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Functional Genomics in Aquaculture
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Functional Genomics in Aquaculture

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

Deadline for manuscript submissions: closed (20 May 2022) | Viewed by 6141

Special Issue Editors

Dr. Beth M Cleveland

E-Mail Website
Guest Editor
USDA ARS National Center for Cool and Cold Water Aquaculture, Kearneysville, WV 25430, USA
Interests: rainbow trout; gene editing; genotype–environment interaction; nutritional biochemistry; physiology; functional genomics
Special Issues, Collections and Topics in MDPI journals
Dr. Albert Caballero-Solares

E-Mail Website
Guest Editor
Department of Ocean Sciences, Memorial University of Newfoundland, St. John’s, NL A1C 5S7, Canada
Interests: immune responses; fish genomics; aquaculture; fish nutrition; immunology; genomics

Special Issue Information

Dear Colleagues,

Advancements in functional genomics technologies combined with improved genome assemblies have enhanced understanding of genetic regulation of economically important traits in fish and shellfish species relevant to the aquaculture industry. For example, genomic modification strategies such as gene editing are valuable for characterizing the relationship between genes, protein function, and phenotypes, and useful for validating candidate loci that support precision breeding strategies. Technologies in transcriptome analysis have advanced knowledge of regulatory mechanisms controlling biological processes and responses to environmental factors. In addition, the field of epigenetics has progressed our understanding of both informational transmission through generations and how environmental factors affect gene expression.

This Special Issue welcomes manuscripts that apply these technologies in functional genomics in fish and shellfish. Studies that utilize gene editing to understand the relationship between genotype and phenotype are encouraged, as are manuscripts that characterize the transcriptomic and epigenetic response to various stimuli (nutrients and nutritional programming, environmental influences, pathogen exposure, maternal imprinting, etc.). Research that utilizes bioinformatics approaches to integrate data from different -omics applications is also welcome. Collectively, this Special Issue is intended to contribute to the development of novel husbandry strategies and breeding tools for superior genetics that advance aquaculture production efficiency and improve global food security.

Dr. Beth M Cleveland
Dr. Albert Caballero-Solares
Guest Editors

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.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Genes is an international peer-reviewed open access monthly journal published by MDPI.

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

  • functional genomics
  • aquaculture
  • gene editing
  • transcriptomics
  • epigenetics
  • bioinformatics

Published Papers (3 papers)

