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Genomic Prediction and Functional Genomics in Aquaculture
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Genomic Prediction and Functional Genomics in Aquaculture

A special issue of Journal of Marine Science and Engineering (ISSN 2077-1312). This special issue belongs to the section "Marine Biology".

Deadline for manuscript submissions: closed (30 June 2021) | Viewed by 13796

Special Issue Editors

Dr. Nguyen Hong Nguyen

E-Mail Website
Guest Editor
Faculty of Science, Health, Education & Engineering, University of the Sunshine Coast, Maroochydore, Australia
Interests: quantitative genetics; genomics; selective breeding; genetic improvement; DNA markers; gene mapping, genome analysis and applied statistics
Prof. Dr. Kyall Zenger

E-Mail Website
Guest Editor
Centre for Sustainable Tropical Fisheries and Aquaculture and College of Science and Engineering, James Cook University, Townsville, QLD 4811, Australia
Interests: quantitative genetics; adaptive traits; genomics; selective breeding; evolutionary and population genetics; genome structure

Special Issue Information

Dear Colleagues,

This Special Issue focuses on two major research areas: genomic prediction/selection and functional genomics in aquaculture. We call for review and research papers in relation to these main themes. Topics considered by this Issue include but are not restricted to the following:

  1. Genomic prediction for complex quantitative traits of commercial importance in aquaculture species
  2. Development and use of advanced on-farm data collection systems for improving aquaculture breeding programs;
  3. Relationship between genotype and phenotype on a genome-wide (genome-, transcriptome-, proteome-, metabolome or epigenome-wide) scale.
  4. Utilization of ‘natural’ genetic variation (germplasm, diversity, genetically divergent populations to identify useful alleles) to enhance aquaculture breeding
  5. Functional genomic resources, such as expressed sequence tags, full-length cDNAs, and gene expression profiles (transcriptome, proteome, and metabolome)
  6. Understanding and manipulating key biological genetic pathways for genetic improvement of important aquaculture species
  7. RNA silencing and CRISPR/CAS9 applications in aquaculture
  8. Bioinformatics tools that integrate and analyze data obtained from multiple ‘omics’ platforms
  9. Improving aquaculture genetic improvement programs through the incorporation of G×E effects.

Dr. Nguyen Hong Nguyen
Prof. Kyall Zenger
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. Journal of Marine Science and Engineering 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

  • genomic selection
  • genome-wide analysis
  • functional genomics
  • system biology
  • multi-omics
  • selective breeding
  • genetic improvement and aquaculture species

Published Papers (5 papers)

