn-CTSD dsRNA inhibits ovarian maturation in M. nipponense, highlighting its important role in ovarian maturation in this species and suggesting an approach to controlling ovarian maturation during M. nipponense aquaculture. Full article
(This article belongs to the Special Issue Genetic Breeding of Aquaculture)
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12 pages, 1791 KiB  
Article
Microsatellite Characteristics of Silver Carp (Hypophthalmichthysmolitrix) Genome and Genetic Diversity Analysis in Four Cultured Populations
by Yajun Wang, Hang Sha, Xiaohui Li, Tong Zhou, Xiangzhong Luo, Guiwei Zou, Yi Chai and Hongwei Liang
Genes 2022, 13(7), 1267; https://doi.org/10.3390/genes13071267 - 16 Jul 2022
Cited by 2 | Viewed by 1703
Abstract
Hypophthalmichthys molitrix is one of the four most important fish in China and has high breeding potential. However, simple sequence repeat (SSR) markers developed on H. molitrix genome level for genetic diversity analysis are limited. In this study, the distribution characteristics of SSRs [...] Read more.
Hypophthalmichthys molitrix is one of the four most important fish in China and has high breeding potential. However, simple sequence repeat (SSR) markers developed on H. molitrix genome level for genetic diversity analysis are limited. In this study, the distribution characteristics of SSRs in the assembled H. molitrix genome were analyzed, and new markers were developed to preliminarily evaluate the genetic diversity of the four breeding populations. A total of 368,572 SSRs were identified from the H. molitrix genome. The total length of SSRs was 6,492,076 bp, accounting for 0.77% of the total length of the genome sequence. The total frequency and total density were 437.73 loci/Mb and 7713.16 bp/Mb, respectively. Among the 2–6 different nucleotide repeat types, SSRs were dominated by di-nucleotide repeats (204,873, 55.59%), and AC/GT was the most abundant motif. The number of SSRs on each chromosome was positively correlated with the length. The 13 pairs of markers developed were used to analyze the genetic diversity of four cultivated populations in Hubei Province. The results showed that the genetic diversity of the four populations was low, and the ranges of alleles (Na), effective alleles (Ne), observed heterozygosity (Ho), and Shannon’s index information (I) were 3.538–4.462, 2.045–2.461, 0.392–0.450, and 0.879–0.954, respectively. Genetic variation occurs mainly among individuals within populations (95.35%). UPGMA tree and Bayesian analysis showed that four populations could be divided into two different branches. Therefore, the genome-wide SSRs were effectively in genetic diversity analysis on H. molitrix. Full article
(This article belongs to the Special Issue Genetic Breeding of Aquaculture)
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