JP2010148505A - Marker and identification method of fishery fish and shellfish by base sequence of mitochondoria dna variable region - Google Patents

Abstract

<P>PROBLEM TO BE SOLVED: To provide a simple and accurate method for marking-identifying fishery fishes and shellfishes, especially, fishery fishes and shellfishes derived from a specific production area, excellent fishery seeds and seedlings having one or plural excellent characters, or fishery fishes and shellfishes of a specific kind. <P>SOLUTION: There are provided a method for tracing the production history of a fishery fish or shellfish of an individual or a group of individuals, or a part or manufactured goods thereof by using a base sequence of mitocondria DNA D-loop, and a method for determining a marker gene usable for such a method. <P>COPYRIGHT: (C)2010,JPO&INPIT

Description

  The present invention relates to gene identification and labeling methods for marine fish and shellfish in natural and cultivated fisheries. More specifically, the present invention relates to a method for identifying and labeling varieties, production areas, lines (seed seedlings) of seafood based on the difference in the base sequence of the D loop of seafood mitochondrial DNA, and aquaculture business (cultivation fishery) The present invention relates to a method for identifying and labeling larvae of seedlings bred in Japan, and a method for determining and detecting a marker gene used in such a method.

  In Japan, technological development of sea surface aquaculture and cultivated fisheries has been progressing, but in particular, adult fish that can reproduce from eggs in red sea bream, flounder, white eel, etc. The technology of complete aquaculture that does not depend on natural resources is being established to produce the next generation from adult fish. Today, food prices are rising due to a global food shortage, Japan's food self-sufficiency rate is falling, and safety issues related to imported foods are urgent issues. Today, it is a source that can provide safer, cheaper and higher-quality food. As a result, interest in aquaculture and cultivated fisheries has increased.

  In aquaculture and cultivated fisheries, high quality artificial seedlings can be obtained by selecting and breeding excellent strains, for example, strains with high resistance to pathogens such as viruses and bacteria, strains with high growth rates, and strains with high breeding ability. Is trained. An enormous amount of capital is required for the breeding of artificial seedlings, especially the attempt to completely cultivate fish that is edible by subculture, and the recovery of the capital is not easy. In addition, in the case of marine seedlings, it is technically and ethically difficult to introduce sterile techniques by genetic manipulation, such as plant seedlings, so if you sell or transfer breeding / established excellent seedlings (fry), the assignee Propagation (breeding) and sales are easy, and it is very difficult to protect the rights of seed breeders. In addition, for plant seeds and seeds, the rights of seed and seedling (variety) growers registered by the Seed and Seed Law are protected, but for seeds of animals, especially fishery products, the rights of the growers are legally substantial protection. Has not been made. Therefore, in order to protect the rights of breeders and release operators of excellent seedlings in the field of aquaculture and cultivating fisheries and to activate the fishery industry, establishment of a registration system for aquatic seedlings and methods for labeling and identifying seedlings and adult fish Development is desired.

  In addition, it is also desired to develop a method for labeling fry for cultivating fisheries, especially for investigating changes in recruitment in the discharge business. For example, in recent years, Atlantic bluefin tuna has been designated as an endangered species following SBT, and fishing has been restricted. For such species, it is considered possible to release artificially nurtured fry and restore natural populations. In some cases, there is concern that large-scale release of genetically uniform seedlings will reduce biodiversity and thus lead to a decline in marine resources. This will contribute to the recovery of the fishing ground, as it will increase the diversity of genes in the ecosystem. In order to restore the fishing grounds by releasing seedlings, it is necessary to conduct research on the release of new seedlings with different genetic compositions and a recruitment fluctuation survey that accurately evaluates the release. Surveys on recruitment fluctuations are also important for understanding fluctuations in marine resources in nature. Accurate recruitment fluctuation surveys on specific species, varieties, strains and seedlings in fishing grounds are important for the release of ecosystems into the ecosystem. It is necessary for understanding the impacts and for sustainable catch planning.

  As conventional signs for tracking released larvae, for example, excision of oil salmon fry (Oppeikawa Salmon Science Museum, Sapporo City, Hokkaido), blackening of the unaided side of flounder fry and branding (Miyazu Cultivation Fisheries Center), ALC (Alizarin Complexon) pigment labeling and bellows extraction labeling for larval otoliths in madara and tiger pufferfish (Noto Cultivation Fishery Center and Minamiizu Cultivation Fishery Center), and more recently, electronic tags using IC tags and communication satellites have been implemented. ing. All of them are used for physically labeling fry, and means such as cutting of salmon and branding have the risk of damaging seedlings and may impair the commercial value of the market. ALC dye labeling has the advantage that it does not affect the growth and viability after release because labeling is done without damaging the seedlings, but for investigation, fish are collected and disassembled to collect otoliths, Confirmation with a fluorescence microscope must be performed. In addition, labeling by these methods is not only necessary for labeling all released individuals, but is limited to only one labeled individual and is not identifiable over generations after F1. Furthermore, in the case of high-grade fish such as tuna and tiger puffer, it is practically impossible to purchase fish for inspection due to the huge cost, and in the case of bluefin tuna it is not only expensive. Many problems remain in conducting the survey, such as the difficulty of collecting samples and marking itself due to the large size of the fish.

  Another concern in the fishery industry is the issue of labeling marine products when they are distributed to the market. As a result of the revision of the JAS Act in 1999, it is obliged to display the name, place of origin (name of the catchment / produced water area or name of the exporting country), and thawing / culture for fresh seafood sold to general consumers. However, since it is practically difficult to determine the authenticity of these indications at the distribution site, disguised seafood production areas (fishing grounds / ports) by sellers (selling foreign eels with false indications with domestic eels) For example), and disguise of seeds or varieties (for example, selling yellowfin tuna by false indication with bluefin tuna). The quality and original price of food varies depending on the variety and fishing ground, but verification when there is a suspicion of impersonation is not easy, and there is no system that can accurately and easily track production history without depending on display, Confidence in food labeling is being lost. Therefore, in order to make the display of fishery products more rigorous and, in turn, the local consumers can select the fishery products with more peace of mind, the production history of fishery products is displayed strictly in the distribution process, and can be judged quickly and accurately as needed. Development is also desired.

  The method of identifying a species or subspecies based on the difference in DNA base sequence is very useful in the fields of molecular genetics, phylogenetic chemistry, etc., especially in the fields of medicine and forensic medicine in humans. It's being used. In fish, for example, a method for discriminating flounder that tends to whiten using a specific gene marker has been developed (Patent Document 1). However, in the method using the genetic polymorphism that brings about a specific trait as a marker, it is necessary to identify the genotype that becomes the marker for each trait, and in order to solve the problems in the fields of aquaculture and cultivated fishery as described above It is not valid.

  Attempts have also been made to use genomic polymorphism markers such as MHC microsatellite for genetic labeling of seedlings, but the diversity of MHC sequences is extremely high even in a fertilization tank with a limited genetic composition. It was difficult to label and identify seedlings with MHC haplotypes (experiment by the inventors: data not shown).

  Mitochondria have a circular double-stranded DNA of about 15,000 to 17,000 base pairs (16,569 base pairs in humans) containing 10 unique gene groups independent of the nuclear genome. Mitochondrial DNA (mtDNA) is used in the field of genetics because it is transmitted to offspring by maternal inheritance. In addition, mtDNA is used for haplotype identification because its base substitution rate is 5 to 10 times faster than that of the nuclear genome and has many mutations within the same species. For example, a method has been developed in which polymorphisms in the mtDNA control region (control region, D-loop) of chum salmon are detected by hybridization to determine the haplotype (Patent Document 2).

