Tag: Genotyping

Reports

Optimization of Icelandic turbot culture / Profitability increase in Icelandic sandeel farming

Published:

01/07/2012

Authors:

Sigurlaug Skírnisdóttir, Kristinn Ólafsson, Eirik Leknes, Jón Árnason, Snorri Gunnarsson, Benedikt Kristjánsson, Sigurbjörg Hauksdóttir, Steinunn Magnúsdóttir, Aðalheiður Ólafsdóttir, María Pétursdóttir, Helgi Thorarensen, Soizic Le Deuff, Arnþór Gústavsson, Gunnar Örn Kristjánsson, Trond Bjørndal, Sigríður Hjörleifsdóttir, Albert Imsland

Supported by:

Technology Development Fund

Contact

Sigurlaug Skírnisdóttir

Project Manager

sigurlaug.skirnisdottir@matis.is

Optimization of Icelandic turbot culture / Profitability increase in Icelandic sandeel farming

The main goal of the project "Increasing profitability in Icelandic sandeel farming (MAXIMUS)" was to develop methods to reduce production costs in sandeel farming in Iceland. Sandhverfa is for the most part raised in pots on land and is therefore very suitable for farming in Iceland, in addition to which the market price is high (about 1500 ISK / kg) and stable. Land farming, on the other hand, is costly and therefore new and better technical solutions must be sought to increase the efficiency of farming. The MAXIMUS project worked on the development of a new light cycle control that makes it possible to increase growth by up to 20%. Work was done on the development of new feed types which sought to reduce the weight of sea protein and managed to reduce feed costs by up to 10% compared to conventional feed. This will make it possible to increase the efficiency of aquaculture in the later stages of the aquaculture process. The project also developed a multiplex genetic marker kit for a sandeel that has made it possible to genotype large numbers of juveniles quickly and safely. This genetic marker kit will be used to accelerate genetic progress in sandeel farming in the future. Market research was carried out and an attempt was made to examine the future prospects of the farm. Sandeel production will probably increase considerably in the coming years, but despite an increase in recent years, prices have remained stable. The results of the project strongly indicate that sandeel farming is economical in Iceland and the methods that have been developed in the project will increase the likelihood of development and investment in sandeel farming in Iceland.

The overall aim of this project, MAXIMUS, was to develop methods to significantly reduce production costs in farming of turbot (Scophthalmus maximus). Production of turbot in Iceland has been growing and therefore it is important to develop technology to lower the production costs. Turbot is an ideal species for farming in land ‐ based stations in Iceland, having many good characteristics as an aquaculture species and high (1500 kr / kg) and stable market value. Rearing fish in land ‐ based farms comes however with a cost and it is important to constantly strive to develop new technology to reduce cost of production. Firstly, methods to use photoperiod control to increase growth rate up to 20% compared to traditional methods were developed. Secondly, it was found that crude protein in turbot feed can be reduced by approximately 10% compared to current level in commercial feed without negative effects on growth. This will make production of a more cost efficient and less expensive feed for large turbot possible. Thirdly, multiplex genotyping systems were developed, making it possible to determine the pedigree of the parent fish during breeding to ensure genetic diversity leading to high growth rate. Finally, the current and future developments in turbot production and markets were analyzed. Production of this species is likely to increase considerably in coming years. In addition, there are important developments in technology that may impact on future supply and cost of production. An estimate of the economic implications of optimized turbot farming system in Iceland, profitability and revenue, was also investigated. Overall the results from this project will make turbot production in Iceland more feasible, and profitable, in the future.

Report closed until 01.12.2013

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Reports

Population genetics of the Icelandic Nephrops norvegius stock / Stofnerfðafræði leturhumars á Íslandsmiðum

Published:

01/06/2010

Authors:

Sigurlaug Skírnisdóttir, Sigurbjörg Hauksdóttir, Kristinn Ólafsson, Christophe Pampouli, Hrafnkell Eiríksson, Steinunn Á. Magnúsdóttir, Guðmundur H. Gunnarsson, Guðmundur Ó. Hreggviðsson, Sigríður Hjörleifsdóttir

Supported by:

The Icelandic Fisheries Research Fund, the Student Innovation Fund

Contact

Sigurlaug Skírnisdóttir

Project Manager

sigurlaug.skirnisdottir@matis.is

Population genetics of the Icelandic Nephrops norvegius stock / Stofnerfðafræði leturhumars á Íslandsmiðum

