Tetra-Repeat Microsatellite Markers for the Masu Salmon (Oncorhynchus masou masou) and Its Application in Cross-Subspecies Amplification

Yamamoto, Shoichiro; Kurokawa, Tadahide; Sekino, Masashi; Yasuike, Motoshige; Saitoh, Kenji

doi:10.3390/ijms141123153

Cited by 4 publications

(2 citation statements)

References 12 publications

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“…For the 38 populations, selected mainly by sample size within populations (Table ), microsatellite DNA analysis was carried out using 13 loci: OMAS‐3, OMAS‐4, OMAS‐5, OMAS‐10, OMAS‐18 (Yamamoto, Kurokawa, Sekino, Yasuike, & Saitoh, ), OMM‐1311, OMM‐1344 (Palti, Fincham, & Rexroad, ), Ssa‐197 (O'Reilly, Hamilton, McConnel, & Wright, ), One‐111 (Olsen, Wilson, Kretschmer, Jones, & Seeb, ), Omy‐325 (Olsen, Wenburg, & Bentzen, ) Oma‐02, Oma‐3ke and Ots‐520 (Noguchi, Ikeda, Nakajima, & Taniguchi, ). After conjugating 6‐FAM, HEX, NED or PET fluorescent dyes to the 5′ end of each forward primer with tailed reverse primer (Thermo Fisher Scientific, Inc.), we analysed three multiplex PCR sets (Set‐A: OMAS‐3, OMAS‐4, OMAS‐5, OMAS‐10 and OMAS‐18; Set‐B: Oma‐02, Oma‐3ke, Ots‐520, Omy‐325 and OMM‐1311; Set‐C: OMM‐1344, One‐111 and Ssa‐197) using a Type‐it Microsatellite PCR Kit (Qiagen, Inc.).…”

Section: Methodsmentioning

confidence: 99%

Phylogeography of a salmonid fish, masu salmon Oncorhynchus masou subspecies‐complex, with disjunct distributions across the temperate northern Pacific

et al. 2019

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Climate oscillations during the Pleistocene had profound effects on the evolutionary history of freshwater fishes now distributed across northern temperate regions. The extent of continental glaciation on the western side of the North Pacific, including areas of East Asia, was more limited as compared with regions of North America, Europe and high‐latitude areas of the North Pacific. Therefore, the effects of climate oscillations might have influenced species in dissimilar ways depending on the species' distribution. We used mitochondrial DNA (mtDNA) and microsatellite DNA (msDNA) markers to clarify the evolutionary history of masu salmon Oncorhynchus masou subspecies‐complex (family Salmonidae) distributed in historically non‐glaciated regions in the western North Pacific. No marked regional or subspecies‐specific mtDNA haplotype associations were recognised, except for O. masou subsp., a lacustrine form endemic to Lake Biwa, an ancient lake in central Honshu. The landlocked subspecies O. masou formosanus, with a disjunct distribution on Taiwan Island, exhibited no diagnostic population features differing from the other subspecies, in either mtDNA or msDNA markers. Mismatch distribution and Bayesian skyline plot analyses indicated relatively recent range expansion and rapid population growth for masu salmon during the last glacial period (c. 0.1–0.15 Ma). Contrary to the mtDNA genealogy, Bayesian clustering using msDNA showed two main genetic clusters, mainly northern populations of the subspecies O. m. masou and populations of the subspecies O. m. ishikawae in southern areas of the Japanese Archipelago. Notably, O. m. formosanus on Taiwan Island was included in the O. m. masou group, and O. masou subsp. was included in the O. m. ishikawae group. Our results suggest that the masu salmon subspecies‐complex in historically non‐glaciated regions of the Temperate Northern Pacific is characterised by weak population structuring and shallow genetic differentiation among the subspecies, except for O. masou subsp. owing to its long isolation in Lake Biwa. Incomplete lineage sorting and historical inter‐subspecies hybridisation, possibly due to secondary contact, seem to be plausible explanations for discrepancies in the mitochondrial DNA genealogy and nuclear DNA genetic structure.

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Section: Methodsmentioning

confidence: 99%

Phylogeography of a salmonid fish, masu salmon Oncorhynchus masou subspecies‐complex, with disjunct distributions across the temperate northern Pacific

et al. 2019

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“…These methods are laborious and difficult to use. With technological advances, such as next generation sequencing [14,15,16], the emerging sequencing platforms now allows us to quickly achieve a large number of SSR markers [17,18]. In this study, we utilized shotgun 454 pyrosequencing technology to isolate SSR markers from the C. coggygria genome.…”

Section: Introductionmentioning

confidence: 99%

Isolation and Characterization of Microsatellite Markers for Cotinus coggygria Scop. (Anacardiaceae) by 454 Pyrosequencing

Wang

2014

Molecules

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Abstract:Cotinus coggygria Scop. (Anacardiaceae) is a deciduous shrub or small tree that is native to a large area covering from southern Europe, east across central Asia, and the Himalayas in northern China. Shotgun 454 pyrosequencing was used to develop microsatellite markers from the genome of C. coggygria. In this study, 349 microsatellite loci were identified from 40,074 individual sequence reads produced by one-sixteenth run, and primer pairs were designed for these loci. To test the primer amplification efficiency, 50 microsatellite primer pairs were tested across 12 individuals from two C. coggygria populations (Wuzhi Mountain: 36°30'N, 113°39'E; Tianlong Mountain: 37°42'N, 112°26'E). Among the 50 tested primer pairs, eight were found to be polymorphic. The average allele number of the microsatellites was 3.5 per locus, with a range from two to five. The inbreeding coefficient ranged from −0.478 to 0.222. The observed and expected heterozygosities varied from 0.167 to 0.750 and from 0.163 to 0.743, respectively. This set of markers is potentially useful for assessing the genetic diversity, as well as for understanding the population structure and phylogeographical and landscape genetic patterns, of C. coggygria.

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Isolation and characterization of microsatellite markers for Forsythia suspensa (Thunb.) Vahl (Oleaceae) using 454 sequencing technology

Fu¹,

Li²,

Li³

2014

Biochemical Systematics and Ecology

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Tetra-Repeat Microsatellite Markers for the Masu Salmon (Oncorhynchus masou masou) and Its Application in Cross-Subspecies Amplification

Cited by 4 publications

References 12 publications

Phylogeography of a salmonid fish, masu salmon Oncorhynchus masou subspecies‐complex, with disjunct distributions across the temperate northern Pacific

Phylogeography of a salmonid fish, masu salmon Oncorhynchus masou subspecies‐complex, with disjunct distributions across the temperate northern Pacific

Isolation and Characterization of Microsatellite Markers for Cotinus coggygria Scop. (Anacardiaceae) by 454 Pyrosequencing

Isolation and characterization of microsatellite markers for Forsythia suspensa (Thunb.) Vahl (Oleaceae) using 454 sequencing technology

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