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Molecular Biology and the Genetic Breeding of Aquatic Animals: Breakthroughs and Challenges

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A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Biology".

Deadline for manuscript submissions: closed (20 May 2025) | Viewed by 8512

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Prof. Dr. Hongyan Xu

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Integrative Science Center of Germplasm Creation in Western China (CHONGQING) Science City & College of Fisheries, Southwest University, Chongqing 402460, China
Interests: molecular biology and genetic breeding of aquatic animals; biodiversity and conservation of aquatic animals; sustainable development of fishery
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Dear Colleagues,

Aquatic animals are important for ensuring the aquatic product supply in terms of high levels of proteins, unsaturated fatty acids, vitamins, and microelements. Recently, the increasing demands for aquatic products have resulted in the rapid depletion of fishery stocks all over the world. With decreasing water resources, it has become urgent to improve the aquaculture industry’s efficiency and sustainability. Thus, to obtain new breeds with desirable traits such as a rapid growth, a high meat quality, and stress resistance, a variety of technologies have been developed by the molecular biology and genetic breeding fields. The present Special Issue will focus on aquaculture industry improvements in molecular biology, such as genomic sequencing and gene-editing technologies, as well as genetic breeding, such as markers’ assistant selective, integration, and modification breeding. We welcome original research article and review submissions that contribute to progress in molecular biology and the genetic breeding of aquatic animals.

Prof. Dr. Hongyan Xu
Guest Editor

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Keywords

transgenic
genetic breeding
omics
gene expression and regulation
aquatic animals

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Published Papers (8 papers)

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Research

21 pages, 3359 KiB

Open AccessArticle

Developing Efficient Methods of Sperm Cryopreservation for Three Fish Species (Cyprinus carpio L., Schizothorax prenanti, Glyptosternum maculatum)

by Zheng Zhu, Jingting Yao, Linghui Zeng, Ke Feng, Chaowei Zhou, Haiping Liu, Wanliang Wang, Jianshe Zhou and Hongyan Xu

Int. J. Mol. Sci. 2025, 26(10), 4648; https://doi.org/10.3390/ijms26104648 - 13 May 2025

Viewed by 225

Abstract

Sperm cryopreservation is helpful for maintaining the genetic diversity of fish species. This study was aimed at developing efficient methods to cryopreserve the sperm of three fish species, including koi carp (Cyprinus carpio L.), Ya fish (Schizothorax prenanti), and Glyptosternum maculatum. Firstly, based on the analysis of sperm viability, the cryomedium, dilution ratio, volume, and cooling procedure were assessed and optimized in koi carp. The results showed that the highest sperm viability was up to 63.23 ± 1.36% after a 14-day cryopreservation using the optimal method, briefly, sperm frozen with a volume of 50 μL (Vol.sperm:Vol.cryomedium = 1:9) of cryomedium containing 10% DMSO and 3% sucrose in D17 through ultrarapid cooling. Secondly, both the mitochondrial membrane potential and the DNA fragmentation index of sperm were examined and found to be significantly damaged after the cryopreservation. Intriguingly, the fertilization rate of sperm after 14-day cryopreservation is up to 63.03 ± 1.36% and the elongation of cryopreservation time (210 days) just slightly affected the fertilization rate (55.09 ± 4.70%) in koi carp. Thirdly, the optimal cryopreservation method was applied to cryopreserve Glyptosternum maculatum sperm; the cell viability was 45.39 ± 4.70%. And then this method, after a minor modification (3% sucrose of cryomedium replaced with 3% SMP) was adopted to cryopreserve Ya fish sperm, the cell viability was up to 70.45 ± 2.23%. Lastly, the ultrastructure and morphology of sperm was observed by SEM, and it was found that the cryopreservation prominently caused sperm head swelling and tail shortening in three fish species. In conclusion, this study established effective methods for cryopreserving sperm in three fish species and elaborated the injuries on sperm caused by cryopreservation. And the findings facilitate developing more protocols with practical value to cryopreserve sperm in different fish species. Full article

(This article belongs to the Special Issue Molecular Biology and the Genetic Breeding of Aquatic Animals: Breakthroughs and Challenges)

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18 pages, 2080 KiB

Open AccessArticle

Evaluation of Low-Coverage Sequencing Strategies for Whole-Genome Imputation in Pacific Abalone Haliotis discus hannai

by Chengxia Fei, Shoudu Zhang, Xiangrui Chen, Junyu Liu, Wenzhu Peng, Guofan Zhang, Weiwei You and Fucun Wu

Int. J. Mol. Sci. 2025, 26(10), 4598; https://doi.org/10.3390/ijms26104598 - 11 May 2025