  The D loop is an untranslated hypervariable region in mtDNA, and many mutations occur within the same species. In Non-Patent Document 1, for the purpose of comparing the genetic composition of Ryukyu Ayu to the natural population and the introduced population introduced into different environments from the natural population, the microsatellite of the mtDNA D-loop is a restriction enzyme-cut fragment length polymorphism. It is described that haplotype analysis was performed by (RFLP) analysis, and it was confirmed that the genetic composition was similar between the natural population of Ryukyu Ayu and the introduced population. Further, Non-Patent Document 2 shows that the base substitution rate of the mitochondrial control region (D-loop) of the three species of the genus Kinmeida was 15.5%, and that the goldfish collected from different fishing grounds. All of these show their own haplotypes, indicating that none of them showed a common sequence.

  Non-Patent Document 3 investigated the genetic correlation between geographical subspecies of bluefin tuna and swordfish using the sequence of the hypervariable region in the mitochondrial control region. As a result, the gene of bluefin tuna captured in the Atlantic and the Mediterranean It states that no separation was found in the composition. On the other hand, Non-Patent Document 4 investigated the genetic composition of each population of Atlantic bluefin tuna fish using the microsatellite locus and the mitochondrial control region. It describes that a significant association was found. In addition, Non-Patent Document 5 describes investigating geographical gene inflows of bigeye tuna by population statistics using two clades separated by haplotypes at the 5 ′ end of the mitochondrial control region. ing.

  The methods disclosed in these documents are for investigating the relationship between individual groups by determining the haplotype of an individual and examining the haplotype frequency in a specific area. For example, as understood from Patent Document 2, a specific haplotype is observed in a plurality of individuals and distributed over a plurality of different regions. Thus, depending on these methods, a haplotype or haplotype composition can be determined for a particular individual or population, but the population (lineage or place of origin) to which the individual belongs cannot be determined, and the individual or It was also impossible to label populations with genes. Further, as understood from Non-Patent Document 2, for example, the base sequence of the D-loop has a large difference in haplotypes even among individuals of the same species, and thus cannot be used for identification of species or strains. .

  Non-Patent Document 6 describes the breeding of bluefin tuna cultured with respect to hatched larvae obtained from about 20 natural parent fish in ginger for the purpose of monitoring genetic diversity when breeding by breeding the aquaculture line. The sequence 20 analysis of the first half of the D-loop of mitochondrial DNA was performed for the estimation of the mitochondrial DNA, and the microsatellite marker analysis was performed for the paternal estimation. Three to eight mitochondrial DNA haplotypes are observed in each lot (fertilized eggs collected on the same day), and the haplotype frequency varies greatly between lots, and the genetic composition between lots also differs in microsatellite marker analysis. It became clear that the parent fish involved in the spawning of the school of fish in the cage differed depending on the spawning date. However, no method has yet been found for labeling specific seedlings and managing and tracking their history after release and during the distribution process.

  In this way, for a specific individual or group of marine fish and shellfish, the species, variety, strain or production area can be easily and accurately identified, and a large number of individuals can be labeled by any conventional method. Development of such a method has been desired.

JP 2007-312645 Japanese Patent Laid-Open No. 2003-180397

Ikeda et al., “Genetic evaluation of Ryukyuyu population introduced by PCR-RFLP analysis of microsatellite DNA and mitochondrial DNA D-loop”, Fishery Breeding, 2001, Vol. 31, pp. 33-37 Akimoto et al., “Analysis of population genetic structure of damselfish in fishing grounds around Japan by base sequence analysis of mitochondrial control region”, Kensui Kenken No. 8, 2003, pp.89-97 Carlsson et al., "Microsatellite and mitochondrial DNA analyzes of Atlantic bluefin tuna (Thunnus thynnus thynnus) population structure in the Mediterranean Sea", Molecular Ecology, 2004, vol.13, pp.3345-3356 Martinez et al., "Genetic diversity and historial demography of Atlantic bigeye tuna (Thunnus obesus)", Molecular Phylogenetics and Evolution, 2006, vol.39, pp.404-416 Alvarado Bremer et al., "Comparative phylogeography of Atlantic bluefin tuna and swordfish: the combined population expansion on the regional phylogenies of two highly migratetory pelagic fishes", Molecular Phylogenetics and Evolution, 2005, vol.36, pp.169-187 Morishima et al., "Research for genetic management of cultured bluefin tuna", 2007 Annual Meeting Program of the Japan Society of Fisheries Science Kinki Branch, 109-D, December 1, 2007, Japanese Society of Fisheries Science (http: // www. suisan-kinki.org/reikai/h19reikai/h19_kouki/9.pdf)

  Therefore, in view of the above-mentioned problems, the present invention provides marine fish and shellfish, in particular, marine fish and shellfish derived from a specific production area, excellent fishery seedlings having one or more excellent traits, or fisheries of a specific species or variety. It is an object of the present invention to provide a simple and accurate method for labeling / identifying one to a large number of individuals of seafood.

  The present inventors paid attention to the behavioral pattern and the breeding form of fish. For example, in bluefin tuna laying, a single female parent lays and hatches about 2 million to 10 million eggs at a time. It is thought that several male parents are involved in the fertilization. In particular, in the case of aquaculture, the number of female parent individuals that lay eggs in one aquaculture tank per day is small, and fertilized eggs hatch in about one day, float on the surface of the water, and can be collected every egg laying day. is there. In conjunction with this, the present inventors focused on the fact that mitochondrial DNA (mtDNA) is maternally specific. Mitochondrial DNA is generally small in size and recombination does not occur, so it is highly conserved among individuals, but mutations are concentrated in a short region of the D loop. As a result of diligent research focusing on these matters, it was found that it was possible to identify the profile of aquatic fishery products, such as production history, species, varieties, strains, or production areas. It came to complete.

That is, the present invention relates to a method for identifying the profile of a fishery product or processed product thereof by determining the base sequence of the mitochondrial DNA D loop of the fishery product or processed product thereof.
The invention further relates to the method, wherein the profile is a seed, variety, line, seedling, production history and / or production area.

The present invention also relates to the method, further comprising determining a karyotype by microsatellite.
The present invention further relates to said method, further comprising determining whether the species-specific base sequence of the mitochondrial DNA D-loop can be aligned by inserting one or more gaps.
The present invention also relates to the above method, further comprising amplifying the full-length D-loop base sequence of mitochondrial DNA using a mitochondrial proline tRNA-specific primer and a mitochondrial phenylalanine tRNA-specific primer and determining by double-stranded sequencing. .

The present invention also relates to the above-mentioned method for comparing the base sequences of mitochondrial DNA D loops of two or more fishery products or processed products thereof.
Furthermore, the present invention relates to the above method, wherein the comparison of the base sequence of the mitochondrial DNA D loop is a comparison of whether or not the maternal specific base sequence is completely matched.

The present invention also provides that at least one of the two or more marine fish and shellfishes is a single female parent whose base sequence of the mitochondrial DNA D loop has been previously identified, or a fertilized egg, larvae derived from the female parent, The method relates to a fry or adult fish.
Furthermore, the present invention relates to the above method, wherein fertilized eggs, larvae, fry or adult fish derived from a female parent are laid and / or hatched in the same farm or ginger.

