Genetics and Genomics Applied to Aquatic Animal Science—2nd Edition

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

Deadline for manuscript submissions: closed (25 December 2024) | Viewed by 3950

Special Issue Editors


E-Mail Website
Guest Editor
College of Life Sciences, Huzhou University, Huzhou 313000, China
Interests: RNA-seq; bioinformatics; functional genomics; GWAS; livestock genomics; conservation of animal genetic resources

E-Mail Website
Guest Editor
Institute of Hydrobiology, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
Interests: population genetics; genetic breeding of aquatic organisms

Special Issue Information

Dear Colleagues,

Aquatic animals play a critical role in the global food supply and have become a primary source for human diets. Compared to crops and livestock, the production of aquatic animals is fast-growing due to modern aquaculture and the genetic improvement of aquatic animals. The genetic improvement of economic traits via molecular selective breeding has become increasingly important to help meet the rising food demand driven by human population growth. In particular, the genetics and genomics of aquatic animals provide huge opportunities for genetic gains in breeding programs.

With the continuous advances in sequencing techniques and bioinformatics, genetics and genomics have been widely used in breeding studies of aquatic animals in recent years. For instance, ultra-long reads generated by PacBio or Nanopore sequencing platforms allow us to obtain a large number of genetic variations and candidate functional genes associated with breeding traits. Additionally, with the aid of RNA-seq and whole-genome sequencing or resequencing methods, we can accurately evaluate the genetic regulation patterns and genetic backgrounds of aquatic resources.

In this Special Issue, we welcome papers in the field of the genetics and genomics of aquatic animals, such as fish, crustaceans, and turtles, including the identification of candidate functional genes or QTLs related to important traits and genetic resource evaluation with genome-wide markers. Manuscripts focusing on the application of high-throughput sequencing approaches and biotechnological innovations, such as RNA-seq, gene editing, WGS, genome resequencing in genome selection, and BS-seq, are encouraged.

Dr. Shaokui Yi
Dr. Xiaojun Xu
Guest Editors

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Keywords

  • breeding trait
  • gene function
  • genetic map
  • gene editing
  • transcriptome
  • GWAS
  • QTL
  • genome resequencing
  • molecular marker

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Published Papers (4 papers)

