Discrimination of chum salmon stocks by stock-specific PCR based on single nucleotide polymorphisms

The chum salmon (Oncorhynchus keta) is an anadromous fish distributed all around the North Pacific. Artificial production and release of the juveniles are being made by Korea, Japan, Russia, Canada and the United States for enrichment of the stocks. Since the released salmons migrate through EEZ of the neighboring countries and intermix in the open ocean, it becomes important to set up some criteria and methods discriminating each stock in order to clarify each nation's right of harvest of the salmon resources. Here, we report a few stock-specific single nucleotide polymorphisms (SNPs) in the COIII-ND3-ND4L region of the mitochondrial DNA and present a simple method of stock separation by polymerase chain reaction(PCR) utilizing the SNPs. A total of 141 chum salmons from Korea, Japan, Canada, and the United States were analyzed and 744 nucleotide sequences of the COIII-ND3-ND4L region were compared each other in this study. Several SNPs were observed in the region, some of which were stock-specific (e.g., positions 57, 70, 246, 303, 307, 534, 591). Based on these SNPs, 20-25 nucleotide long stock-specific PCR primers were designed so that a single PCR with these primers could discriminate salmon stocks among Korea, Japan, Canada and the United States. The primers have the most 3'end nucleotide identical to the SNPs and the second to the 3'end being a mismatch to any of the sequences. With such primer design, a PCR with SF0 (a primer of a conserved sequence) and SR1 (a primer with Korea stock-specific SNP) amplified DNA only from the Korea salmons. This study suggests that SNPs in the COIII-ND3-ND4L region would be useful genetic markers for stock separation and PCR with the modified primers utilizing the SNPs provide a simple method for such purpose.2

Discrimination of chum salmon stocks by stock-specific PCR based on single nucleotide polymorphisms

The chum salmon (Oncorhynchus keta) is an anadromous fish distributed all around the North Pacific. Artificial production and release of the juveniles are being made by Korea, Japan, Russia, Canada and the United States for enrichment of the stocks. Since the released salmons migrate through EEZ of the neighboring countries and intermix in the open ocean, it becomes important to set up some criteria and methods discriminating each stock in order to clarify each nation's right of harvest of the salmon resources. Here, we report a few stock-specific single nucleotide polymorphisms (SNPs) in the COIII-ND3-ND4L region of the mitochondrial DNA and present a simple method of stock separation by polymerase chain reaction(PCR) utilizing the SNPs. A total of 141 chum salmons from Korea, Japan, Canada, and the United States were analyzed and 744 nucleotide sequences of the COIII-ND3-ND4L region were compared each other in this study. Several SNPs were observed in the region, some of which were stock-specific (e.g., positions 57, 70, 246, 303, 307, 534, 591). Based on these SNPs, 20-25 nucleotide long stock-specific PCR primers were designed so that a single PCR with these primers could discriminate salmon stocks among Korea, Japan, Canada and the United States. The primers have the most 3'end nucleotide identical to the SNPs and the second to the 3'end being a mismatch to any of the sequences. With such primer design, a PCR with SF0 (a primer of a conserved sequence) and SR1 (a primer with Korea stock-specific SNP) amplified DNA only from the Korea salmons. This study suggests that SNPs in the COIII-ND3-ND4L region would be useful genetic markers for stock separation and PCR with the modified primers utilizing the SNPs provide a simple method for such purpose.2

How to discriminate the aggregated stocks of migratory species according to their origins: a simple and quick PCR method utilizing stock-specific single nucleotide polymorphisms

Migratory fishes often intermix in the open ocean among stocks of different origins sometime during their life. The chum salmon (Oncorhynchus keta), an anadromous fish that distributes in the North Pacific is one of such examples. The fish reproduces in the river, migrates into the open ocean for growth and becomes intermixed. To study stock-specific migratory routes and other ecological characteristics, it will be necessary to develop a method discriminating each stock. Here, we present a simple polymerase chain reaction (PCR) method utilizing single nucleotide polymorphisms (SNPs) observed in the COIII-ND3-ND4L region of the mitochondrial DNA. From a 744 nucleotide-long sequence of the region, several stock-specific SNPs were observed (e.g., positions 57, 70, 246, 303, 307, 534, 591) among 141 chum salmons of Korea, Japan, Canada, and the United States. Based on these SNPs, 20-25 nucleotide-long stock-specific PCR primers were designed in a way that the most 3'end nucleotide becomes identical to the SNPs and that the second to the 3'end mismatches the conserved nucleotide. With primer pairs designed as such, PCR amplified DNA distinctively among the Korea, Japan, Canada and the United States chum salmons: e.g. primer pairs of SF0 and SR1 for Korea and of SF1 and SR2 for America salmons. Because of its simplicity, this method would be useful for processing many specimens of aggregated stocks collected during any open ocean sampling cruise.1

How to discriminate the aggregated stocks of migratory species according to their origins: a simple and quick PCR method utilizing stock-specific single nucleotide polymorphisms