Furthermore, this invention relates to the said method for the identification of the seedling seedling in the recruitment amount fluctuation | variation investigation or culture | cultivation in a discharge business or a cultivation fishery.
The present invention also relates to the above-mentioned method for identifying the species, production history and / or production area of marine seafood as a food or processed product thereof.

  As used herein, a breed is a subclass within the same species and has characteristics that can be distinguished from other groups by morphology, physiology, and genetics. Sometimes it is divided as a subspecies. For example, bluefin tuna is generally classified into two subspecies: Atlantic, Mediterranean and Black Sea (Apis bluefin tuna), and Pacific (Apis bluefin tuna). Although it was supposed to be divided into groups having different genetic characteristics, the analysis of the inventors described below in this specification classifies Atlantic bluefin tuna and Atlantic bluefin tuna as separate varieties.

  As used herein, seedlings (artificial seedlings) are artificially selected and mated with individuals having excellent characteristics (or suitable for sacrifice farming or release), and the next generation is trained as a line. By selecting individuals or strains, this refers to those established for breeding with excellent traits, including fertilized eggs, larvae, larvae and adult fish, and released to sea rivers even for aquaculture It may be for that.

  As used herein, production history refers to the production area (place for aquaculture, harvesting or processing), production, etc., when an individual or part of a fishery product or a processed product thereof is in the process of distribution. Means information such as methods (culture, collection or processing methods or conditions, etc.), storage or distribution methods or conditions, or species, varieties or strains of marine fish and shellfish used as raw materials in the case of processed products. The production area means a water area or facility from which the target seafood is derived, and includes a spawning ground, a feeding ground, a playground, a fishing ground, a landing ground, a hatchery, and a farm.

  As used herein, the maternal-specific sequence refers to the alignment (alignment) of the D-loop base sequence of the mitochondrial DNA of the individual to be tested with the D-loop base sequence of the mitochondrial DNA of the individual to be compared. When comparing homology, individuals from the same maternal line are completely identical, but with different mothers, they can be aligned by inserting about 0 to 2 gaps, and show a high degree of homology. This refers to the base sequence of a region that does not completely match. The species-specific sequence refers to a base sequence having high homology between different species when a plurality of different species of D-loop base sequences can be aligned by inserting several or more gaps. Furthermore, the present inventors have found that there are short regions in the maternal-specific sequence where particularly many mutations are concentrated between different maternals even among the same species. This region is referred to herein as a maternal mutation concentration region. Similarly, it is found that there is a short region in which many gaps can be aligned, but this region is referred to as a heterogeneous mutation concentration region.

  According to the present invention, it is possible to easily and quickly identify the seedlings, production areas and varieties of aquatic fish and shellfish, and therefore, the display of the production history and varieties of the fishery products and seafood can be strictly managed. It becomes possible to provide marine seafood as food more safely and fairly. In particular, it is possible to manage the production history of fishery products that have been distributed by importing or selling on the Internet, where it was difficult to keep track of production history in the past. . Further, according to the present invention, it becomes possible to identify genes of excellent seedlings of cultured seafood, for example, excellent seedlings such as GTL and virus resistance, and it becomes easier to brand seeds and protect the rights of breeders. In addition, according to the present invention, it is possible to mass-produce seeds and seedlings labeled with a maternal-specific gene sequence, and at the same time, by constructing a database of maternal-specific sequences, it becomes possible to investigate the recruitment variation in the discharge business. In addition, it becomes easy to monitor the increase and decrease of the number of individuals of a specific strain in the ecosystem, and can provide useful data for maintaining the genetic diversity of fishery products.

It is a figure which shows the comparison of the D loop base sequence of the tuna mitochondrion. It is a figure which shows the comparison of the D loop base sequence of the tuna mitochondrion. It is a figure which shows the comparison of the D loop base sequence of the tuna mitochondrion. It is a figure which shows the comparison of the D loop base sequence of the tuna mitochondrion. It is a figure which shows the comparison of the D loop base sequence of the tuna mitochondrion. It is a figure which shows the comparison of the D loop base sequence of the tuna mitochondrion. It is a figure which shows the comparison of the D loop base sequence of the tuna mitochondrion. It is a figure which shows the comparison of the D loop base sequence of the tuna mitochondrion. It is a figure which shows the comparison of the D loop base sequence of the tuna mitochondrion. It is a figure which shows the comparison of the D loop base sequence of the tuna mitochondrion. It is a figure which shows the comparison of the D loop base sequence of the tuna mitochondrion.

The result of the electrophoresis of the maternal-specific DNA in the Tuna genus amplified by PCR is shown. It is a figure which shows the diversity of the mitochondrial DNA D loop base sequence of a natural and cultured red sea bream. It is a figure which shows the diversity of the mitochondrial DNA D loop base sequence of a natural and cultured red sea bream. It is a figure which shows the diversity of the mitochondrial DNA D loop base sequence of a natural and cultured red sea bream. It is a figure which shows the diversity of the mitochondrial DNA D loop base sequence of a natural and cultured red sea bream.

The results of electrophoresis of maternally specific DNA in red sea bream amplified by PCR are shown. It is a figure which shows the comparison of the mitochondrial DNA D loop base sequence of a tuna genus. It is a figure which shows the comparison of the mitochondrial DNA D loop base sequence of a tuna genus. It is a figure which shows the comparison of the mitochondrial DNA D loop base sequence of a tuna genus. FIG. 5 shows a comparison of mitochondrial DNA D-loop sequences of natural and farmed tuna. It is the photograph of gel electrophoresis which shows the result of four types of microsatellite analysis of the cultured bluefin tuna fry belonging to the same mother system.

  In one aspect, the present invention provides a method for identifying a profile of aquatic seafood or a processed product thereof. In this method, a base sequence of a mitochondrial DNA D loop of a fishery product collected in advance is determined, and the determined base sequence and a mitochondrial DNA D loop of a fishery product or processed product thereof as a specimen to be identified The profile of the specimen is identified by comparing with the base sequence. A profile is preferably a species, variety, line, production history and / or place of production, but is not limited thereto. Although it is not easy to find genetic markers specific to seeds and seedlings of a specific species and variety lineage, in the method of the present invention, marine fishery products that produce a large number of next-generation individuals from a single female parent. Using the characteristics, the difference in the base sequence of the mitochondrial D-loop region, which is particularly highly variable between different species, strains or maternal lines, is used as a marker for species, strains, etc. Mitochondrial DNA is most suitable as an information source for fish profiles because it has a high copy number from a small sample and is highly stable even under conditions where the nuclear DNA is degraded.

  In one embodiment, the method of the present invention comprises collecting a sample containing mitochondrial DNA from an aquatic seafood or a part thereof, a processed product thereof, or a female parent individual thereof in advance in a production history. Including. The initial stage of production history means, for example, a place for collection (fishing), production, wholesale, distribution, sales, etc. A sample (sample) containing mitochondrial DNA of the fish and shellfish such as salmon and small pieces of meat can be collected and stored frozen. In addition, when selling larvae (fry) cultivated from fertilized eggs, one or more fertilized eggs, larvae or fry, or nesting scales, etc. (same litter) laid by the same female parent shall be collected and stored frozen. Can do. Since all fry of the same maternal line are labeled with the same marker (maternal line specific sequence) according to the method of the present invention, a single sample of litter fry can be stored to track all released or sold individuals. It becomes possible to do. Alternatively, for example, when dismantling and distributing and selling such as tuna, a sample of each individual can be collected and stored frozen in a wholesale area, a market, or a store. In this way, by selling a part of an individual in advance as a sample and storing it, after selling all or a part of a specific individual (fillet, processed product, etc.), a commercial product derived from the individual And mitochondrial DNA contained in a sample of the same individual collected in advance can be compared.

