Genetic differentiation between collections of hatchery and wild masu salmon (Oncorhynchus masou) inferred from mitochondrial and microsatellite DNA analyses

Yu, Jeong-Nam; Azuma, Noriko; S, Abe

doi:10.1007/s10641-011-9869-0

Cited by 24 publications

(10 citation statements)

References 28 publications

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“…To determine genetic distances among farms, the data were examined using the chord distance ( D C ) method of Cavalli‐Sforza and Edwards (). This method has been widely used to calculate genetic distance in captive and wild populations of marine and freshwater species (Bai et al ; Iwamoto et al ; Yu et al ). The neighbor‐joining dendrogram resulting from this analysis was corroborated statistically by a bootstrap analysis of 1000 replicates.…”

Section: Methodsmentioning

confidence: 99%

Identification of Two Channel Catfish Stocks, Ictalurus punctatus, Cultivated in Northeast Mexico

Rosa-Reyna

Sifuentes‐Rincón

Parra‐Bracamonte

et al. 2014

J World Aquaculture Soc

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The channel catfish farming in Mexico began in the 1970s. One of the most important areas of production is its northeastern region. Traditionally, the channel catfish farmers have attempted to preserve their original genetic stock. After more than 30 yr of production, the genetic relationship between stocks has not been assessed. The goal of this study was to evaluate the genetic differentiation between five channel catfish farm populations, using 13 microsatellite markers. A total of 154 fin clip samples were collected from five channel catfish farms in Tamaulipas. We also included 31 individuals of the commercial strain NWAC103. In each population, we calculated parameter of genetic variability: inbreeding coefficient (FIS), pairwise differentiation (FST), and genetic distance (DC). For the inference of populations and individual assignment two Bayesian methods were used. Genetic variability parameters were NA = 9.54–11.08 and AE = 5.40–6.67. Hardy–Weinberg equilibrium deviations were observed for all farm populations examined, and a deficit of heterozygotes was found. Signals of inbreeding were observed, particularly for the ACU (Acuamex) hatchery. Populations EKA (Empresas Karol) and ACU showed higher genetic differentiation values with respect to the commercial strain (FST = 0.107; FST = 0.082, respectively). Moderated genetic differences (FST = 0.067; DC = 0.080) were observed between the EKA and ACU. Clustering analysis revealed a well‐defined group between EKA and TPA (El Tiron Parejo). In the Bayesian analysis three groups were defined. The first group was formed by EKA and TPA, the second group included ACU, LAJ (La Lajilla), and PRO (Prodatec). In the third group was the commercial strain. In the assignment of individuals, EKA and ACU were represented by exclusive genotypes. Identification of two genetic stocks, one located in the EKA and the other in the ACU population, will be relevant for future management of these hatcheries. Additionally, the information from microsatellites and the statistical procedures presented will be important tools for genetic monitoring of these farm populations.

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Section: Methodsmentioning

confidence: 99%

Identification of Two Channel Catfish Stocks, Ictalurus punctatus, Cultivated in Northeast Mexico

Rosa-Reyna

Sifuentes‐Rincón

Parra‐Bracamonte

et al. 2014

J World Aquaculture Soc

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“…Mitochondrial markers are currently one of the most popular molecular markers, particularly in studies of molecular evolution, species identification, and genetic diversity (Yu et al, 2012;Sahoo et al, 2015;Korkmaz et al, 2016). The mitochondrial genome is usually a closed circular molecule, and contains 13 protein-coding genes, 22 transfer RNA (tRNA) genes, 2 ribosomal RNA (rRNA) genes, and a control region.…”

Section: Introductionmentioning

confidence: 99%

Characterization of the complete mitochondrial genome and phylogenetic relationships of the three-spot swimming crab (Portunus sanguinolentus)

Zhu

et al. 2016

Genet. Mol. Res.