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Research

17 pages, 5392 KiB  
Article
Research on SSR Genetic Molecular Markers and Morphological Differences of Different Pelodiscus sinensis Populations
by Yixin Liang, Changqing Huang, Pei Wang, Hewei Xiao, Zi’ao Wang, Jiawei Zeng, Xiaoqing Wang, Shuting Xiong, Yazhou Hu and Qin Qin
Genes 2025, 16(3), 318; https://doi.org/10.3390/genes16030318 - 7 Mar 2025
Viewed by 504
Abstract
Background/Objectives: The Chinese soft-shelled turtle (Pelodiscus sinensis) is an important species in freshwater aquaculture. Genetic admixture and degradation due to rapid industry expansion threaten sustainable development. This study aims to assess the genetic diversity and structure of six P. sinensis populations [...] Read more.
Background/Objectives: The Chinese soft-shelled turtle (Pelodiscus sinensis) is an important species in freshwater aquaculture. Genetic admixture and degradation due to rapid industry expansion threaten sustainable development. This study aims to assess the genetic diversity and structure of six P. sinensis populations for better management. Methods: We combined morphological analysis and microsatellite markers to evaluate the genetic diversity of six populations. A discriminant function based on morphology was developed, achieving 71.4% classification accuracy. Two SSR markers were identified to specifically distinguish the HS population. Results: The six populations were classified into three subgroups. Frequent gene flow was observed among the CY, W, and DT populations, with most genetic variation occurring within individuals. However, significant genetic differentiation was detected between populations. While gene flow enhanced diversity, it suppressed differentiation. Conclusions: This study provides insights into the genetic structure and diversity of six P. sinensis populations. The discriminant function and SSR markers offer a basis for germplasm conservation and management, supporting sustainable aquaculture development. Full article
(This article belongs to the Special Issue Genetics and Genomics Applied to Aquatic Animal Science—2nd Edition)
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15 pages, 23444 KiB  
Article
Construction of the Red Swamp Crayfish (Procambarus clarkii) Family Selection Population and Whole Genome Sequencing to Screen WIPFI Candidate Genes Related to Growth
by Xing Tian, Xiudan Yuan, Zhigang He, Weiguo Li, Jinlong Li, Yong He, Shiming Deng, Jiarong Guo, Miaoquan Fang and Dongwu Wang
Genes 2025, 16(2), 174; https://doi.org/10.3390/genes16020174 - 31 Jan 2025
Viewed by 843
Abstract
Background/Objectives: Procambarus clarkii is an important freshwater aquaculture species in China which has the characteristics of rich nutrition and delicious taste. However, the expansion of aquaculture scale, germplasm degradation, and other problems that have become increasingly prominent seriously restrict the sustainable development [...] Read more.
Background/Objectives: Procambarus clarkii is an important freshwater aquaculture species in China which has the characteristics of rich nutrition and delicious taste. However, the expansion of aquaculture scale, germplasm degradation, and other problems that have become increasingly prominent seriously restrict the sustainable development of the crayfish industry. Genetic improvement is an urgent need for the crayfish aquaculture industry, and selective breeding is an important way to improve the crayfish varieties. Methods: We established full-sibling family populations of the red swamp crayfish and performed whole-genome resequencing of the F3 family-selected red swamp crayfish population and wild red swamp crayfish populations from four regions of Hunan Province (Nanx, Mil, Caish, and Wangc). Results: The results showed that there was a clear separation between the wild population and the family population, and the decline rate was slightly faster in the wild population than that of the family breeding population. There was local gene flow between family populations, as well as gene flow between Mil, Caish, and families. In addition, 52 SNP loci related to body weight traits were identified by genome-wide association analysis, and the candidate gene WIPF1 related to growth was screened out. Conclusions: We established a line selection population of red swamp crayfish and obtained more stable candidate lines. In addition, this study identified Wiskott–Aldrich syndrome protein-interacting protein family member 1 (WIPF1) as a candidate gene related to body weight for the first time. The results provide a theoretical basis for exploring the growth mechanism of P. clarkii and carrying out in-depth genetic improvement. Full article
(This article belongs to the Special Issue Genetics and Genomics Applied to Aquatic Animal Science—2nd Edition)
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13 pages, 5625 KiB  
Article
Chromosome-Level Assembly and Annotation of the Endangered Red-Wing Fish (Distoechodon macrophthalmus)
by Xiangyun Zhu, Yanping Luo, Baoshan Ma, Qi Shen, Xingyu Zheng, Mei Xu, Qiang Sheng and Junjie Wu
Genes 2024, 15(12), 1536; https://doi.org/10.3390/genes15121536 - 28 Nov 2024
Viewed by 870
Abstract
Background/Objectives: The red-wing fish (Distoechodon macrophthalmus), an endangered species native to Yunnan, is endemic to Chenghai Lake. The natural population of this species has suffered a sharp decline due to the invasion of alien fish species. Fortunately, the artificial domestication and [...] Read more.
Background/Objectives: The red-wing fish (Distoechodon macrophthalmus), an endangered species native to Yunnan, is endemic to Chenghai Lake. The natural population of this species has suffered a sharp decline due to the invasion of alien fish species. Fortunately, the artificial domestication and reproduction of D. macrophthalmus have been successful and this species has become an economic species locally. However, there is still little research on D. macrophthalmus. Methods: In this study, a high-quality genome of D. macrophthalmus was assembled and annotated. The genome was sequenced and assembled using the PacBio platform and Hi-C method. Results: The genome size is 1.01 Gb and N50 is 37.99 Mb. The assembled contigs were anchored into 24 chromosomes. BUSCO analysis revealed that the genome assembly has 95.6% gene coverage completeness. A total of 455.62 Mb repeat sequences (48.50% of the assembled genome) and 30,424 protein-coding genes were identified in the genome. Conclusions: This study provides essential genomic data for further research on the evolution and conservation of D. macrophthalmus. Meanwhile, the high-quality genome assembly also provides insights into the genomic evolution of the genus Distoechodon. Full article
(This article belongs to the Special Issue Genetics and Genomics Applied to Aquatic Animal Science—2nd Edition)
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11 pages, 3997 KiB  
Article
Germplasm Resources Evaluation of Cultured Largemouth Bass (Micropterus salmoides) in China Based on Whole Genome Resequencing
by Wenzhi Guan, Jieliang Jian, Baolong Niu, Xinhui Zhang, Jiongying Yu and Xiaojun Xu
Genes 2024, 15(10), 1307; https://doi.org/10.3390/genes15101307 - 10 Oct 2024
Cited by 3 | Viewed by 1291
Abstract
Background: Largemouth bass (Micropterus salmoides), a valuable freshwater fish species, has experienced significant genetic decline in China due to prolonged domestic breeding and limited introduction of new genetic material. It is necessary to have a comprehensive understanding of the genetic status [...] Read more.
Background: Largemouth bass (Micropterus salmoides), a valuable freshwater fish species, has experienced significant genetic decline in China due to prolonged domestic breeding and limited introduction of new genetic material. It is necessary to have a comprehensive understanding of the genetic status of largemouth bass populations in China. Method: In this study, we conducted population genetic analyses on nine cultured largemouth bass populations using whole genome resequencing. Results: A total of 3.23 Tb of clean bases were generated, with average Q20 and Q30 values of 98.17% and 94.25%, respectively, and 2,140,534 high-quality SNPs were obtained. Relatively high genetic diversity was observed across all populations. Combined with linkage disequilibrium (LD) patterns, the Wanlu (WL) population possessed the highest genetic diversity, and the Longyou (LY) population possessed the lowest genetic diversity. Additionally, population structure analyses, including pairwise F-statistics, phylogenetic trees, PCA, and admixture analysis, revealed significant genetic differentiation, particularly between the WL, LY, and other 7 populations, while also indicating the occurrence of a common admixture event. Finally, TreeMix inferred migration events from the WL to the Chuanlu (CL) population and from the Taiwan breeding population (TWL) to the Guanglu (GL) population. Conclusions: These findings provide a critical foundation for developing conservation and breeding strategies for largemouth bass in China. Full article
(This article belongs to the Special Issue Genetics and Genomics Applied to Aquatic Animal Science—2nd Edition)
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