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

Ichthyophonus hoferi herring and other fishes / Ichthyophonus hoferi in infected herring and other fishes

Published:

01/12/2009

Authors:

Sigurlaug Skírnisdóttir, Sigurbjörg Hauksdóttir, Eyjólfur Reynisson, Sigurður Helgason, Guðmundur Óskarsson, Sigríður Hjörleifsdóttir

Supported by:

AVS small project

contact

Sigurlaug Skírnisdóttir

Project Manager

sigurlaug.skirnisdottir@matis.is

Ichthyophonus hoferi herring and other fishes / Ichthyophonus hoferi in infected herring and other fishes

The aim of the project was to set up a simple DNA analysis method to detect the parasite Ichthyophonus hoferi in infected fish and to check if there is a difference between the parasite found in herring and plaice in Iceland. The intention was also to investigate whether I. hoferi was found in cod that had eaten infected herring, both fresh and salted fish. The objectives of the project were achieved, but the method development was more extensive than expected in the application. In this project, technology was developed for the genetic analysis of the Ihoferi infection in herring and plaice in Iceland. Methods based on conventional PCR and sequencing were tested and developed, in fact time PCR but also genetic analysis with the size analysis of the 18S mark, but to the best of our knowledge, the latter two methods have not been used before to analyze the I. hoferi. The method can be used both to diagnose infection in blood-rich organs such as the heart and kidneys but also in infected flesh. The cod could not be detected in cod. In the future, the method can be used for further research into the infection to try to shed light on the extent and extent of the infection and to try to identify the origin of the infection by applying the method to the different food types of herring.

The goal of the project was to develop a genetic analysis method to diagnose if the parasite Ichthyophonus hoferi was found in herring and other fish species. Furthermore, to determine if the same parasite species was infecting herring and infecting European plaice (Pleuronectes platessa) in Icelandic waters. Another goal was to analyze if I. hoferi could be found in cod (Gadus morhua) either salted or fresh which had been caught from infected herring areas during 2009. The goal of the project was reached and four different genetic methods were tested and all were successful. Conventional PCR technique as well as sequencing was used in the project. Real-time PCR and genotyping on ABI3730 sequencing machine were also developed successfully. The most sensitive technique is the last one (genotyping on ABI3730). The last two methods have not been published to our knowledge in this purpose. We detected I. hoferi parasite both in hearts, kidneys and fresh fillets of the fish. The parasite could not be detected in cod. In future studies, these techniques may be used for research of the origin of the parasite in the herring feed and to determine the distribution of the parasite.

Report closed until 01-01-2012

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Reports

Genetic analysis services for Icelandic commercial stocks

Published:

01/10/2008

Authors:

Sigríður Hjörleifsdóttir

Supported by:

Agricultural Productivity Fund

Genetic analysis services for Icelandic commercial stocks

Development of a genetic analysis kit for cows with 11 repeated microsatellite markers (BM1824, BM2113, INRA023, SPS115, TGLA122, TGLA126, TGLA227, ETH10, ETH225, TGLA53, E18). Prokaria offers services and participation in research projects on cow genetics. The development of a genetic kit for sheep has begun. It contains 11 genetic markers (CSRD0247, HSC, INRA0063, MAF0214, OarAE0129, OarCP0049, OarFCB0011, OarFCB0304, INRA0005, INRA0023, OaRFCB0020). The development work has come a long way.

A genotyping protocol for cows with 11 microsatellite markers (BM1824, BM2113, INRA023, SPS115, TGLA122, TGLA126, TGLA227, ETH10, ETH225, TGLA53, ETH3) has been developed. Prokaria offers genotyping service and participation in research projects on cow genetics. A genotyping protocol was started for 11 microsatellite markers for sheep (CSRD0247, HSC, INRA0063, MAF0214, OarAE0129, OarCP0049, OarFCB0011, OarFCB0304, INRA0005, INRA0023, OaRFCB0020). The final optimizations of conditions are not finished.

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