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ABSTRACT. In this study, we determined the whole mitochondrial genome profile of the three-spot swimming crab (Portunus sanguinolentus) and elucidated phylogenetic relationships between representative species in the order Decapoda. The mitochondrial genome was 16,024 bp in length and consisted of 13 protein-coding genes, 22 transfer RNA genes, two ribosomal RNA genes, and a putative control region. Of the 37 genes, 23 were encoded by the heavy strand while 14 were encoded by the light strand. Four types of start codons were identified; ATG initiated nine genes, ATT initiated two genes, and ATC and GTG each started one gene. Nine protein-coding genes ended with a complete TAA or TAG stop codon, and four genes ended with an incomplete T or TA codon. Fourteen non-coding regions were found, which ranged from 1 to 34 bp in length. Nine overlaps were observed, with lengths between 1 and 7 bp. Phylogenetic analysis suggested that P. sanguinolentus is genetically closest to P. trituberculatus and P. pelagicus. Charybdis feriata, C. japonica, and Thalamita crenata formed a single cluster, and were close to the genera Callinectes and Portunus. Therefore, the genera Charybdis and Thalamita should be classified into the subfamily Portuninae.

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“…Complete mitochondrial genome sequence information is useful in studying genome-level characteristics and phylogenetic relationships (Knudsen et al, 2006), because of its high mutation rate, simple structure, abundant distribution, and maternal inheritance (Yu et al, 2012;Ma et al, 2013;Baek et al, 2014). With the development of molecular techniques, it has become easier to obtain complete mitochondrial genome sequences (Wang et al, 2015), and they have been reported in many crustacean species (Shen et al, 2007;Liu and Cui, 2010;Jondeung et al, 2012;Ma et al, 2013).…”

Section: Introductionmentioning

confidence: 99%

Characterization of the complete mitochondrial genome of Portunus pelagicus with implications for phylogenomics

Ren

et al. 2016

Genet. Mol. Res.

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ABSTRACT. This study determined the mitochondrial genome structure of the blue swimming crab (Portunus pelagicus), and elucidated its phylogenetic relationships among the species within the order Decapoda. The complete mitochondrial genome was 16,155 bp long, and contained 13 protein-coding genes, 22 transfer RNA genes, 2 ribosomal RNA genes, and 1 DNA control region. The gene order of the genome was the same as that found within the family Portunidae. Twenty-three genes were on the heavy strand and 14 were on the light strand. Almost all of the protein-coding genes were initiated by an ATG codon, except for three genes (ATP6, ND1, and ND3) that started with a rare ATT codon. Of the 13 protein-coding genes, 10 ended with complete TAA or TAG stop codons and three ended with an incomplete T codon. Thirteen non-coding regions were identified that ranged from 1 to 30 bp in length. Nine overlaps were found, which ranged from 1 to 7 bp in length. Phylogenetic analyses based on 12 concatenated protein-coding genes revealed that P. pelagicus formed a monophyletic group with Portunus trituberculatus, which were in a larger group with Callinectes sapidus, while the genera Charybdis and Thalamita formed another group. These two groups clustered together and grouped with the genus Scylla. The phylogenetic analysis supported the inclusion of Charybdis in subfamily Portuninae of the family Portunidae, and revealed a close relationship between Charybdis and Thalamita. We suggest that Thalamita should also be classified into the subfamily Portuninae. The results can be used in the study of phylogenetic, population genetic and conservation genetics of P. pelagicus.

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Genetic differentiation between collections of hatchery and wild masu salmon (Oncorhynchus masou) inferred from mitochondrial and microsatellite DNA analyses

Cited by 24 publications

References 28 publications

Identification of Two Channel Catfish Stocks, Ictalurus punctatus, Cultivated in Northeast Mexico

Identification of Two Channel Catfish Stocks, Ictalurus punctatus, Cultivated in Northeast Mexico

Characterization of the complete mitochondrial genome and phylogenetic relationships of the three-spot swimming crab (Portunus sanguinolentus)

Characterization of the complete mitochondrial genome of Portunus pelagicus with implications for phylogenomics

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