Special Issue "Genetic Breeding Technology and Its Application in Marine Aquaculture"

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A special issue of Journal of Marine Science and Engineering (ISSN 2077-1312).

Deadline for manuscript submissions: closed (31 January 2015)

Special Issue Editors

Guest Editor
Prof. Dean Jerry

Head of Aquaculture and Fisheries; Director ARC ITRH for Advanced Prawn Genetics and Breeding; Deputy Director Centre for Sustainable Tropical Fisheries and Aquaculture; College of Marine and Environmental Science; James Cook University; Townsville, 4811 QLD Australia
Website | E-Mail
Interests: aquaculture; aquaculture genetics; genetic improvement of aquaculture animals; conservation genetics of fish
Guest Editor
Dr. Nick Robinson

Senior Research Scientist, Breeding and Genetics, Nofima, PO Box 210, 1431 Ås, Norway
Website | E-Mail
Phone: +61 448984002
Interests: aquaculture; disease resistance; expressed sequences and polymorphisms revealed by mRNA-seq; microsatellite evolution; population genetics; gene marker discovery; bioeconomic modeling; selective breeding and marker assisted selection

Special Issue Information

Dear Colleagues,

Application of modern genetic breeding approaches to marine farmed species will dramatically boost productivity, whilst also allowing aquaculture to proceed in a sustainable fashion to help meet the future challenges of providing animal protein to the human population. Most gains in productivity of important farmed species over the last decade have come from traditional phenotypic-based breeding programs. However, similar to that being experienced in livestock and plant production, marine aquaculture breeding programs have been undergoing a renaissance through the increased incorporation and acquisition of molecular genetics and genomic data. This data has come from intensive sequencing and mapping studies of the genomes of important species and linking them to phenotypic traits, as well as the increased use of molecular-marker determined pedigrees of breeding candidates and other genetic technologies.

New exciting technologies are now also being developed and trialed, including prediction of breeding merit using genome-wide association markers (GWAS), genomic selection, RNAi for disease prevention, sex manipulation through gene regulation, and so on.

This special issue will capture what has been done to date in marine aquaculture breeding programs and highlight the current genetic advances being made and applied in the endeavor to further boost their productivity and resilience. It will cover articles not just on the approaches themselves, but where they have been used successfully in a whole range of aquaculture species.

Kindest regards,

Prof. Dean Jerry
Dr. Nick Robinson
Guest Editor

Submission

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. Papers will be published continuously (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as 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 refereed through a 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 quarterly 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 300 CHF (Swiss Francs). English correction and/or formatting fees of 250 CHF (Swiss Francs) will be charged in certain cases for those articles accepted for publication that require extensive additional formatting and/or English corrections.


Keywords

  • aquaculture breeding programs
  • genetic selection
  • genome-wide association studies
  • genomic selection
  • DNA parentage
  • molecular breeding
  • marine aquaculture
  • linkage mapping

Published Papers (8 papers)