Migratory fishes often intermix in the open ocean among stocks of different origins sometime during their life. The chum salmon (Oncorhynchus keta), an anadromous fish that distributes in the North Pacific is one of such examples. The fish reproduces in the river, migrates into the open ocean for growth and becomes intermixed. To study stock-specific migratory routes and other ecological characteristics, it will be necessary to develop a method discriminating each stock. Here, we present a simple polymerase chain reaction (PCR) method utilizing single nucleotide polymorphisms (SNPs) observed in the COIII-ND3-ND4L region of the mitochondrial DNA. From a 744 nucleotide-long sequence of the region, several stock-specific SNPs were observed (e.g., positions 57, 70, 246, 303, 307, 534, 591) among 141 chum salmons of Korea, Japan, Canada, and the United States. Based on these SNPs, 20-25 nucleotide-long stock-specific PCR primers were designed in a way that the most 3'end nucleotide becomes identical to the SNPs and that the second to the 3'end mismatches the conserved nucleotide. With primer pairs designed as such, PCR amplified DNA distinctively among the Korea, Japan, Canada and the United States chum salmons: e.g. primer pairs of SF0 and SR1 for Korea and of SF1 and SR2 for America salmons. Because of its simplicity, this method would be useful for processing many specimens of aggregated stocks collected during any open ocean sampling cruise.1

The complete mitochondrial genome of an Antarctic Collembola Cryptopygus antarcticus

2

Genetic structure and the evolutionary history of the North Pacific chum salmon populations

Chum salmon populations are widely distributed in the North Pacific. To find influence of historical events on population genetic structure of the North Pacific chum salmon, we analyzed the 730bp region of mtDNA, COIII-ND3-ND4L, from a total of 201 individuals, 48 from Korea, 44 from Japan, 45 from Alaska, 29 from Canada, 20 from the United States and 15 from Russia. These sequences comprised 51 different haplotypes. There were four major haplotypes: haplotype A was found most of the Korea and Japan salmons, haplotype B was from the majority of Canada, Alaska and Russia salmons, haplotypes C and D were specific to America and Korea salmons, respectively. Such association of the haplotypes with geographical distribution was supported by the haplotype network constructed by TCS analysis. Fst and AMOVA analyses of the populations showed close relationship between Korea and Japan populations and that among Canada, Alaska and Russia populations. Nested clade analysis (NCA) using the GeoDis program which analyzes spatial distribution of genetic variance in terms of phylogeography summarized the current population structure and the evolutionary history of the chum salmon populations in the North Pacific as Past fragmentation and/or long distance colonization. This result could be explained by the glaciation event in the North Pacific during the Pleistocene period.2

The complete Mitochondrial Genome of Antarctic Collebola <i>Cryptopygus antarcticus</i> and the Molecular Evolution

2

Genetic stock identification and gene flow estimation among the chum salmon populations in the North Pacific using the nucleotide variations in mtDNA, COIII-ND3-ND4L region

Genetic stock identification has employed a number of different methods. In terms of accuracy, reproducibility and comparability, single nucleotide polymorphisms (SNPs) which use difference in DNA sequences are getting more acceptances. For the chum salmon, we identified 53 variable sites within the 744 nucleotide&#8208;long region of mtDNA, COIII&#8208;ND3&#8208;ND4L, from the comparison of 186 individuals, 48 from Korea, 44 from Japan, 45 from Alaska, 29 from Canada and 20 from the United States. SNPs in these variable sites comprise 49 haplotypes, some of which are specific to a certain population. Based on these SNPs, population&#8208;specific PCR primers were designed in a way that the most 3&apos;end nucleotide becomes specific to each haplotype and that the second to the last nucleotide at the 3&apos;end mismatches the conserved nucleotide at the site.&nbsp;PCR with these primers amplified DNA distinctively depending on the origin of samples. On the other hand, some haplotypes are common in different populations, indicating presence of individual migration among them. Parsimony network of individual genealogies corroborates such gene flow and shows close genetic relationship between Korea and Japan populations and among Canada, Alaska, and the United States populations. Major gene flow occurs asymmetrically from Alaska to Canada populations (16±6 individuals per generation), from the United States to Canada populations (5.7±1.9), from the North America to the Asia populations (1.4±0.2), and from Japan to Korea populations (10±3). In the last example of the gene flows, however, human&#8208;mediated transplantation of stocks for hatchery operation should be considered in its interpretation.1

Genetic stock identification and gene flow estimation among the chum salmon populations in the North Pacific using the nucleotide variations in mtDNA, COIII-ND3-ND4L region

Genetic stock identification has employed a number of different methods. In terms of accuracy, reproducibility and comparability, single nucleotide polymorphisms (SNPs) which use difference in DNA sequences are getting more acceptances. For the chum salmon, we identified 53 variable sites within the 744 nucleotide‐long region of mtDNA, COIII‐ND3‐ND4L, from the comparison of 186 individuals, 48 from Korea, 44 from Japan, 45 from Alaska, 29 from Canada and 20 from the United States. SNPs in these variable sites comprise 49 haplotypes, some of which are specific to a certain population. Based on these SNPs, population‐specific PCR primers were designed in a way that the most 3'end nucleotide becomes specific to each haplotype and that the second to the last nucleotide at the 3'end mismatches the conserved nucleotide at the site.&nbsp;PCR with these primers amplified DNA distinctively depending on the origin of samples. On the other hand, some haplotypes are common in different populations, indicating presence of individual migration among them. Parsimony network of individual genealogies corroborates such gene flow and shows close genetic relationship between Korea and Japan populations and among Canada, Alaska, and the United States populations. Major gene flow occurs asymmetrically from Alaska to Canada populations (16±6 individuals per generation), from the United States to Canada populations (5.7±1.9), from the North America to the Asia populations (1.4±0.2), and from Japan to Korea populations (10±3). In the last example of the gene flows, however, human‐mediated transplantation of stocks for hatchery operation should be considered in its interpretation.1

Technological development for inducing artifical fish hibernation and manipulation of fish biorhythm

한국해양연구