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Research

13 pages, 3823 KiB  
Article
Whole Genome Sequence of the Newly Prescribed Subspecies Oreochromis spilurus saudii: A Valuable Genetic Resource for Aquaculture in Saudi Arabia
by Mohammed Othman Aljahdali, Mohammad Habibur Rahman Molla and Wessam Mansour Filfilan
J. Mar. Sci. Eng. 2021, 9(5), 506; https://doi.org/10.3390/jmse9050506 - 8 May 2021
Cited by 7 | Viewed by 2943
Abstract
Tilapia (Oreochromis spp.) have significant potential for aquaculture production around the world. There is an increasing demand among tilapia producers for strains with higher yields and for fish that can survive in highly saline water. Novel strains and consistent seedstock are critically [...] Read more.
Tilapia (Oreochromis spp.) have significant potential for aquaculture production around the world. There is an increasing demand among tilapia producers for strains with higher yields and for fish that can survive in highly saline water. Novel strains and consistent seedstock are critically important objectives for sustainable aquaculture, but for these required targets there is still not enough progress. Therefore, this study describes the genome sequence of Oreochromis spilurus to support the seawater culture of tilapia. The draft genome is 0.768 Gb (gigabases), with a scaffold N50 (the genome (50%) is in fragments of this length) of 0.22 Mb (megabases). The GC content is 40.4%, the heterozygosity rate is 0.35%, and the repeat content is 47.97%. The predicted protein-coding peptide encoded 51,642 and predicted 10,641 protein-coding genes in the O. spilurus genome. The predicted antimicrobial peptides were 262, bringing new hope for further research. This whole genome sequence provides new insights for biomedical and molecular research and will also improve the breeding of tilapia for high yields, resistance to disease, and adaptation to salt water. Full article
(This article belongs to the Special Issue Genomic Prediction and Functional Genomics in Aquaculture)
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9 pages, 452 KiB  
Article
Genome-Wide Marker Analysis for Traits of Economic Importance in Asian Seabass Lates calcarifer
by Nguyen Hong Nguyen and Pham Van Khang
J. Mar. Sci. Eng. 2021, 9(3), 282; https://doi.org/10.3390/jmse9030282 - 5 Mar 2021
Cited by 2 | Viewed by 1719
Abstract
To date, it is not known whether animal breeding values in Asian seabass (Lates calcarifer) can be estimated using single nucleotide polymorphisms (SNPs) generated from new high-throughput genotyping by sequencing platforms. The principal aim of the present study was to assess [...] Read more.
To date, it is not known whether animal breeding values in Asian seabass (Lates calcarifer) can be estimated using single nucleotide polymorphisms (SNPs) generated from new high-throughput genotyping by sequencing platforms. The principal aim of the present study was to assess the genomic prediction accuracy for growth traits, survival, cannibalism, and disease resistance against Streptococcus iniae in this species L. calcarifer. Additionally, this study attempted to identify markers associated with the five traits studied as well as to understand if the genotype data can be used to estimate genetic parameters for these complex traits. The genomic best linear unbiased prediction (gBLUP) method was used to analyze 11,084 SNPs and showed that the prediction accuracies for growth traits (weight and length) were high (0.67–0.75). By contrast, these estimates for survival were low (0.25). Multi-locus mixed model analyses identified four SNPs significantly associated with body weight (p < 5 × 10−8 or −log10 p ≥ 5). There were, however, no significant associations detected for other traits. Similarly, the SNP heritability was moderate, while the estimates for other traits were approximated to zero and not significant. Genetic correlations between body weight and standard length were close to unity. Collectively, the results obtained from this study suggest that genotyping by sequencing platforms can provide informative DNA markers to conduct genome-wide association analysis, estimation of genetic parameters, and evaluation of genomic prediction accuracy for complex traits in Asian seabass. Full article
(This article belongs to the Special Issue Genomic Prediction and Functional Genomics in Aquaculture)
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11 pages, 1259 KiB  
Article
Molecular Cloning and Polymorphism Analysis of PmFGF18 from Pinctada fucata martensii
by Ruijuan Hao, Chuchu Mo, Linda Adzigbli, Chuangye Yang, Yuewen Deng and Qingheng Wang
J. Mar. Sci. Eng. 2020, 8(11), 896; https://doi.org/10.3390/jmse8110896 - 10 Nov 2020
Cited by 2 | Viewed by 1895
Abstract
Fibroblast growth factor 18 (FGF18) plays an important functional role in skeletal growth and development. The FGF18 gene was characterized in pearl oyster Pinctada fucata martensii (PmFGF18) with the full-length sequence containing an open reading frame of 714 bp encoding 237 [...] Read more.
Fibroblast growth factor 18 (FGF18) plays an important functional role in skeletal growth and development. The FGF18 gene was characterized in pearl oyster Pinctada fucata martensii (PmFGF18) with the full-length sequence containing an open reading frame of 714 bp encoding 237 amino acids. The domain analysis of PmFGF18 showed a distinctive FGF domain, with a high similarity to FGF18 protein sequences from Crassostrea gigas (43.35%) and C. virginica (37.43%). PmFGF18 expression was revealed in all analyzed tissues with a significantly higher expression level in the fast-growing group than the slow-growing group. The analysis of PmFGF18 polymorphism demonstrated 33 SNPs (single nucleotide polymorphisms) in the CDS and promoter region of PmFGF18 sequence. Association analysis revealed 19 SNPs (2 SNPs from CDS and 17 SNPs from the promoter region) associating significantly with growth traits. Among the associated SNPs, one SNP g.50918198 A > C was verified in the other breeding line. Therefore, PmFGF18 can be utilized as a candidate gene for growth, and its related SNPs could be used in selective breeding of P. f. martensii for the improvement of growth traits. Full article