Viewed by 297

Abstract

Low-coverage whole-genome sequencing (lcWGS) followed by imputation is emerging as a cost-effective method for generating a substantial number of single nucleotide polymorphism (SNP) in aquatic species with highly heterozygous and complex genomes. This study represents the first systematic investigation into the application of low-coverage whole-genome sequencing (lcWGS) combined with imputation for genotyping in Pacific abalone (Haliotis discus hannai) without a reference panel. We utilized 1059 Pacific abalone individuals sequenced at an average depth of 7.86×, as well as 16 individuals sequenced at 20×, as sample materials. To assess the genotype imputation accuracy for lcWGS without a reference panel, we simulated data with varying sequencing depths (0.5–4×) and examined the effects of sample size, chromosome length, and minor allele frequency (MAF) using BaseVar and STITCH strategies. Results showed that STITCH achieved high accuracy when the sample size exceeded 400, with a genotype correlation (R²) of 0.98 ± 0.002 and genotype concordance (GC) of 0.99 ± 0.001. Imputation accuracy plateaued when the sample size exceeded 400 and sequencing depth surpassed 1×. Chromosome length had minimal effects, with all three chromosomes achieving an accuracy of approximately 0.98. However, the accuracy for rare MAF (<0.05) was lower, falling below 0.99. A second imputation with Beagle significantly increased SNP detection by 3.9–8.3 folds for a sequencing depth of 0.5–4×, apparently without sacrificing accuracy. To our knowledge, this is the first study of lcWGS analysis conducted in abalone. The findings demonstrate that lcWGS with imputation can achieve high accuracy with moderate sample sizes (n ≥ 400) in Pacific abalone, offering a cost-effective approach for genotyping in aquaculture species. Full article

(This article belongs to the Special Issue Molecular Biology and the Genetic Breeding of Aquatic Animals: Breakthroughs and Challenges)

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13 pages, 3264 KiB

Open AccessArticle

Integrative Utilization of Transcriptomics and Metabolomics Sheds Light on Disparate Growth Performance of Whiteleg Shrimp, Litopenaeus vannamei

by Xin Zhang, Bo Ma, Pengying Li, Ting Chen, Chunhua Ren, Chaoqun Hu and Peng Luo

Int. J. Mol. Sci. 2025, 26(7), 3133; https://doi.org/10.3390/ijms26073133 - 28 Mar 2025

Viewed by 418

Abstract

Litopenaeus vannamei is a key economic species in aquaculture, yet the molecular mechanisms underlying its growth variability remain unclear. This study conducted transcriptomic and metabolomic analyses of fast-growing (NL) and slow-growing (NS) shrimp under identical conditions. A total of 1280 differentially expressed genes (DEGs) related to protein processing, ribosomes, and oxidative phosphorylation, along with 5297 differentially abundant metabolites (DMs) involved in arginine biosynthesis, amino acid metabolism, and pantothenate and CoA biosynthesis, were identified and analyzed. An integrative analysis revealed that the NL shrimp exhibited an enhanced retinol, glutathione, riboflavin, and purine metabolism, which implies a higher tolerance to environmental stress. In contrast, the NS shrimp showed increased fatty acid degradation and an accelerated TCA cycle. This suggests that NS shrimp might require a substantial amount of energy to cope with environmental changes, consequently resulting in increased energy expenditures. This study provides significant insights into the molecular mechanisms underlying the growth disparity in L. vannamei, offering valuable data for future research aimed at optimizing shrimp growth performance and enhancing aquaculture productivity. Full article

(This article belongs to the Special Issue Molecular Biology and the Genetic Breeding of Aquatic Animals: Breakthroughs and Challenges)

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18 pages, 9644 KiB

Open AccessArticle

ctdsp2 Knockout Induces Zebrafish Craniofacial Dysplasia via p53 Signaling Activation

by Xin Xia, Wenjie Song, Fuyu Zhang, Yue Fan, Bo Zhang and Xiaowei Chen

Int. J. Mol. Sci. 2025, 26(3), 1297; https://doi.org/10.3390/ijms26031297 - 3 Feb 2025

Viewed by 1010

Abstract

Hemifacial microsomia (HFM) is a rare congenital craniofacial deformity that significantly impacts the appearance and hearing. The genetic etiology of HFM remains largely unknown, although genetic factors are considered to be primary contributors. We previously identified CTDSP2 as a potential causative gene in HFM cases. Utilizing CRISPR/Cas9, we knocked out ctdsp2 in zebrafish and analyzed the spatiotemporal expression of ctdsp2 and neural crest cell (NCC) markers through in situ hybridization (ISH). Craniofacial cartilage and chondrocyte phenotypes were visualized using Alcian blue and wheat germ agglutinin (WGA) staining. Cell proliferation and apoptosis were assessed via immunofluorescence with PH3 and TUNEL. RNA sequencing was performed on ctdsp2^−/− embryos and control siblings, followed by rescue experiments. Knockout of ctdsp2 in zebrafish resulted in craniofacial defects characteristic of HFM. We observed abnormalities in NCC apoptosis and proliferation in the pharyngeal arches, as well as impaired differentiation of chondrocytes in ctdsp2^−/− embryos. RNA-Seq analysis revealed significantly higher expression of genes in the p53 signaling pathway in mutants. Furthermore, ctdsp2 mRNA injection and tp53 knockout significantly rescued pharyngeal arch cartilage dysplasia. Our findings suggest that ctdsp2 knockout induces zebrafish craniofacial dysplasia, primarily by disrupting pharyngeal chondrocyte differentiation and inhibiting NCC proliferation through p53 signaling pathway activation. Full article