  In a preferred embodiment, the method of the present invention is a mitochondrial DNA control region (D) contained in a sample (first sample, standard sample) collected from a marine fishery product or processed product thereof, or in the case of a seedling, from a female individual. -Determining a maternal-specific or species-specific base sequence in the base sequence of the loop. For example, in order to determine a species-specific base sequence, it is first necessary to obtain a sequence that serves as an index for the target species. Specifically, from public databases such as GeneBank and MitoFish (public database of seafood mitochondria (http://mitofish.ori.u-tokyo.ac.jp/)) You may search and use the base sequence of mtDNA of a marginal species. In order to obtain a maternal-specific sequence for the labeling of cultured larvae, mitochondrial DNA is obtained from a female parent or at least one fertilized egg, larva or fry laid by the female parent, and a known molecular biological technique is used. And the base sequence of the D loop may be determined. By comparing this D-loop base sequence with the D-loop base sequences of databases or other individuals, a maternal mutation concentration region can be determined and used as a maternal-specific sequence. The fertilized egg laid by the same female parent and the larvae or fry derived therefrom all have the same maternal-specific sequence, and this maternal-specific sequence is different from individuals derived from other female parents. Therefore, the maternal-specific sequence of one fertilized egg, larvae or fry is the maternal-specific sequence of all individuals in the same maternal population.

  To determine maternal-specific or species-specific sequences, mtDNA D loop sequences of aquatic fish and shellfish from a particular species, breed, line or place, and individuals from other species, breeds, lines or places To the corresponding sequence to determine the region where base substitution occurs in a discernable percentage.

This region is 5 to 10 (1%), preferably 11 to 15 (1.5%), more preferably 16 if the region is between 800 to 1600 bases, for example, among individuals of different maternal systems. A region with -30 (3%) base substitutions. It is preferable that the base sequences of this region completely match between individuals of the same maternal system. However, as long as it can be distinguished from other maternal systems, substitution of about 1 or 2 bases may be included. For more accurate identification, the base substitution between individuals of the same mother line may be about 0.2% or less, preferably about 0.1% or less, and more preferably 0% (perfect match). preferable.
The typical position of the maternal specific sequence is present in the base sequence between about 100 to 600, preferably about 150 to 450, with the base at the proline side end of the D loop as the first base. For example, in bluefin tuna, the maternal-specific sequence is present in the base sequence between about 150-350th and in red sea bream between about 250-450th.

The region for identifying a species is a base sequence showing homology between different species when the D loop sequence can be aligned by inserting one or more gaps between a plurality of different species. The homology between different species is 90 to 97%, preferably 90 to 95%, more preferably 90 to 93%. For multiple alignment analysis (multi-alignment) comparing a plurality of sequences, for example, MEGA4 (registered trademark, Molecular Evolutionary Genetic Analysis Software Version 4.0, Tamura et al., Mol. Biol. Evol., 2007, 24 (8): 1596-1599), SEQUENCHER® (Gene Codes, USA), and public or commercial software for sequence analysis can be used.
The typical position of the species specific sequence may partially overlap with the maternal specific sequence. For example, in bluefin tuna, species-specific sequences can be found at about 150-700, particularly about 150-250 and about 600-700.

Next, the mitochondrial D-loop DNA contained in the sample (second sample, sample ) collected from the marine fish and shellfish serving as the sample is compared with the above-mentioned maternal-specific sequence or species-specific sequence to obtain the species. It is possible to identify the type, system, production history and production area. For example, by using a primer or probe designed based on the above-mentioned maternal or heterospecific base sequence, a sequence identical to the maternal specific base sequence or heterospecific base sequence is present in the mtDNA of the specimen by a known means. Whether it is included or not can be easily detected. Known means for this purpose include, but are not limited to, PCR, RCA, direct sequencing, TaqMan, DNA array, FISH and the like.

  In the method of the present invention, the discrimination may be made more rigorously by combining other haplotype comparisons in addition to the maternal or species-specific sequence of the mitochondrial DNA D-loop. In normal haplotype analysis, there is a large difference between individuals, so it cannot be used for identification of seeds and seedlings. For example, as shown in Non-Patent Document 2, even in the mitochondrial DNA of litters, the microsatellite haplotypes are different. However, in aquaculture where breeding is performed with a limited number of individuals, the number of haplotypes in F1 is relatively small. For example, in 11 juveniles originating from the same female parent, haplotypes identified by four microsatellite are There were 4 types (Reference Example 1). This can be used to reinforce identification by the D-loop. For example, as a marker for the released artificial seedling (fry), not only the D-loop mother line or species-specific sequence, but also the karyotype haplotype is determined by microsatellite, etc. Even if an individual belonging to the group exists in nature, it is possible to reliably determine whether the collected (fished) sample is a natural sample or an artificial seedling.

  In a preferred embodiment, the method of the present invention includes preparation of a primer or a probe based on the maternal specific base sequence, the maternal mutation concentration region or the heterospecific base sequence. The primer includes a primer for amplification of the full length of the D loop, or a primer for specific amplification of a maternal-specific base sequence, a maternal mutation concentration region or a species-specific base sequence. The probe includes a nucleic acid, such as an oligonucleotide, that specifically binds to a maternal-specific base sequence, a maternal mutation concentration region, or a species-specific base sequence. Using a primer or probe designed to be at least partially complementary to a portion of the target maternal-specific or species-specific base sequence, mtDNA containing the target sequence in the sample is obtained by a conventional method. It can be easily determined whether or not it is included. Specifically, for example, in a recruitment amount variation survey in cultivated fisheries, PCR is performed using primers designed based on sequences specific to the seeds and seedlings (maternal line) to be studied, using the mtDNA of the individual fish as a template as a template. Or by performing direct sequencing, it is possible to easily determine whether or not the individual is a target seedling. Alternatively, whether or not the specimen corresponds to the production area or system described in the database by comparing a plurality of maternal-specific sequences in the database according to the production area or system and the sequence of the specimen using the DNA array method or the like. Can be easily determined.

  In another embodiment, a document or label may be attached to the aquatic seafood or a part thereof, or a processed product thereof, which describes that they are labeled with the maternal-specific or heterospecific base sequence. . This document or label also includes the marine fish and seafood to which they are attached, either pre-sampled and stored early in the production history, and / or already maternal or species-specific sequences determined, It is possible to compare the base sequence of mitochondrial DNA contained in the fishery product with a maternal or species-specific sequence as required (for example, at the request of the purchaser or user of the fishery product) Can show. It is possible to track the production history of fishery products and processed products attached with such documents or labels even after they have been distributed away from the producers, and the production areas and varieties for inspection by genetic labeling. Therefore, it becomes possible to provide food with higher safety.

