New polymorphic microsatellite markers for the Korean manila clam (Ruditapes philippinarum) and their application to wild populations

Kim, Eun Mi; An, Hye Suck; Kang, Jung-Ha; An, Cheul Min; Dong, Chun Mae; Hong, Y.K.; Park, J.Y.

doi:10.4238/2014.october.7.11

Cited by 8 publications

(7 citation statements)

References 34 publications

(49 reference statements)

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“…showed the presence of null alleles (range from 0.109 to 0.277) in 10 loci out of 19. Another study aiming to examine the genetic variability and relationships between two shellfish ( Ruditapes philippinarum ) populations in Korea also reported the occurrence of null alleles in 7 loci out of 1046. The presence of null alleles has also been reported in a study that assessed the genetic diversity of four wild and six hatchery stocks of the hard clam ( Mercenaria mercenaria) in Florida.…”

Section: Discussionmentioning

confidence: 76%

Implications for management and conservation of the population genetic structure of the wedge clam Donax trunculus across two biogeographic boundaries

Marie

Lejeusne

Karapatsiou

et al. 2016

Sci Rep

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In a resource management perspective, the understanding of the relative influence of the physical factors on species connectivity remains a major challenge and is also of great ecological and conservation biology interest. Despite the overfishing threat on the wedge clam Donax trunculus in Europe, relatively little information is known about its population genetic structure and connectivity and their consequences on conservation policies. We employed 16 microsatellite loci to characterise the genetic diversity and population structure of D. trunculus. A total of 514 samples from seven different localities along the Atlantic-Mediterranean transition, from the Atlantic (Gulf of Cádiz) to the north-western Mediterranean were genotyped. The analysis of the population genetic structure displayed a clear distinction along the Atlantic-Mediterranean transition with different clusters in the Atlantic Ocean, the Alboran Sea and the northwestern Mediterranean. Consequently, we recommend that these three areas should be considered as different management units. We showed that all populations seem to be at high long-term risk of extinction with the exception of the protected Doñana National Park population which still seems to have evolutionary potential. Therefore, our results emphasized the necessity of protection of this economic resource and the validity of molecular tools to evaluate the population dynamics.

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Section: Discussionmentioning

confidence: 76%

Implications for management and conservation of the population genetic structure of the wedge clam Donax trunculus across two biogeographic boundaries

Marie

Lejeusne

Karapatsiou

et al. 2016

Sci Rep

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“…Of the 19 loci characterised in this study, at least 10 showed the presence of null alleles with frequencies ranging from 0.109 to 0.277. Another study aiming to examine the genetic variability and relationships between two Manila clam ( Ruditapes philippinarum ) populations in Korea also suggested the occurrence of null alleles in 7 loci out of 10 (Kim et al, 2014). More recently Chiesa et al (2016) demonstrated the occurrence of null alleles through rigorous analytical tests in this species.…”

Section: Introductionmentioning

confidence: 99%

Null alleles are ubiquitous at microsatellite loci in the Wedge Clam (Donax trunculus)

Rico

Cuesta

Drake

et al. 2017

PeerJ

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Recent studies have reported an unusually high frequency of nonamplifying alleles at microsatellite loci in bivalves. Null alleles have been associated with heterozygous deficits in many studies. While several studies have tested for its presence using different analytical tools, few have empirically tested for its consequences in estimating population structure and differentiation. We characterised 16 newly developed microsatellite loci and show that null alleles are ubiquitous in the wedge clam, Donax trunculus. We carried out several tests to demonstrate that the large heterozygous deficits observed in the newly characterised loci were most likely due to null alleles. We tested the robustness of microsatellite genotyping for population assignment by showing that well-recognised biogeographic regions of the south Atlantic and south Mediterranean coast of Spain harbour genetically different populations.

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“…Following the library construction, 10 polymorphic loci out of 45 loci (22.22%) were screened that contained two to six different nucleotide repeat motifs. This rate of polymorphism is slightly higher than the 16.1% found in the same species (Kim et al, 2014). In our study, six monomorphic loci were also identified.…”

Section: Discussionmentioning

confidence: 44%

“…Different methods used to develop SSR loci for the same species differ in efficiency. In this study, we had a 77.78% positive rate of cloning, which greatly exceeded the 0.52% achieved in Kim et al (2014). This phenomenon could be due to the construction of an aimed SSR gene library.…”

Section: Discussionmentioning

confidence: 92%

“…We developed a relatively small number of loci, due to the limitation in sample collection from different sites. To investigate genetic diversity of two Korean populations, Kim et al (2014) developed 10 polymorphic loci from expressed sequence tag-derived microsatellite markers, using next-generation sequencing. Different methods used to develop SSR loci for the same species differ in efficiency.…”

Section: Discussionmentioning

confidence: 99%

See 1 more Smart Citation

Isolation and characterization of microsatellite markers in Ruditapes philippinarum

Zb¹,

Yf²,

Jb³

et al. 2016

Genet. Mol. Res.

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ABSTRACT. Ruditapes philippinarum is considered a commercially valuable species, which is commonly found in tidal flats along West Pacific coasts. In China, it is mainly distributed in the southeast sea. In this study, 16 novel microsatellite loci from the R. philippinarum genome were developed, using the protocol of fast isolation by amplified fragment length polymorphism of sequence containing repeats. Thirty-two wild-caught individuals were used to evaluate the degree of polymorphism of these markers. Our results show that there were 10 polymorphic loci and 6 monomorphic loci. The number of alleles per locus and the polymorphism information content ranged from 2 to 6 and from 0.199 to 0.751, respectively. The observed and expected heterozygosities varied from 0.1333 to 0.6207 and 0.1603 to 0.7412, respectively. Of all loci, only one locus was found to deviate significantly from Hardy-Weinberg equilibrium after Bonferroni correction. The loci identified here will provide useful information for future population genetic studies of R. philippinarum.

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New polymorphic microsatellite markers for the Korean manila clam (Ruditapes philippinarum) and their application to wild populations

Cited by 8 publications

References 34 publications

Implications for management and conservation of the population genetic structure of the wedge clam Donax trunculus across two biogeographic boundaries

Implications for management and conservation of the population genetic structure of the wedge clam Donax trunculus across two biogeographic boundaries

Null alleles are ubiquitous at microsatellite loci in the Wedge Clam (Donax trunculus)

Isolation and characterization of microsatellite markers in Ruditapes philippinarum

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