(This article belongs to the Special Issue Molecular Biology and the Genetic Breeding of Aquatic Animals: Breakthroughs and Challenges)

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14 pages, 3408 KiB

Open AccessArticle

Characterization of Feeding Behaviors, Appetite Regulation and Growth Performance of All-Female (cyp17a1+/−;XX Genotype) Common Carp (Cyprinus carpio)

by Xuehui Li, Qingqing Zou, Xuebo Liu, Qiyong Lou, Xia Jin, Jiangyan He, Zhan Yin, Gang Zhai, Ming Duan and Guanghui Chen

Int. J. Mol. Sci. 2024, 25(23), 12517; https://doi.org/10.3390/ijms252312517 - 21 Nov 2024

Cited by 1 | Viewed by 1057

Abstract

Genome editing has the potential to improve growth and traits of aquatic animals. Assessment of the feeding habits of the genetically modified farmed fish is necessary, as this is closely related to the assessment of their growth performance, which is one of the most important economic traits. Previously, we developed a novel strategy to produce all-female (AF) common carp (cyp17a1+/−;XX genotype) with genome editing, which exhibited a growth advantage compared to the control carp (including control male and female carp). However, the feeding behavior related to the growth performance of wild-type control and AF common carp remains elusive. The results of feeding and swimming behaviors showed that AF common carp exhibited a faster feeding activities and more active swimming activities, which probably enhanced its growth performance. Brain gene expression analysis revealed AF common carp had a significant upregulation of the orexigenic factors gene expression levels in the fed state, which would further promote the growth of AF carp. Here, AF carp exhibited higher growth performance with higher growth hormone (gh) gene expression. This study provided insight into the growth performance, feeding behaviors and appetite regulation of the genetically modified AF carp and the assessment of feeding behaviors in other genetically modified farmed fish. Full article

(This article belongs to the Special Issue Molecular Biology and the Genetic Breeding of Aquatic Animals: Breakthroughs and Challenges)

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12 pages, 2332 KiB

Open AccessArticle

Optimization of Whole-Genome Resequencing Depth for High-Throughput SNP Genotyping in Litopenaeus vannamei

by Pengfei Lin, Yang Yu, Zhenning Bao and Fuhua Li

Int. J. Mol. Sci. 2024, 25(22), 12083; https://doi.org/10.3390/ijms252212083 - 11 Nov 2024

Viewed by 1152

Abstract

The application of whole-genome resequencing in genetic research is rapidly expanding, yet the impact of sequencing depth on data quality and variant detection remains unclear, particularly in aquaculture species. This study re-sequenced 31 Litopenaeus vannamei (L. vannamei) samples at over 28× sequencing depth using the Illumina NovaSeq system and down-sampled the data to simulate depths from 0.5× to 20×. Results showed that when the sequencing depth was below 10×, the number of SNP identifications increased sharply with the rise in depth, with single nucleotide polymorphisms (SNPs) detected at 10× accounting for approximately 69.16% of those detected at 20×. The genotyping accuracy followed a similar trend to SNP detection results, being approximately 0.90 at 6×. Further analyses showed that the main cause of genotyping errors was the misidentification of heterozygous variants as homozygous variants. Therefore, considering both the quantity and quality of SNPs, a sequencing depth of 10× is recommended for whole-genome studies and genetic mapping, while a depth of 6× is more cost-effective for population structure analysis. This study underscores the importance of selecting optimal sequencing depth to ensure reliable variant detection and high data quality, providing valuable guidance for whole-genome resequencing in shrimp and other aquatic species. Full article

(This article belongs to the Special Issue Molecular Biology and the Genetic Breeding of Aquatic Animals: Breakthroughs and Challenges)

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16 pages, 1589 KiB

Open AccessArticle

GWAS Enhances Genomic Prediction Accuracy of Caviar Yield, Caviar Color and Body Weight Traits in Sturgeons Using Whole-Genome Sequencing Data

by Hailiang Song, Tian Dong, Wei Wang, Xiaoyu Yan, Chenfan Geng, Song Bai and Hongxia Hu

Int. J. Mol. Sci. 2024, 25(17), 9756; https://doi.org/10.3390/ijms25179756 - 9 Sep 2024