  In one embodiment, a plurality of maternal-specific or species-specific sequences derived from a plurality of female parents belonging to the same species, variety, line, production history and / or production area are pooled by the production area, breed or line and made into a database. It can also be used for specimen identification. For example, by obtaining a maternal-specific sequence of a female individual constantly in a farm and creating a database, a farm where fishery products such as yellowtail and tuna that have been subcultured and distributed are derived and shipping time Can be tracked. Alternatively, a similar database can be constructed for a specific production area, which can be used to determine the authenticity of the production area display. Specifically, based on a control sample obtained by sampling in a target water area, the production area is identified as a group in which one or more mother systems exist. For example, if a population has a high degree of fixation in a specific water area and a relatively small number of maternal lines, a database in which the maternal specific sequences in the group are pooled is created, and the locality is determined by the maternal specific sequences included in the database. Can be specified.

  In another embodiment, the present invention includes collecting and storing a sample containing mitochondrial DNA from aquatic seafood as a specimen, a part thereof, or a processed product thereof in the above method. The aquatic seafood or a part thereof or a processed product thereof whose production history can be traced by the method of the present invention may be a live seafood, or a fresh, cooked, dried or frozen seafood Even those scales, eyelids, eyelids, tails, skin, bones, body fluids, muscles or visceral tissues may be used. In general, since mitochondria are present in large numbers (hundreds to thousands) in a single cell, sufficient mtDNA can be obtained from a small amount of sample, and because it is structurally stable compared to nuclear DNA, Extraction is also possible under conditions where the nuclear DNA deteriorates. Therefore, according to the method of the present invention, it is possible to investigate the production history of fish or seafood processed as food or animal feed or raw materials thereof. In particular, the determination of fish species and subspecies is expected to be performed mainly downstream in the distribution route, that is, in a situation where the target fish and shellfish have already been sold, processed and cooked, but the method of the present invention. By using mitochondrial DNA according to the above, the fish species can be determined if a small amount of sample is obtained even after processing such as processing, cooking, freezing, and thawing. For a more accurate production history survey, the tissue sample is preferably about 0.2 g or more (several scales) in the case of an unheated sample, and about 1 g to 5 g in the case of a heated sample. . The collected sample is sealed in a sample tube and stored frozen at −20 ° C. to −80 ° C. Mitochondrial DNA is extracted and purified by an alkaline method or the like according to a conventional method and dissolved in TE. In the case of long-term storage, a method of precipitating with alcohol and storing at −20 ° C. to −80 ° C. or storing DNA at room temperature for a long time using a carrier such as polymer, beads or paper has been developed (for example, "DNA book": see Kawai et al., Genome Research, 2003, 13: 1488-1495).

  In one aspect of the present invention, a method for tracking the production history of fertilized eggs, larvae or fry of seedlings grown in aquaculture or cultivated fisheries is provided. In aquaculture or cultivated fishery, it is possible to obtain a group of fertilized eggs and larvae (fry) of the same litter (same female parents) by observing the spawning season of the parent fish. According to the method of the present invention, a population floating at the same time can be regarded as a seedling that is genetically labeled with the same maternal-specific sequence. Therefore, by distinguishing excellent seedlings grown by subculture and breeding with excellent strains as groups divided by female parents, each group's mtDNA D-loop parentage-specific base sequence was labeled. It can be a parent group. For example, in the case of tuna and the like, uniform labeling can be performed on all the seedlings of millions to tens of millions produced from a single female fish without damaging the fish or performing genetic recombination. It is possible to easily follow-up after discharge, especially to investigate the recruitment variation by parent system. In addition, it is possible to provide an index for avoiding genetic damage due to inbreeding of seedlings. In addition, it is technically possible to detect a seedling that has been duly copied by another person, which can be used to protect a trader who grows the seedling.

  The method of the present invention is not limited by the type of aquatic seafood, but in particular, the production history of aquatic seafood that is distributed in a wide area and whose safety, nutritional value, price, etc. vary depending on the variety, production area or seedling. It is particularly useful for tracking. Specific examples include Persidaceae, Subfamily Sabaaceae (for example, Bluefin Tuna, Southern Bluefin Tuna, Yellowfin Tuna, Bigeye Tuna, Bluefin Tuna, etc.), Sawara (Sawara, etc.) Glyceridae (Buri, amberjack, Hiramasa, etc.) and Ganoderma (Majia, etc.), Perciformes, Perciformes, Perciformes (Perch, etc.) Pufferfish (Traphug, pufferfish, etc.), flatfish, flatfish (flounder, flatfish), salmonid, salmonids (sockeye salmon, chum salmon, coho salmon, calaph trout, trout salmon, etc.), eels, eel subs (eels, anagos, sea breams) ), Shellfish (clams, clams, scallops, swordfish, and tuna).

  In one aspect, the method of the present invention further comprises determining the base sequence of the full D loop of mitochondrial DNA by double-stranded sequencing using a mitochondrial proline tRNA-specific primer and a mitochondrial phenylalanine tRNA-specific primer. The arrangement and base sequence of genes contained in mitochondrial DNA are highly conserved, except for D-loops, among related species of marine fish and shellfish. The D loop is a highly variable region having a base length of about 0.8 to 1.5 kb, but the base sequences of the proline tRNA gene adjacent on the 3 ′ end side and the phenylalanine tRNA gene adjacent on the 5 ′ end side are conserved. High nature. Therefore, by designing primers for the proline tRNA and phenylalanine tRNA sequences with the D loop in between, the entire length of the D loop can be amplified by PCR. After amplifying D-loop DNA by PCR with primers of proline tRNA and phenyllanine tRNA, the primers in the PCR product are digested with enzymes and the like to inactivate unreacted dNTP, and then the two PCR primers used for amplification Each is used to sequence from each end. From the viewpoint of sequence reliability, it is preferable to perform double-stranded sequencing. In order to improve the sequence accuracy, the base sequence of the D loop is used only when the complementary strands match. The region where both strands do not overlap is sequenced again from the inside of the obtained D loop.

  Hereinafter, the present invention will be described in more detail with reference to examples. However, the scope of the present invention is not limited to these examples. Moreover, it is within the ordinary skill of a person skilled in the art to appropriately modify the method of the present invention.

Materials and Methods Mitochondrial DNA extraction / purification method Reagent composition:
(1) P1 solution (Resuspended reagent: 250 ml, stored at 2-8 ° C.)
0.5M EDTA 5.0ml
1M Tris-HCl (pH 8.0) 12.5 ml
The volume is increased to 250 ml with sterilized water and autoclaved.
(2) P2 solution (lysis reagent: 250 ml, stored at room temperature)
SDS 2.5g
NaOH 2.0g
Increase to 250 ml with sterile water.
(3) P3 solution (deproteinization precipitation reagent: 500 ml, stored at 4-8 ° C.)
147.3g of potassium acetate
Acetic acid 60.0ml
The volume is increased to 500 ml with sterilized water, adjusted to pH 5.5, and autoclaved.

Extraction of mitochondrial DNA:
(1) Transfer a sample of about 0.2 g (a few in the case of scales) of fishery products to a sample tube, add 0.4 ml of the P1 solution, and crush the sample with a pestle stick.
(2) Add 0.4 ml of P2 solution and mix gently with a pestle stick.
(3) Add 0.4 ml of P3 solution, and stir the bottom of the tube with your fingers.
(4) Centrifuge at 20,000 × g for 5 minutes at room temperature, and transfer the supernatant to another tube.
(5) Add 0.4 ml of phenol / chloroform solution and apply to vortex mixer.
(6) Centrifuge again and collect the supernatant.
(7) Repeat steps 5 and 6.
(8) Add 0.6 volume of isopropanol to the obtained supernatant.
(9) Centrifuge at 20,000 × g for 30 minutes, discard the supernatant, and wash the precipitate with 70% ethanol.
(10) After centrifuging again, the supernatant is discarded and allowed to stand at 65 ° C. for 5 minutes to dry.
(11) Dissolve in 30 μl of 0.1M TE to obtain a mitochondrial DNA solution.