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Research

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Open AccessArticle Domestication of Marine Fish Species: Update and Perspectives
J. Mar. Sci. Eng. 2015, 3(4), 1227-1243; doi:10.3390/jmse3041227
Received: 31 July 2015 / Accepted: 12 October 2015 / Published: 15 October 2015
Cited by 2 | PDF Full-text (1057 KB) | HTML Full-text | XML Full-text
Abstract
Domestication is a long and endless process during which animals become, generations after generations, more adapted to both captive conditions and humans. Compared to land animals, domestication of fish species has started recently. This implies that most farmed marine fish species have only
[...] Read more.
Domestication is a long and endless process during which animals become, generations after generations, more adapted to both captive conditions and humans. Compared to land animals, domestication of fish species has started recently. This implies that most farmed marine fish species have only changed slightly from their wild counterparts, and production is based partly or completely on wild inputs. In the past decades, global marine fish production has increased tremendously, particularly since the 1990s, to reach more than 2.2 million tons in 2013. Among the 100 marine fish species listed in the FAO’s database in 2013, 35 are no longer produced, and only six have a production higher than 100,000 tons. The top ten farmed marine species accounted for nearly 90% of global production. The future growth and sustainability of mariculture will depend partly on our ability to domesticate (i.e., control the life cycle in captivity) of both currently farmed and new species. Full article
(This article belongs to the Special Issue Genetic Breeding Technology and Its Application in Marine Aquaculture)
Open AccessArticle Genotype by Environment Interaction for Growth in Atlantic Cod (Gadus morhua L.) in Four Farms of Norway
J. Mar. Sci. Eng. 2015, 3(2), 412-427; doi:10.3390/jmse3020412
Received: 10 February 2015 / Accepted: 26 May 2015 / Published: 3 June 2015
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Abstract
We studied genotype by environment interaction (G × E) for body weight (BW) of Atlantic cod (Gadus morhua L.) from the National cod breeding program in Norway. Records of 13,811 fish in a nucleus farm (NUC) and two test farms (PENorth,
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We studied genotype by environment interaction (G × E) for body weight (BW) of Atlantic cod (Gadus morhua L.) from the National cod breeding program in Norway. Records of 13,811 fish in a nucleus farm (NUC) and two test farms (PENorth, PESouth) in year-class (YC) 2007, and for 9149 fish in NUC and one test farm in YC 2010 were available. Heterogeneity of variances and heritabilities ( ) were estimated using a univariate animal model with environmental effects common to full-sibs (full-model). Genetic correlations ( ) between farms were estimated using a multivariate full-model and a reduced-model (without ) for each YC. Heterogeneity of  was observed in both YC 2007 (0.10 to 0.16) and YC 2010 (0.08 to 0.26). The estimates of  between NUC and test farms were relatively high for both models (0.81 ± 0.19 to 0.96 ± 0.17) and (0.81 ± 0.08 to 0.86 ± 0.04), suggesting low re-ranking of genotypes. Strong re-ranking of genotypes between PESouth and PENorth may be less important because most cod producers are situated close to the breeding nucleus. In conclusion, G × E between NUC and test farms were low and at present there is no need for separate breeding programs for BW in cod. Full article
(This article belongs to the Special Issue Genetic Breeding Technology and Its Application in Marine Aquaculture)
Open AccessArticle Transcriptome Survey of a Marine Food Fish: Asian Seabass (Lates calcarifer)
J. Mar. Sci. Eng. 2015, 3(2), 382-400; doi:10.3390/jmse3020382
Received: 12 May 2015 / Accepted: 22 May 2015 / Published: 2 June 2015
Cited by 1 | PDF Full-text (1154 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
The Asian seabass (or barramundi; Lates calcarifer) is a marine teleost and a popular food fish in Southeast Asia and Australia. To date, comprehensive genome and transcriptome sequence information has not been available for this species in public repositories. Here, we report