Cited by 1 | Viewed by 1695

Abstract

Caviar yield, caviar color, and body weight are crucial economic traits in sturgeon breeding. Understanding the molecular mechanisms behind these traits is essential for their genetic improvement. In this study, we performed whole-genome sequencing on 673 Russian sturgeons, renowned for their high-quality caviar. With an average sequencing depth of 13.69×, we obtained approximately 10.41 million high-quality single nucleotide polymorphisms (SNPs). Using a genome-wide association study (GWAS) with a single-marker regression model, we identified SNPs and genes associated with these traits. Our findings revealed several candidate genes for each trait: caviar yield: TFAP2A, RPS6KA3, CRB3, TUBB, H2AFX, morc3, BAG1, RANBP2, PLA2G1B, and NYAP1; caviar color: NFX1, OTULIN, SRFBP1, PLEK, INHBA, and NARS; body weight: ACVR1, HTR4, fmnl2, INSIG2, GPD2, ACVR1C, TANC1, KCNH7, SLC16A13, XKR4, GALR2, RPL39, ACVR2A, ADCY10, and ZEB2. Additionally, using the genomic feature BLUP (GFBLUP) method, which combines linkage disequilibrium (LD) pruning markers with GWAS prior information, we improved genomic prediction accuracy by 2%, 1.9%, and 3.1% for caviar yield, caviar color, and body weight traits, respectively, compared to the GBLUP method. In conclusion, this study enhances our understanding of the genetic mechanisms underlying caviar yield, caviar color, and body weight traits in sturgeons, providing opportunities for genetic improvement of these traits through genomic selection. Full article

(This article belongs to the Special Issue Molecular Biology and the Genetic Breeding of Aquatic Animals: Breakthroughs and Challenges)

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16 pages, 14420 KiB

Open AccessArticle

Characterization and Functional Analysis of the 17-Beta Hydroxysteroid Dehydrogenase 2 (hsd17b2) Gene during Sex Reversal in the Ricefield Eel (Monopterus albus)

by Ruyi Chen, Haoyu Zhu, Xiaoling Zhang, Lingli Li, Jinglin Xu, Zhimin Tan, Jialin Su, Ke Feng, Kaili Chen and Hongyan Xu

Int. J. Mol. Sci. 2024, 25(16), 9063; https://doi.org/10.3390/ijms25169063 - 21 Aug 2024

Cited by 1 | Viewed by 1610

Abstract

In mammals, 17-beta hydroxysteroid dehydrogenase 2 (Hsd17b2) enzyme specifically catalyzes the oxidation of the C17 hydroxyl group and efficiently regulates the activities of estrogens and androgens to prevent diseases induced by hormone disorders. However, the functions of the hsd17b2 gene involved in animal sex differentiation are still largely unclear. The ricefield eel (Monopterus albus), a protogynous hermaphroditic fish with a small genome size (2n = 24), is usually used as an ideal model to study the mechanism of sex differentiation in vertebrates. Therefore, in this study, hsd17b2 gene cDNA was cloned and its mRNA expression profiles were determined in the ricefield eel. The cloned cDNA fragment of hsd17b2 was 1230 bp, including an open reading frame of 1107 bp, encoding 368 amino acid residues with conserved catalytic subunits. Moreover, real-time quantitative reverse transcription polymerase chain reaction (RT-qPCR) analysis showed that hsd17b2 mRNA expressed strongly in the ovaries at early developmental stages, weakly in liver and intestine, and barely in testis and other tissues. In particular, hsd17b2 mRNA expression was found to peak in ovaries of young fish and ovotestis at the early stage, and eventually declined in gonads from the late ovotestis to testis. Likewise, chemical in situ hybridization results indicated that the hsd17b2 mRNA signals were primarily detected in the cytoplasm of oogonia and oocytes at stage I–II, subsequently concentrated in the granulosa cells around the oocytes at stage Ⅲ–Ⅳ, but undetectable in mature oocytes and male germ cells. Intriguingly, in ricefield eel ovaries, hsd17b2 mRNA expression could be significantly reduced by 17β-estradiol (E2) or tamoxifen (17β-estradiol inhibitor, E2I) induction at a low concentration (10 ng/mL) and increased by E2I induction at a high concentration (100 ng/mL). On the other hand, both the melatonin (MT) and flutamide (androgen inhibitor, AI) induction could significantly decrease hsd17b2 mRNA expression in the ovary of ricefield eel. This study provides a clue for demonstrating the mechanism of sexual differentiation in fish. The findings of our study imply that the hsd17b2 gene could be a key regulator in sexual differentiation and modulate sex reversal in the ricefield eel and other hermaphroditic fishes. Full article

(This article belongs to the Special Issue Molecular Biology and the Genetic Breeding of Aquatic Animals: Breakthroughs and Challenges)

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