2. Amplification of D-loop DNA For example, the D-loop base sequence of mitochondrial DNA is amplified according to the following procedure:
(1) The base sequence of seafood mitochondrial DNA is MitoFish (http://mitofish.ori.u-tokyo.ac.jp/), GeneBank (http://www.ncbi.nlm.nih.gov/Genbank) PCR) from the gene sequences of proline tRNA and phenyllanine tRNA on both sides of the D loop in the mtDNA base sequence of the same species as that of the target species or closely related species obtained from a public database such as /) Make a primer. In the case of a new sample not included in the db, the sequence is obtained by replacing with a closely related primer (success example: yellowtail (see Example 3)) or by shotgun sequencing of mitochondrial DNA. .

(2) Prepare a cocktail for PCR reaction with the following composition, and add 0.5 μl of sample mitochondrial DNA:
10 × PCR buffer: 2 μl, 25 mM MgCl ₂ : 2 μl, 2 mM dNTPs: 2 μl, 5 U / μl Taq polymerase: 0.1 μl, 16.7 pmol / μl primer (forward): 1 μl, 16.7 pmol / μl primer (reverse): 1 μl, purified water: 11.3 μl.

(3) Thermal denaturation 95 ° C for 10 minutes, DNA amplification (95 ° C for 1 minute, 65 ° C for 30 seconds, 72 ° C for 1 minute) x 34 cycles, 72 ° C for 5 minutes under the reaction conditions.
(4) Dispense 7.1 μl of the PCR reaction solution to a 384 well PCR plate, and add 2.9 μl of Exo SAP IT (USB Co.).
(5) After reaction at 37 ° C. for 15 minutes, heat denaturation at 80 ° C. for 15 minutes.

3. D-loop DNA double-strand sequencing method After amplification of DNA by PCR, the primers in the PCR product are digested by Exo SAP IT (USB Co.), etc. and unreacted dNTPs are inactivated, and then the two types used for amplification Using each of the PCR primers, sequencing is performed from the respective ends, for example, by the following procedure.

(1) Divide the Exo SAP IT reaction solution into two (5 μl each) and transfer to an empty well of a 384 well PCR plate.
(2) A sequencing cocktail is prepared according to the ABI manual with the following composition:
Forward (or reverse) primer: 1 μl of 16.7 pmol / μl, 5 × sequence buffer: 2 μl, Bigdye: 2 μl.
(3) Seal by heat sealing, and perform a cycle sequence reaction under conditions of heat denaturation 96 ° C. for 1 minute and elongation (96 ° C. for 10 seconds, 50 ° C. for 5 seconds, 60 ° C. for 4 minutes) × 30 cycles.
(4) Peel off the heat seal, add 2.5 μl of 125 mM EDTA and 25 μl of ethanol and let stand at room temperature for 1 hour.
(5) Centrifuge at 4 ° C. and 3,273 × g for 30 minutes.
(6) The ethanol is removed by turning the PCR plate upside down.
(7) Add 35 μl of cooled 70% ethanol and centrifuge under the same conditions.
(8) Remove ethanol and place at 65 ° C. for 5 minutes to dry.
(9) Add 5 μl of formamide and heat denature.
(10) Sequence with an ABI373 type sequencer.

4). Multiple alignment analysis The analysis procedure when “SEQUENCHER (registered trademark)” is used is shown below.
(1) Import sequence data into SEQUENCHER (registered trademark).
(2) Remove sequences with low end quality.
(3) Import the database or past sequence data into the sequencer.
(4) For example, under the following condition setting, a contig of a plurality of sequences is created, and a maternal specific sequence, a maternal variation concentration region, and a cognate heterospecific sequence are determined based on homology:
Assembly Algorithm: Check Dirty Data
Optimize Gap placement: Check Use Re Aligner, Prefer 3 'Gap Placement
Minimum Match Percentage: 80
Minimum Overlap: 20.

Example 1: Extraction of bluefin tuna maternal-specific base sequence and gene labeling of seedlings Seed method
1) From "MitoFish" (http://mitofish.ori.u-tokyo.ac.jp), the base sequence of mitochondrial DNA of this tuna (Tunanus orientalis) (GeneBank accession number AB185022: SEQ ID NO: 1, below) and a PCR primer for D-loop amplification was prepared as follows from the base sequences of proline tRNA and phenylalanine tRNA.
PCR common primer sequence for D loop DNA amplification of this tuna Forward primer (proline side):
5'-TACCCCTAACTCCCAAAGCTAGG-3 '(SEQ ID NO: 2)
Reverse primer (phenylalanine side):
5'-GCTTTCTAGGGCCCATCTTAAC-3 '(SEQ ID NO: 3)

2) Adult natural tuna (Pacific bluefin tuna) and adult cultured tuna (Pacific bluefin tuna) landed in Sakaiminato and Fukuoka, each one and each, and tuna larvae collected from 11 tuna juveniles hatched at the same time. This was extracted and used as a template DNA for PCR.
3) After the D-loop DNA was amplified by the above method, the base sequence was determined and compared with the base sequence of the D-loop (SEQ ID NO: 1) of the tuna (db) in the database.

result:
The results of multiple alignment are shown in FIG. 1 (note that each D-loop base sequence is Sakaiminato: SEQ ID NO: 20, Fukuoka: SEQ ID NO: 21, cultured adult fish: SEQ ID NO: 22, cultured fry 1-11: SEQ ID NO: 23- 33). In the figure, the lower sequence is from nt (nucleotide) 1 to nt865 in the base sequence of the mitochondrial D loop of Pacific bluefin tuna in the database (db), and the black dot at the bottom is the other tuna compared with the db Pacific bluefin tuna It shows that there is a base difference between. The D-loop DNA of 14 Pacific bluefin tuna individuals determined using the above primers had the same 865 bases as db, and each base sequence could be multiple aligned without adding a gap. Between natural and aquaculture adults, the sequence base homology between individuals is high, with only 6-22 different base differences present at 29 sites between nt175-586 in the first half of Pacific bluefin tuna (db). (Table 1).

  The base differences were concentrated at 7 sites in nt175 to 200 and 5 sites in nt273 to 305, and the sequence between them was defined as a maternal-specific base sequence. On the other hand, because the sequence is exactly the same among the 11 cultured larvae, the simultaneously fertilized eggs are derived from the same female parent, and the differences from other adult fish with different female parents are concentrated in specific sites. It became clear that. The results also indicate that fertilized eggs and fry derived from the same female parent can easily label all individuals as the same maternal population by determining the base sequence of one mitochondrial D-loop. It was.

Application example 1: Bluefin tuna maternal-specific base sequence identification and simple detection method By preparing PCR primers that amplify maternal-specific base sequences, especially base sequence of maternal mutation concentration region, by simple and rapid method from the sample A maternal-specific signal can be obtained, and the production history of the specimen can be traced from the maternal nature. An example is shown below.