(This article belongs to the Special Issue Genomic Prediction and Functional Genomics in Aquaculture)
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16 pages, 1378 KiB  
Article
Population Genomic Analyses of Wild and Farmed Striped Catfish Pangasianodon Hypophthalmus in the Lower Mekong River
by Nguyen Thanh Vu, Tran Thi Thuy Ha, Vo Thi Bich Thuy, Vu Thi Trang and Nguyen Hong Nguyen
J. Mar. Sci. Eng. 2020, 8(6), 471; https://doi.org/10.3390/jmse8060471 - 25 Jun 2020
Cited by 4 | Viewed by 3091
Abstract
The striped catfish Pangasianodon hypophthalmus is an important freshwater fish cultured in many countries where the collection of wild brooders is still widely practiced. Global farming development of this species makes use of significant natural resources that pose challenges for the genetic diversity [...] Read more.
The striped catfish Pangasianodon hypophthalmus is an important freshwater fish cultured in many countries where the collection of wild brooders is still widely practiced. Global farming development of this species makes use of significant natural resources that pose challenges for the genetic diversity of striped catfish. Hence, this study aims to conduct a systematic genetic diversity assessment of wild and farmed catfish stocks collected from four major pangasius-farming countries, using a new genotyping by sequencing platform known as DArT-seq technology. Our population genomic analyses using 7263 single-nucleotide polymorphisms (SNPs) after high-quality-control showed that there were two distinct populations of striped catfish in the lower Mekong river: (i) wild catfish from Thailand and (ii) catfish from Cambodia and Vietnam. The genetic diversity was greatest (0.363) in the wild stock from Thailand, but it was lower in farmed and wild stocks in other countries (0.049 to 0.088). The wild stocks were more genetically diverse than the farmed animals (0.103 vs. 0.064). The inbreeding coefficient ranged from 0.004 and 0.109, with the lowest value (−0.499) in the wild animals from Thailand. Molecular inference methods revealed high degree of historical effective population size (1043.9–1258.4), but there was considerable decline in the contemporary estimates in all populations (10.8 to 73.6). Our additional analyses calculating divergent times and migration patterns showed that the wild catfish from Thailand stand out as separate lineages, while those from Cambodia and Vietnam are genetically identical. Our results also indicated that the cultured stock in Bangladesh originated from the lower part of the Mekong river. These findings have significant practical implications in the context of genetic selection and conservation of striped catfish in the region. Collectively, they will contribute to the sustainable development of the striped catfish sector in these countries. Full article
(This article belongs to the Special Issue Genomic Prediction and Functional Genomics in Aquaculture)
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14 pages, 303 KiB  
Article
Prospects for Genetic Improvement in Objective Measurements of Body Colour in Pacific Whiteleg Shrimp (Litopenaeus vannamei)
by Cao Truong Giang, Wayne Knibb, Tran The Muu, Nguyen Huu Ninh and Nguyen Hong Nguyen
J. Mar. Sci. Eng. 2019, 7(12), 460; https://doi.org/10.3390/jmse7120460 - 14 Dec 2019
Cited by 9 | Viewed by 2989
Abstract
Body colour, together with growth and survival, are traits of commercial importance in Pacific whiteleg shrimp (Litopenaeus vannamei). However, heritability estimates for objective measurements of body colour are not available in Whiteleg shrimp species, including L. vannamei. Further, the effect [...] Read more.
Body colour, together with growth and survival, are traits of commercial importance in Pacific whiteleg shrimp (Litopenaeus vannamei). However, heritability estimates for objective measurements of body colour are not available in Whiteleg shrimp species, including L. vannamei. Further, the effect of genotype by environment interactions (G × E) on this trait (i.e., the objective measures of body colour) and its genetic associations with growth are not known in this species. The present study presented the first attempt at understanding the genetic architecture of this complex character (body colour) that is of economic significance to the shrimp aquaculture sector world-wide. Specifically, we investigated the quantitative genetic basis of shrimp colour, while using the measurement tool (colorimeter) for a Whiteleg shrimp population reared in two contrasting environments. A total of 5464 shrimp had the objective measurements of body colour (lightness, yellowness, and redness) and growth trait records (weight, length and width). They were the offspring of 204 dams and 197 sires. The restricted maximum likelihood mixed model analysis showed that there were heritable additive genetic components for all of the measurements of shrimp colour, with the heritability (h2) ranging from 0.11–0.55. The h2 estimates for redness and yellowness traits differed between the two environments (h2 = 0.66–0.82 in Khanhhoa vs. 0.00–0.03 in Haiphong). However, the heritability for colour traits was moderate (0.11–0.55) when the two environments were combined. There is existence of (co)-genetic variances between the studied traits. The genetic correlations of body traits with redness or yellowness colour of the shrimp were moderate and positive (a*: 0.13–0.32 for redness and b*: 0.19–0.40 for yellowness). The effect of G × E interactions on shrimp colours could be important, as the genetic correlations for these traits between the two environments were low (−0.41 to 0.16). Our results showed that the genetic improvement for body colour can be achieved through direct selection and the increased redness colour is also expected to have favorable impacts on growth traits. Breeding programs to improve shrimp colour should account for the effects of environmental factors. Full article
(This article belongs to the Special Issue Genomic Prediction and Functional Genomics in Aquaculture)
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