[...] Read more.
The Asian seabass (or barramundi; Lates calcarifer) is a marine teleost and a popular food fish in Southeast Asia and Australia. To date, comprehensive genome and transcriptome sequence information has not been available for this species in public repositories. Here, we report a comprehensive de novo transcriptome assembly of the Asian seabass. These data will be useful for the development of molecular tools for use in aquaculture of Asian seabass as well as a resource for genome annotation. The transcriptome was obtained from sequences generated from organs of multiple individuals using three different next-generation sequencing platforms (454-FLX Titanium, SOLiD 3+, and paired-end Illumina HiSeq 2000). The assembled transcriptome contains >80% of the expected protein-coding loci, with 58% of these represented by a predicted full-length cDNA sequence when compared to the available Nile tilapia RefSeq dataset. Detailed descriptions of the various steps involved in sequencing and assembling a transcriptome are provided to serve as a helpful guide for transcriptome projects involving de novo assembly of short sequence reads for non-model teleosts or any species of interest. Full article
(This article belongs to the Special Issue Genetic Breeding Technology and Its Application in Marine Aquaculture)
Open AccessArticle Can the Global Adoption of Genetically Improved Farmed Fish Increase Beyond 10%, and How?
J. Mar. Sci. Eng. 2015, 3(2), 240-266; doi:10.3390/jmse3020240
Received: 19 April 2015 / Accepted: 11 May 2015 / Published: 19 May 2015
Cited by 3 | PDF Full-text (709 KB) | HTML Full-text | XML Full-text
Abstract
The annual production from global aquaculture has increased rapidly from 2.6 million tons or 3.9% of the total supply of fish, shellfish and mollusks in 1970, to 66.7 million tons or 42.2% in 2012, while capture fisheries have more or less leveled out
[...] Read more.
The annual production from global aquaculture has increased rapidly from 2.6 million tons or 3.9% of the total supply of fish, shellfish and mollusks in 1970, to 66.7 million tons or 42.2% in 2012, while capture fisheries have more or less leveled out at about 90 million tons per year since the turn of the century. Consequently, the future seafood supply is likely to depend on a further increase of aquaculture production. Unlike terrestrial animal farming, less than 10% of the aquaculture production comes from domesticated and selectively bred farm stocks. This situation has substantial consequences in terms of poorer resource efficiency, poorer product quality and poorer animal welfare. The history of biological and technical challenges when establishing selective breeding programs for aquaculture is discussed, and it is concluded that most aquaculture species may now be domesticated and improved by selection. However, the adoption of selective breeding in aquaculture is progressing slowly. This paper reports on a study carried out in 2012 to identify key issues to address in promoting the development of genetically improved aquaculture stocks. The study involved semi structured interviews of 34 respondents from different sectors of the aquaculture society in East and Southeast Asia, where 76% of the global aquaculture production is located. Based on the interviews and literature review, three key factors are identified: (i) long-term public commitment is often needed for financial support of the breeding nucleus operation (at least during the first five to ten generations of selection); (ii) training at all levels (from government officers and university staff to breeding nucleus and hatchery operators, as well as farmers); and (iii) development of appropriate business models for benefit sharing between the breeding, multiplier and grow-out operators (whether being public, cooperative or private operations). The public support should be invested in efforts of selective breeding on the most important and highest volume species, which may not be a priority for investment by private breeders due to, for instance, long generation intervals and delays in return to investment. Full article
(This article belongs to the Special Issue Genetic Breeding Technology and Its Application in Marine Aquaculture)