Method:
The following primer pairs were prepared and amplified by touch-down PCR using mitochondrial DNA extracted from 3 natural and cultured adult Pacific bluefin tuna and 11 juvenile fish as well as from each of southern bluefin tuna and bluefin tuna.
Maternal-specific PCR forward primer (FIG. 1, identical maternal Pacific bluefin tuna nt.175-200: 7 maternal-specific mutation points):
5'-CTTTCAACATCTTACTTACATCACG-3 '(SEQ ID NO: 4)
Maternal-specific PCR reverse primer (FIG. 1, identical maternal Pacific bluefin tuna nt.273-305: 5 maternal-specific mutation points):
5'-TTCTTACTGCGTTTAAGTTTACCAG-3 (SEQ ID NO: 5)

result:
FIG. 2 shows the result of agarose electrophoresis of the PCR amplification product. No signal was detected from natural and cultured Pacific bluefin tuna with different maternal lines, but 135 base pairs of maternal-specific DNA were amplified from 11 cultured juveniles of the same maternal line. Therefore, cultured fry (seedlings) of the same maternal system are genetically labeled with a maternal-specific base sequence, and can be easily detected by PCR using primers specifically designed for the maternal-specific base sequence. confirmed. In the case of seedlings other than the lines or production areas shown in the present specification, maternal identification can be performed simply and rapidly depending on the presence or absence of signals by similarly designing maternal-specific primers and performing real-time PCR of the specimen.

Example 2: Red sea bream maternal-specific base sequence and seed gene seeding method:
1) Obtain the mitochondrial DNA base sequence (GeneBank accession number AP002949: SEQ ID NO: 6) of red sea bream (Pagrus major) from “MitoFish” and design the following PCR primers from the base sequences of proline tRNA and phenylalanine tRNA. Used for loop amplification and sequencing:
Forward primer (substitute from bluefin tuna (db) phenylalanine tRNA base sequence):
5'-GCTTTCTAGGGCCCATCTTAAC-3 '(SEQ ID NO: 7)
Reverse primer I (designed from madai db proline tRNA):
5'-TTTAACCCCCACCATTGGCTCCC-3 '(SEQ ID NO: 8)
Reverse primer II (Redesigned from the base sequence in red sea bream D loop):
5'-AGAGGGGGGTAACAATGAGATC-3 '(SEQ ID NO: 9)

  2) Although the base sequences of red sea bream proline tRNA and phenylalanine tRNA all coincided with the corresponding sequences of bluefin tuna, but one base was different on the reverse side, the base sequence of red sea bream dbalan tRNA was used (reverse primer). I). Regarding the base sequence, a second reverse primer II was prepared from the base sequence of the D-loop 3 'end that was read first, and the base sequences of both strands were completely read.

  3) Mitochondria were extracted from the template DNA of PCR, from each of cultured aquacultured fish in Fukuoka Genkai, one each of Yamaguchi and one of Fukuoka's natural adult fish, and 10 cultured seedlings hatched and grown on the same day. PCR template DNA. D-loop DNA amplification and base sequence determination were performed by the above method, and multiple alignment was performed based on the base sequence of the red sea bream (hereinafter referred to as db) in the database (FIG. 3).

result:
The red sea bream D loop consists of about 1054 base pairs, which is 189 base pairs longer than the Pacific bluefin tuna (db) D loop (869 base pairs). Multiple alignment was made possible by inserting gaps at four locations (FIG. 3). In particular, the sequence of the D-loop was the same among 10 cultured fry. Since the mitochondrial D-loops of juveniles generated from fertilized eggs floating and collected at the same time have the same base sequence, it becomes clear that these juveniles are derived from the same female parent, and fertilized eggs derived from the same female parent. It was shown that larvae and larvae can easily label all individuals as the same maternal population by determining the base sequence of the mitochondrial D-loop of one of them. On the other hand, there were differences of 9 to 24 bases in about 1054 base pairs between individuals with different production areas (Table 2). Among these mutations, 9 sites were concentrated between D loops nt.273 to 311 and 9 sites between nt370 to 416 of red sea bream db.

Application Example 2: Identification of Madam Maternal Specific Base Sequence and Simple Detection Method:
The following primers were designed based on the base sequence of the maternal specific region determined in Example 2, and touchdown was performed using mitochondrial DNA extracted from 3 native and farmed red sea bream adults and 5 identical maternal larvae as templates. Amplification was performed by PCR:
Red sea bream maternal specific PCR forward primer (Fig. 3, red sea bream nt.273-308: 8 maternal specific mutation points):
5'-AGAAATAGCAAGTGTTCAAGTATTTATCCCCAAAAC-3 '(SEQ ID NO: 10)
Red sea bream maternal specific PCR reverse primer (FIG. 3, red sea bream nt. 402-375: 5 maternal specific mutation points):
5'-GTGTTGGTACTTGGTAGACATTTGTCG-3 '(SEQ ID NO: 11)

result:
FIG. 4 shows the result of agarose electrophoresis of the PCR amplification product. No signal was detected from natural and cultured adult fish with different maternal lines, but 129 base pair maternal-specific DNA was amplified from 5 cultured juveniles of the same maternal line. Therefore, cultured fry (seedlings) of the same maternal system are genetically labeled with a maternal-specific base sequence, and can be easily detected by PCR using primers specifically designed for the maternal-specific base sequence. confirmed.

Example 3: Comparison of yellowfin D-loop analysis examples with bluefin tuna and red sea bream Red sea bream, yellowtail and bluefin tuna account for 90% of cultured fish sales. The subfamily Sabaceae and yellowtail belong to the sea bass subfamily Ajiaceae. The perch includes many other important migratory fish such as skipjack and mackerel. The D loops were compared to find out their genetic affinity. However, since the yellow mitochondrial DNA base sequence was not registered in the database, the bluefin tuna tRNA primer was substituted.

Method:
About 900 base pairs of DNA were amplified using the bluefin tuna D-loop end primers (SEQ ID NOs: 2 and 3) used in Example 1, using mitochondrial DNA of natural yellowtails landed in Tottori and Fukuoka as templates. When double-stranded sequencing was performed using each of the primers at both ends, the full length could not be read at once on the phenylalanine side, so the next primer was designed from the partial sequence obtained with the first primer, and the full-length base sequence It was determined.
Yellowtail reverse primer: 5'-GGTTTAACGCGCAAAAGCCGAG-3 '(SEQ ID NO: 12)

result:
In order to align the D-loop base sequences of Tottori yellowtail (SEQ ID NO: 13) and Fukuoka yellowtail (SEQ ID NO: 14), a gap was required at one position in the sequence. The 690 base sequences out of 699 bases were homologous, and the different bases were 8 bases. Furthermore, by increasing the number of samples, the variety (subspecies) can be identified by the base sequence of the mitochondrial DNA D loop of yellowtail.
In addition, among the same perch, there are short (up to 33) homologous bases everywhere between red sea bream, tuna and yellowtail, but there were many gap insertions, and multiple alignment was impossible.