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Research

15 pages, 14868 KiB  
Article
Mechanisms of Caspases 3/7/8/9 in the Degeneration of External Gills of Chinese Giant Salamanders (Andrias davidianus)
by Shijun Yang, Caixia Tan, Xuerong Sun, Xiong Tang, Xiao Huang, Fan Yan, Guangxiang Zhu and Qin Wang
Genes 2022, 13(8), 1360; https://doi.org/10.3390/genes13081360 - 29 Jul 2022
Viewed by 1478
Abstract
Metamorphosis is a critical stage in the adaptive development of amphibians from aquatic to terrestrial animals. Metamorphosis of the Chinese giant salamander is mainly manifested by the loss of external gills with consequent changes in the respiratory pattern. The loss of the external [...] Read more.
Metamorphosis is a critical stage in the adaptive development of amphibians from aquatic to terrestrial animals. Metamorphosis of the Chinese giant salamander is mainly manifested by the loss of external gills with consequent changes in the respiratory pattern. The loss of the external gill is regulated by the pathway of apoptosis in which caspase genes are the key factors. This study cloned and expressed the caspase 3/7/8/9 genes of the Chinese giant salamander. The main results were as follows: the complete open reading frames (ORFs) were 885 bp, 960 bp, 1461 bp and 1279 bp, respectively; caspase 3/7/8/9 genes all contained the CASc domain, and most of the motifs were located in CASc domain; and caspase 8 possessed two DED structural domains and caspase 9 possessed a CARD structural domain. Furthermore, results from the tissue distribution analysis indicated that caspase 3/7/8/9 genes were all significantly expressed in the external gill, and at 9 and 10 months of age (MOA), which is the peak time for the loss, the EXPRESSION level of caspase 3/7/8/9 genes was obviously high, which was consistent with the histological result. Moreover, the loss of external gills of the Chinese giant salamander may result from activation of both the apoptosis-related death receptor pathway and the mitochondrial pathway. Finally, it was discovered that thyroid hormone (TH) treatment could both advance the time point at which the external gills of the Chinese giant salamander began to degenerate and shorten this process. Interestingly, at the peak of its metamorphosis (9 MOA), the Chinese giant salamander further accelerated the metamorphosis rate of TH treatment, which suggested a promotive effect on the loss of external gills via the superimposition of the exogenous TH and caspase genes. The study of caspase genes in this experiment was conducive to understanding the mechanism of external gill loss in the Chinese giant salamander, as well as improving our understanding of the metamorphosis development of some Caudata species. Full article
(This article belongs to the Special Issue Functional Genomics in Aquaculture)
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18 pages, 1291 KiB  
Article
Weighted Single-Step GWAS Identifies Genes Influencing Fillet Color in Rainbow Trout
by Ridwan O. Ahmed, Ali Ali, Rafet Al-Tobasei, Tim Leeds, Brett Kenney and Mohamed Salem
Genes 2022, 13(8), 1331; https://doi.org/10.3390/genes13081331 - 26 Jul 2022
Cited by 4 | Viewed by 2133
Abstract
The visual appearance of the fish fillet is a significant determinant of consumers’ purchase decisions. Depending on the rainbow trout diet, a uniform bright white or reddish/pink fillet color is desirable. Factors affecting fillet color are complex, ranging from the ability of live [...] Read more.
The visual appearance of the fish fillet is a significant determinant of consumers’ purchase decisions. Depending on the rainbow trout diet, a uniform bright white or reddish/pink fillet color is desirable. Factors affecting fillet color are complex, ranging from the ability of live fish to accumulate carotenoids in the muscle to preharvest environmental conditions, early postmortem muscle metabolism, and storage conditions. Identifying genetic markers of fillet color is a desirable goal but a challenging task for the aquaculture industry. This study used weighted, single-step GWAS to explore the genetic basis of fillet color variation in rainbow trout. We identified several SNP windows explaining up to 3.5%, 2.5%, and 1.6% of the additive genetic variance for fillet redness, yellowness, and whiteness, respectively. SNPs are located within genes implicated in carotenoid metabolism (β,β-carotene 15,15′-dioxygenase, retinol dehydrogenase) and myoglobin homeostasis (ATP synthase subunit β, mitochondrial (ATP5F1B)). These genes are involved in processes that influence muscle pigmentation and postmortem flesh coloration. Other identified genes are involved in the maintenance of muscle structural integrity (kelch protein 41b (klh41b), collagen α-1(XXVIII) chain (COL28A1), and cathepsin K (CTSK)) and protection against lipid oxidation (peroxiredoxin, superoxide dismutase 2 (SOD2), sestrin-1, Ubiquitin carboxyl-terminal hydrolase-10 (USP10)). A-to-G single-nucleotide polymorphism in β,β-carotene 15,15′-dioxygenase, and USP10 result in isoleucine-to-valine and proline-to-leucine non-synonymous amino acid substitutions, respectively. Our observation confirms that fillet color is a complex trait regulated by many genes involved in carotenoid metabolism, myoglobin homeostasis, protection against lipid oxidation, and maintenance of muscle structural integrity. The significant SNPs identified in this study could be prioritized via genomic selection in breeding programs to improve fillet color in rainbow trout. Full article
(This article belongs to the Special Issue Functional Genomics in Aquaculture)
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22 pages, 4551 KiB  
Article
Integrated Analyses of DNA Methylation and Gene Expression of Rainbow Trout Muscle under Variable Ploidy and Muscle Atrophy Conditions
by Mohamed Salem, Rafet Al-Tobasei, Ali Ali and Brett Kenney
Genes 2022, 13(7), 1151; https://doi.org/10.3390/genes13071151 - 26 Jun 2022
Cited by 4 | Viewed by 1891
Abstract
Rainbow trout, Oncorhynchus mykiss, is an important cool, freshwater aquaculture species used as a model for biological research. However, its genome reference has not been annotated for epigenetic markers affecting various biological processes, including muscle growth/atrophy. Increased energetic demands during gonadogenesis/reproduction provoke [...] Read more.
Rainbow trout, Oncorhynchus mykiss, is an important cool, freshwater aquaculture species used as a model for biological research. However, its genome reference has not been annotated for epigenetic markers affecting various biological processes, including muscle growth/atrophy. Increased energetic demands during gonadogenesis/reproduction provoke muscle atrophy in rainbow trout. We described DNA methylation and its associated gene expression in atrophying muscle by comparing gravid, diploid females to sterile, triploid females. Methyl Mini-seq and RNA-Seq were simultaneously used to characterize genome-wide DNA methylation and its association with gene expression in rainbow trout muscle. Genome-wide enrichment in the number of CpGs, accompanied by depleted methylation levels, was noticed around the gene transcription start site (TSS). Hypermethylation of CpG sites within ±1 kb on both sides of TSS (promoter and gene body) was weakly/moderately associated with reduced gene expression. Conversely, hypermethylation of the CpG sites in downstream regions of the gene body +2 to +10 kb was weakly associated with increased gene expression. Unlike mammalian genomes, rainbow trout gene promotors are poor in CpG islands, at <1% compared to 60%. No signs of genome-wide, differentially methylated (DM) CpGs were observed due to the polyploidy effect; only 1206 CpGs (0.03%) were differentially methylated, and these were primarily associated with muscle atrophy. Twenty-eight genes exhibited differential gene expression consistent with methylation levels of 31 DM CpGs. These 31 DM CpGs represent potential epigenetic markers of muscle atrophy in rainbow trout. The DM CpG-harboring genes are involved in apoptosis, epigenetic regulation, autophagy, collagen metabolism, cell membrane functions, and Homeobox proteins. Our study also identified genes explaining higher water content and modulated glycolysis previously shown as characteristic biochemical signs of rainbow trout muscle atrophy associated with sexual maturation. This study characterized DNA methylation in the rainbow trout genome and its correlation with gene expression. This work also identified novel epigenetic markers associated with muscle atrophy in fish/lower vertebrates. Full article
(This article belongs to the Special Issue Functional Genomics in Aquaculture)
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