Fifteen novel polymorphic microsatellites in rock carp, Procypris rabaudi (Tchang), an endemic fish species in the upper reaches of the Yangtze River drainage

Yue, Hao; Yuan, Hui; Zhang, Xiuyue

doi:10.1007/s10592-008-9560-y

Cited by 6 publications

(4 citation statements)

References 4 publications

(4 reference statements)

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“…The genetic diversity of M. pellegrini was similar to that of M. amblycephala (mean N A = 2.9, H O = 0.60, H E = 0.55) [ 30 ]. In addition, the microsatellite diversity in M. pellegrini was slightly lower than those from other endangered fishes endemic to the upper Yangtze River basin, such as largemouth bronze gudgeon ( Coreius guichenoti , mean N A = 5.2, H O = 0.42, H E = 0.63) [ 37 ], Chinese rare minnow ( Gobiocypris rarus , mean N A = 4.4, H O = 0.51, H E = 0.65) [ 38 ], and rock carp ( Procypris rabaudi , mean N A = 6.9, H O = 0.71, H E = 0.77) [ 39 ].…”

Section: Resultsmentioning

confidence: 99%

Microsatellite Development for an Endangered Bream Megalobrama pellegrini (Teleostei, Cyprinidae) Using 454 Sequencing

Wang

Zhao

et al. 2012

IJMS

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Megalobrama pellegrini is an endemic fish species found in the upper Yangtze River basin in China. This species has become endangered due to the construction of the Three Gorges Dam and overfishing. However, the available genetic data for this species is limited. Here, we developed 26 polymorphic microsatellite markers from the M. pellegrini genome using next-generation sequencing techniques. A total of 257,497 raw reads were obtained from a quarter-plate run on 454 GS-FLX titanium platforms and 49,811 unique sequences were generated with an average length of 404 bp; 24,522 (49.2%) sequences contained microsatellite repeats. Of the 53 loci screened, 33 were amplified successfully and 26 were polymorphic. The genetic diversity in M. pellegrini was moderate, with an average of 3.08 alleles per locus, and the mean observed and expected heterozygosity were 0.47 and 0.51, respectively. In addition, we tested cross-species amplification for all 33 loci in four additional breams: M. amblycephala, M. skolkovii, M. terminalis, and Sinibrama wui. The cross-species amplification showed a significant high level of transferability (79%–97%), which might be due to their dramatically close genetic relationships. The polymorphic microsatellites developed in the current study will not only contribute to further conservation genetic studies and parentage analyses of this endangered species, but also facilitate future work on the other closely related species.

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Section: Resultsmentioning

confidence: 99%

Microsatellite Development for an Endangered Bream Megalobrama pellegrini (Teleostei, Cyprinidae) Using 454 Sequencing

Wang

Zhao

et al. 2012

IJMS

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“…Primers for 12 polymorphic microsatellite loci were used to amplify template DNA of all specimens, including loci MFW1, MFW4, MFW7, MFW15, MFW23, MFW24, MFW26 (Croojimans et al 1997), HLJY0708, HLJY3334 (Geng et al 2006), Pra20 (Yue et al 2009), Pra117 (Zhang et al 2008), and YT20 (Xu et al 2007) [Electronic supplementary material (ESM) Appendix S1]. Amplification was performed using GeneAmp 9400 PCR system (Applied Biosystems, Foster City, CA, USA), with an initial denaturing period of 5 min at 95°C, followed by 30 cycles of 94°C for 30 s, primer-specific annealing temperature (ESM Appendix S1) for 30 s, and 72°C for 45 s, followed by a final extension of 7 min at 72°C.…”

Section: Methodsmentioning

confidence: 99%

Microsatellite DNA variation among samples of bronze gudgeon, Coreius heterodon, in the mainstem of the Yangtze River, China

Cheng

et al. 2013

Ichthyol Res

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Bronze gudgeon, Coreius heterodon, is an endemic and economically important fish in the Yangtze River, whose abundance has declined dramatically because of dam construction, overfishing, and water pollution. The Gezhouba and Three Gorges dams block connection of the bronze gudgeon populations above and below the dams. We collected bronze gudgeon from four sites in the mainstem of the Yangtze River, with one site above the dams and three sites below the dams, and studied genetic structure within and among the samples using 12 microsatellite DNA markers. Differences in indexes of genetic diversity were not significant among all the samples. No recent dramatic decrease of effective population size was inferred for all the samples using the population bottleneck test. Overall and pairwise genetic differentiation showed no significant genetic differentiation. Membership proportions of three genetic clusters inferred using assignment analysis were not significantly different among the samples. These results suggested that the genetic diversity and structure of bronze gudgeon were uniform across the samples. However, the Hardy-Weinberg equilibrium test, fixation index and linkage disequilibrium test indicated genetic subdivision of bronze gudgeon in the upper reach of the Three Gorges Dam. The present study and future studies including tributary samples will provide an important baseline of genetic diversity and population structure of bronze gudgeon in the Yangtze River, which is critical for monitoring and evaluating impacts of the large-scale dams on this species.

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“…Microsatellite primers of rock carp were screened [14,15], and 10 highly polymorphic primers were selected to be amplified for all specimens (Table 1). Amplification was performed using a thermal cycler (GeneAmp PCR system 9400, USA) with an initial denaturing period of 5 min at 95°C followed by 30 cycles of 94°C for 30 s, primer-specific annealing temperature (Table 1) for 30 s, and 72°C for 45 s, followed by a final extension of 7 min at 72°C.…”

Section: Microsatellite Genotypingmentioning

confidence: 99%

Impacts of hatchery release on genetic structure of rock carp Procypris rabaudi in the upper Yangtze River, China

Cheng

Liu

et al. 2011

Fish Sci

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Rock carp Procypris rabaudi is a vulnerable endemic fish in the upper Yangtze River. Hatchery release has been carried out as a major stock enhancement strategy for this species. Ten microsatellite loci were chosen to compare genetic variation between one wild population and two hatchery groups to evaluate the potential impacts of hatchery release on the genetic structure of the wild population. Two different models indicated strong evidence of recent bottlenecks in all groups. The hatchery groups were lower in the mean number of alleles per locus, allelic richness, and allelic diversity compared with the wild population. The 80% membership coefficient indicated that 14% of the wild fish could be assigned as hybrids of wild and hatchery fish. Our results suggested that hatchery release will further reduce the natural genetic diversity in the wild population, change the genetic structure of the rock carp population, and may not benefit restoration of this vulnerable fish species.

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Fifteen novel polymorphic microsatellites in rock carp, Procypris rabaudi (Tchang), an endemic fish species in the upper reaches of the Yangtze River drainage

Cited by 6 publications

References 4 publications

Microsatellite Development for an Endangered Bream Megalobrama pellegrini (Teleostei, Cyprinidae) Using 454 Sequencing

Microsatellite Development for an Endangered Bream Megalobrama pellegrini (Teleostei, Cyprinidae) Using 454 Sequencing

Microsatellite DNA variation among samples of bronze gudgeon, Coreius heterodon, in the mainstem of the Yangtze River, China

Impacts of hatchery release on genetic structure of rock carp Procypris rabaudi in the upper Yangtze River, China

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