Example 4: Identification of tuna seeds, varieties and production areas and production history management (traceability)
Using the base sequence of mitochondrial DNA (GeneBank accession number AB185022: SEQ ID NO: 1) of this tuna (Thunnus orientalis) obtained from the MitoFish database as a standard material, the following commercially available tuna species and subspecies A comparative analysis of the base sequence of the D loop was performed between:

Atlantic bluefin tuna (Thunnus thynnus): mitochondrial DNA base sequence (GeneBank accession number AY302574: SEQ ID NO: 15)
Bluefin tuna (Thunnus alalunga): Mitochondrial DNA base sequence (GeneBank accession number AB101291: SEQ ID NO: 16)
Bigeye tuna (Indian Ocean: Thunnus obesus: SEQ ID NO: 17)
Yellowfin tuna (off Miyagi: Thunnus albacares: SEQ ID NO: 18)
Southern bluefin tuna (Australia: Thunnus maccoyii: SEQ ID NO: 19)

result:
The D-loop base sequences of the six tuna species were around 869 bases, but multiple alignments could be performed by inserting gaps of around 10 sites per species. However, there were 22 gap insertions, and 9 sites were particularly concentrated in nt172 to 232 in the first half of the maternal specific sequence. There was a difference of 39 to 77 bases out of 869 bases among the varieties (Table 3), but the homology was maintained in other regions. In particular, different bases were concentrated in 35 sites including a gap 12 site in nt173 to 215 and 20 sites including a gap 3 site in nt628 to 672 (FIGS. 5-1 to 3). Both partially overlap with Pacific bluefin tuna maternal-specific sequences, but the gap position and the number of mutations are clearly different from the maternal-specific sequences, so that it can be specified as a species identification region (cognate heterogeneous identification region) it can.

  According to the conventional method, genetic similarity was determined from the remaining homologous regions. As a result, the number of different bases and gap insertions between Atlantic Bluefin Tuna / Pacific Bluefin Tuna, Southern Bluefin Tuna / Pacific Bluefin Tuna, Atlantic Bluefin Tuna / Southern Bluefin Tuna were 69 (+8) and 77 ( +5), 49 (+2). It became clear that these species, both of which are “Toro” materials, are genetically distant from each other.

  This result suggests that the difference between the base sequences of the mitochondrial D-loop makes it possible to discriminate between the tuna genus and its species, which is useful for prevention and detection of food labeling. However, although there are a maximum of 22 differences between the same Pacific bluefin tuna (Table 1), the identification of species of the genus Tuna can be determined by the number of different bases with the number of gaps taken into account.

Example 5: Tuna production area identification method:
As shown in FIG. 1 and FIG. 3, it became possible to discriminate D-loop base sequences of tuna and red sea bream by maternal system, but the maternal system may be defined by the spawning place, school of fish, or habitat area. The possibility of being used for locality identification was investigated. The degree of D-loop base sequence of tuna, which is a migratory fish with a wide habitat area, varies depending on the place of production, in bigeye tuna and yellowfin tuna.

result:
In the comparison of the D-loop base sequences of individuals with different origins, the sequences could be aligned without adding a gap. The following shows the number of base sequence mutations in the same species of tuna (numbers in parentheses = number of different base sites / number of comparison base sites):
Bigeye tuna: Palau / Indian Ocean (18/569)
Atlantic / Palau (28/569)
Atlantic / Indian Ocean (35/569)
Yellowfin tuna: Indian Ocean / Off Miyagi (12/756)
Pacific Bluefin Tuna: (6-22 / 869)

  Gap insertion was not required for multiple alignments between species, but when the production areas were different, differences were found in the region corresponding to the maternal-specific base sequence of Pacific bluefin tuna. In other words, it is suggested that the polymorphism in this region can be used to identify the production area.

  According to the method of the present invention, the parent system can be identified by the difference in base sequence of red sea bream and tuna D-loops of different production areas. Conversely, when the corresponding production area is estimated from the difference of base sequences, the production history management of the product As with, a comparative sample is required. Preferably, a D-loop base sequence database of a school of fish existing in the production area or the habitat area is created and compared with all sequences in the database. The production area may be identified in parallel with the database creation.

Example 6: Comparison of D-loop sequence of natural and cultured tuna To examine genetic differences between natural tuna populations and cultured larvae, natural bluefin tuna accumulated in the Tsukiji market and from Kinki University Fisheries Research Institute The D-loop base sequences of the donated bluefin tuna fertilized eggs and fry were determined by the above method and compared.
Results Among 535 Pacific bluefin tuna with different fishing grounds and landing sites, there was no individual having the same D-loop sequence as the cultured larvae (Fig. 6). From this result, the method of the present invention can be used in practice to identify, for example, artificial seedlings in the catched population, and to investigate the recruitment variation in the discharge project and determine the contribution of the discharge project to the catch. It has been confirmed that it is possible to track and track seeds that have been cultivated and sold by others.

Reference Example 1: Haplotype analysis with microsatellite For 11 cultured bluefin tuna fry of the same maternal line, known microsatellite markers Tth208, Tth217, Tth4 and Tth7-16 (Clark et al., 2004, Mol. Ecol. Notes, 4:70 -73) was used for haplotype analysis. At least 4 patterns of haplotypes were observed (FIG. 7), suggesting that at least 3 male and female parents (1 individual) were present at the time of egg laying. On the other hand, when the same analysis was performed on natural bluefin tuna, the microsatellite pattern was different among all the individuals analyzed, and there was no individual showing the same haplotype (data not shown). From these results, it is possible to determine the haplotypes of the microsatellite of all fertilized eggs because the number of parent fish existing at the time of spawning is small in the case of farmed fish with low genetic diversity. It is suggested that system identification with higher accuracy becomes possible by combining male identification by microsatellite analysis with maternal identification.

  The present invention makes it possible to provide traceability of fish and shellfish useful as marine resources protection. By providing this traceability, production history of fish and shellfish as food or tracking of fry for aquaculture or cultivated fishery By enabling (investigation), the quality and production area of seafood is guaranteed, the camouflage of production history display is detected and prevented, and the identification of excellent seedlings by genetic markers and the establishment of the rights of aquaculture and breeders To do. The present invention further maintains the genetic diversity of aquatic resources and grows within an exclusive economic zone by enabling the labeling of large numbers of juvenile fish used in the release business and offshore tracking and recruitment changes. Contributes to the development of the fishery.

Claims (11)

  A method for identifying a profile of a fishery product or a processed product thereof by determining a nucleotide sequence of a mitochondrial DNA D loop of the fishery product or a processed product thereof.   The method according to claim 1, wherein the profile is a seed, a variety, a line, a seedling, a production history and / or a production area.   The method according to claim 1 or 2, further comprising determining a karyotype by microsatellite.   The method according to any one of claims 1 to 3, further comprising determining whether or not the species-specific base sequence of the mitochondrial DNA D-loop can be aligned by inserting 1 to 2 or more gaps.   The base sequence of the full-length D loop of mitochondrial DNA is further amplified by using a mitochondrial proline tRNA-specific primer and a mitochondrial phenylalanine tRNA-specific primer, and determined by double-stranded sequencing. The method described in 1.   The method according to any one of claims 1 to 5, for comparing the base sequences of mitochondrial DNA D loops of two or more fishery products or processed products thereof.   The method according to claim 6, wherein the comparison of the base sequence of the mitochondrial DNA D loop is a comparison of whether or not the maternal specific base sequences completely match.   At least one of the two or more marine fish and shellfishes is a single female parent whose nucleotide sequence of the mitochondrial DNA D loop has been previously identified, or a fertilized egg, larva, fry or adult fish derived from the female parent. The method according to claim 6 or 7.   The method according to claim 8, wherein fertilized eggs, larvae, fry or adult fish derived from a dam were laid and / or hatched in the same farm or ginger.   The method according to claim 6, for surveying recruitment variation in a release business or cultivated fishery, or for identification of seedlings in aquaculture.   The method according to claim 6 or 7, for identifying the species, production history and / or production area of marine seafood as a food or a processed product thereof.