As the name of the project "Stock genetics of lobster in Icelandic waters" indicates, the aim of the project was to examine the type of lobster (Nephrops norvegicus) in Icelandic waters, but stock type research is an important factor for sustainable fisheries management. The main objectives of the project were to develop new genetic boundaries to assess genetic variability within and between geographically separated hunting areas in Iceland, to define the paternity of female egg masses from separate hunting areas in order to shed light on the reproductive process of lobster breeding and to stem genetic factors. Genetic analysis involves the use of so-called genetic markers, which are based on specific DNA sequences that are somehow detectable in the genome. Genetic markers based on repeated short sequences (2-6 bases) are most commonly used, which are known to vary between individuals of the same species. These areas therefore vary in length between individuals and make them suitable options. Genetic analysis is a very powerful technology that can be used for individual analysis in a group of organisms. This method is now increasingly used for parental analysis, to assess population structure, for research traceability and to accelerate targeted breeding. Usually 5-15 different genetic markers need to be used to differentiate individuals. A large part of the development work is therefore to find the best conditions for PCR reactions, where as many genetic markers as possible can be used in one reaction (multiplex) and simultaneous runs on a sequencer. Well-made genetic analysis kits that are easy and cheap to use and provide a lot of information and good diagnostic skills are very useful for a variety of uses. They are therefore valuable products and marketers, as both genetic analysis and services based on them can be sold. The project developed eight new genetic markers for lobsters and used them to analyze samples from separate geographical fishing areas around Iceland, while Scottish lobster samples were used as a group. In addition, four previously published genetic markers were used for the analyzes. The results of analyzes with these 12 genetic markers from geographically separated regions (together with the subgroup) did not show a significant genetic difference of lobster between the regions. The results of the project have been published in articles and student projects. The student thesis is entitled "Development of microsatellite multiplex systems for Nephrops norvegicus" and is by Sóleyja Valgeirsdóttir. One article has been approved for publication in the project, which describes eight new genetic markers. The title of the article is: "Isolation and characterization of eight new microsatellite loci in the Norway lobster, Nephrops norvegicus (Linnaeus, 1758)" (approved for publication in the journal Molecular Ecology Resources, Appendix 1). Another article has been submitted for publication in the ICES Journal of Marine Science under the title "A pilot genetic study revealed the absence of spatial genetic structure of the Norway lobster (Nephrops norvegicus) at fishing grounds in Icelandic waters" but it deals with the structure of lobster in Icelandic waters where lobsters from Scotland were kept as an outing group (Appendix 2).

The genetic structure of population and mating behavior of exploited marine species are important criteria for effective fisheries management. The distribution of Nephrops norvegicus, Norway lobster, in Icelandic waters is limited to the warmer sea of the south coast. The distribution of the Icelandic stock can be divided into ten geographical areas but the main aim of this project was to develop microsatellite markers to use for the genetics analysis and to analyze whether the lobsters in each area are a self-contained unit stock or not. The aim was furthermore to determine the paternity of egg masses from individual females, and thus elucidate the breeding structure in Icelandic waters. The final goal was to produce a plan for the conservation and management of genetic resources in the Icelandic Norway lobster stock taking into account possible natural population diversity. Microsatellites are short sequence repeats of 2-6 bases found in all prokaryotic and eukaryotic genomes analyzed to date. Microsatellites are variable, which means the number of repeats in a specific area of the DNA variants between the different members of a species. Consequently, the alleles of the microsatellites differ by the length. The different alleles and thus the different length of the microsatellites can be caused by insertion or deletion of one or more repeats during the DNA replication. These sequences are usually under a high degree of length variability and that makes them as powerful genetic markers. Therefore, microsatellites are suitable for population genetics, for family tracing in breeding programs, genetic monitoring, and kinship studies as well as tracing of origin. Usually, 5-15 microsatellites are enough to discriminate between individuals. A microsatellite multiplex system is the use of multiple, unique primer sets in a single PCR mixture to produce amplicons of varying sizes, specific to different DNA sequences. By targeting multiple loci at once, additional information may be gained from a single reaction. It is a great advantage that microsatellite markers can be run in multiplex assay systems. Larger numbers of samples and smaller DNA quantities can then be genotyped at once, saving time and money. This also minimizes the risk of handling errors. In this study we developed eight new microsatellite markers that were used to characterize the genetic diversity of Norway lobster, in and between isolated geographical areas in Icelandic waters, and an out-group sample from Scotland. In addition, four previously published microsatellite markers were used for the analysis. The microsatellites did not detect significant genetic differentiation among the location sampled, not even among Icelandic samples and the out-group collected in Scotland. The outcomes of the project are two papers and one student report. The report is titled "Development of microsatellite multiplex systems for Nephrops norvegicus" by Sóley Valgeirsdóttir. The first paper is titled; „Isolation and characterization of eight new microsatellite loci in the Norway lobster, Nephrops norvegicus (Linnaeus, 1758)“ where the eight new loci are described (Molecular Ecology Resources; Appendix 1; accepted for publication). The second paper is titled "A pilot genetic study revealed the absence of spatial genetic structure of the Norway lobster (Nephrops norvegicus) at fishing grounds in Icelandic waters" (ICES Journal of Marine Science; Appendix 2; submitted).