Review

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Open AccessReview Sex Control in Fish: Approaches, Challenges and Opportunities for Aquaculture
J. Mar. Sci. Eng. 2015, 3(2), 329-355; doi:10.3390/jmse3020329
Received: 20 April 2015 / Accepted: 20 May 2015 / Published: 28 May 2015
Cited by 2 | PDF Full-text (1403 KB) | HTML Full-text | XML Full-text
Abstract
At present, aquaculture is the fastest growing sector of animal food production and holds great potential as a sustainable solution for world food security. The ability to control sex is one of the most important factors for the commercialisation and efficient propagation of
[...] Read more.
At present, aquaculture is the fastest growing sector of animal food production and holds great potential as a sustainable solution for world food security. The ability to control sex is one of the most important factors for the commercialisation and efficient propagation of fish species, due to influences on reproduction, growth and product quality. Accordingly, there is a large body of research that targets sexual development in commercially important species in an attempt to understand and control fish sex and reproductive function. In this review, we provide an introduction to sex determination and differentiation in fish, including the genetic, epigenetic and environmental factors that can influence fish sex ratios. We also summarise the major approaches used to control sex in fish and discuss their application in commercially important species. Specifically, we discuss the use of exogenous steroid hormones, chromosome ploidy, environmental manipulations, sex-linked genetic markers, selection for altered sex ratios, and transgenics and comment on the challenges associated with controlling sex in a commercial environment. Full article
(This article belongs to the Special Issue Genetic Breeding Technology and Its Application in Marine Aquaculture)
Open AccessReview Epigenetics—Potential for Programming Fish for Aquaculture?
J. Mar. Sci. Eng. 2015, 3(2), 175-192; doi:10.3390/jmse3020175
Received: 25 February 2015 / Accepted: 20 April 2015 / Published: 23 April 2015
Cited by 2 | PDF Full-text (683 KB) | HTML Full-text | XML Full-text
Abstract
Epigenetic marks affecting the expression of genes are triggered by environmental stimuli, can persist throughout life or across multiple generations and can affect an individuals phenotype. In recent years there has been a revival of interest about the possible role of epigenetics in
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Epigenetic marks affecting the expression of genes are triggered by environmental stimuli, can persist throughout life or across multiple generations and can affect an individuals phenotype. In recent years there has been a revival of interest about the possible role of epigenetics in affecting complex or quantitative traits. This growing interest is partly driven by the increasing affordability of ultra-high throughput sequencing methods for studying the epigenome. In this review we focus on some of the possible applications of epigenetic knowledge to the improvement of aquaculture. DNA methylation, in which a methyl group is added to the C5 carbon residue of a cytosine by DNA methyltransferase, has been the most widely studied epigenetic mechanism to date, and methods used to obtain and analyse genome-wide DNA methylation data are outlined. The influence of epigenetic processes on the estimation of breeding values and accuracy of genomic selection for genetic improvement of aquatic species is explored. The possibility of tightly controlling nutritional stimuli found to affect epigenetic processes in order to tailor the development of fish for aquaculture is also discussed. Complex experiments will be required in order to gain a better understanding of the role of epigenetics in affecting quantitative traits in fish. Full article
(This article belongs to the Special Issue Genetic Breeding Technology and Its Application in Marine Aquaculture)
Open AccessReview Disease Resistant Fish and Shellfish Are within Reach: A Review
J. Mar. Sci. Eng. 2015, 3(1), 146-153; doi:10.3390/jmse3010146
Received: 27 January 2015 / Accepted: 18 March 2015 / Published: 20 March 2015
Cited by 1 | PDF Full-text (629 KB) | HTML Full-text | XML Full-text
Abstract
Disease in fish and shellfish is one of the main problems facing aquaculture production. Therefore, all attempts should be made to increase the rate of survival and, thus, reduce economic losses. Much has been done to develop vaccines and medical treatments to reduce
[...] Read more.
Disease in fish and shellfish is one of the main problems facing aquaculture production. Therefore, all attempts should be made to increase the rate of survival and, thus, reduce economic losses. Much has been done to develop vaccines and medical treatments to reduce mortality; and however, farming of aquatic species has a long way to go to optimize the environmental conditions for the animals and, thus, reduce stress and improve animal welfare. However, the good news is that there is the potential to increase disease resistance by selective breeding. By challenge-testing fingerlings from a number of families per generation, and including the rate of survival in the breeding goal, the results so far are very promising. By focusing on one disease at a time it is possible to increase the rate of survival by at least 12.5% per generation for most diseases studied. Unfortunately, selective breeding is only used to a small degree in aquatic species. In 2010, it was estimated that only 8.2% of aquaculture production was based on genetically improved stocks. Full article
(This article belongs to the Special Issue Genetic Breeding Technology and Its Application in Marine Aquaculture)
Open AccessReview Review of the RNA Interference Pathway in Molluscs Including Some Possibilities for Use in Bivalves in Aquaculture
J. Mar. Sci. Eng. 2015, 3(1), 87-99; doi:10.3390/jmse3010087
Received: 28 November 2014 / Accepted: 15 February 2015 / Published: 2 March 2015
Cited by 3 | PDF Full-text (858 KB) | HTML Full-text | XML Full-text
Abstract
Generalised reviews of RNA interference (RNAi) in invertebrates, and for use in aquaculture, have taken for granted that RNAi pathways operate in molluscs, but inspection of such reviews show little specific evidence of such activity in molluscs. This review was to understand what
[...] Read more.
Generalised reviews of RNA interference (RNAi) in invertebrates, and for use in aquaculture, have taken for granted that RNAi pathways operate in molluscs, but inspection of such reviews show little specific evidence of such activity in molluscs. This review was to understand what specific research had been conducted on RNAi in molluscs, particularly with regard to aquaculture. There were questions of whether RNAi in molluscs functions similarly to the paradigm established for most eukaryotes or, alternatively, was it more similar to the ecdozoa and how RNAi may relate to disease control in aquaculture? RNAi in molluscs appears to have been only investigated in about 14 species, mostly as a gene silencing phenomenon. We can infer that microRNAs including let-7 are functional in molluscs. The genes/proteins involved in the actual RNAi pathways have only been rudimentarily investigated, so how homologous the genes and proteins are to other metazoa is unknown. Furthermore, how many different genes for each activity in the RNAi pathway are also unknown? The cephalopods have been greatly overlooked with only a single RNAi gene-silencing study found. The long dsRNA-linked interferon pathways seem to be present in molluscs, unlike some other invertebrates and could be used to reduce disease states in aquaculture. In particular, interferon regulatory factor genes have been found in molluscs of aquacultural importance such as Crassostrea, Mytilus, Pinctada and Haliotis. Two possible aquaculture scenarios are discussed, zoonotic norovirus and ostreid herpesvirus 1 to illustrate the possibilities. The entire field of RNAi in molluscs looks ripe for scientific exploitation and practical application. Full article
(This article belongs to the Special Issue Genetic Breeding Technology and Its Application in Marine Aquaculture)
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