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Reports

Genetics kit for char

Published:

01/02/2008

Authors:

Sigurlaug Skírnisdóttir, Alexandra M. Klonowski, Sigurbjörg Hauksdóttir, Kristinn Ólafsson, Helgi Thorarensen, Einar Svavarsson, Sigríður Hjörleifsdóttir

Supported by:

Tækniþróunarsjóður Rannsóknamiðstöð Íslands

Contact

Sigurlaug Skírnisdóttir

Project Manager

sigurlaug.skirnisdottir@matis.is

Genetics kit for char

The goal of the project was to create a powerful genetic kit for char with 15-20 genetic markers. Many genetic markers have been published for char and other salmonids, but the disadvantage is that no suitable reproduction gene set is known, which is a prerequisite for the efficient use of technology. It is important that the genetic markers show variability within the strain, are of a certain size but of different sizes, work well in a amplification reaction solution and are well readable after the sample has been run on a sequencer. The risk in the project was whether it would be possible to find a suitable genetic marker that could be combined into 2-3 reaction mixtures. 70 pairs of indicators were tested for 56 published genetic markers. The result of the project was that it was possible to combine 17 genetic markers into 3 reaction mixtures. A total of 140 fish were identified from the Hólar fish stock with these 17 genetic boundaries, but in addition, 12 wild fish were identified with them. The results showed that the genetic markers were used to differentiate between different groups of char. The processing of genetic analyzes clearly confirmed that Hólableikjan is mainly made up of two species. Some genetically modified wild charr yielded new isotopes not seen in farmed fish. Therefore, there are now genetic marketing kits that can be used in breeding work, in stock research on wild char and in traceability research. This will strengthen breeding work and is a powerful tool for research on char in the future.

The goal of the project was to develop genotyping protocols for Arctic charr containing multiplexes of 15-20 microsatellite markers. Many microsatellite markers have been published for salmonoid fishes, but no multiplexes are known which are of practical use when analyzing many samples at a time and therefore, to make the research profitable. The microsatellite markers must show variability among the fishes, they must be of certain sizes and of variable sizes, they must be amplifiable in multiplex PCR reactions and they must be easily readable from the machine. The risk of the project was to find published microsatellite markers which would fulfill these criteria and fit into 2-3 multiplex PCR reactions. Seventy primer pairs were tested for 56 published microsatellite markers. The results of the project were that 17 microsatellite markers which fit into 3 multiplex PCR reactions. A total of 140 fish from the brood stock of Arctic charr from the University at Holar was analyzed in the study as well as 12 samples from wild fish of different lakes and rivers. The results indicate that these markers can be used to analyze different stocks of Arctic charr. Furthermore, analyzes of the brood stock confirms that it mainly consists of two different stocks. New alleles were observed in the wild fish compared to the brood stock fish. A genotyping protocol to analyze Arctic charr for use in breeding industry, in wild fish research and in tractability analyzes, is now available. This will help in building up breeding programs and will be a helpful tool of the genetic research of Arctic charr.

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Reports

Genotyping Kits for Cod / Genotyping kits for Atlantic cod

Published:

01/06/2007

Authors:

Sigurlaug Skírnisdóttir, Inga Schulte, Sigurbjörg Hauksdóttir, Kristinn Ólafsson, Steinunn Magnúsdóttir, Klara Björg Jakobsdóttir, Christophe Pampoule, Guðmundur Ó. Hreggviðsson, Sigríður Hjörleifsdóttir

Supported by:

AVS Fisheries Research Fund

Contact

Sigurlaug Skírnisdóttir

Project Manager

sigurlaug.skirnisdottir@matis.is

Genotyping Kits for Cod / Genotyping kits for Atlantic cod

The aim of the project was to develop new coding sets for cod (Gadus morhua) based on repeated DNA short sequences (microsatellites). A total of 118 genetic markers were studied. Two ten genetic marker kits have been developed (CodPrint10a and CodPrint10b) and a patent application has been filed for these genetic markers. Almost 300 Icelandic samples belonging to 3 different sampling areas (N-Iceland, SW-Iceland (shallow waters) and SW-Iceland (deep) were analyzed with these 20 genetic markers, but for comparison the samples were also analyzed with nine well-known and widely used genetic markers. These three sample groups were better distinguished by CodPrint10a and CodPrint10b genetic markers than by previously known genetic markers, and the research shows that the new genetic markers are suitable for both stock studies and parental analyzes.

The goal of the project was to develop new genotyping kits for Atlantic cod (Gadus morhua) based on microsatellite markers. A total of 118 markers were analyzed. Two 10 microsatellite markers sets were developed (CodPrint10a and CodPrint10b) and they were used to analyze approximately 300 samples that were collected in the Northeast Iceland, Southwest inshore Iceland and Southwest offshore Iceland. As a comparison the samples were also analyzed with nine previously known markers. A comparison of the new microsatellite loci and the nine previously used, showed that the power of individual discrimination was much stronger with the new microsatellite loci. Indeed, the discrimination of the samples was clearer with much less overlap of the individuals. Together, these results suggest that the new microsatellite loci are powerful and suitable for both population genetic analysis and paternity analysis, due to their high polymorphism and resolution power.

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