Isolation and characterization of 150 novel microsatellite markers for Zhikong scallop (<i>Chlamys farreri</i>)

Zhan, Aibin; Bao, Zhenmin; Hu, Xiaoli; Hui, Min; Wang, Mingling; Peng, Wei; Zhao, Haibo; Hu, Jiang

doi:10.1111/j.1471-8286.2007.01760.x

Cited by 31 publications

(40 citation statements)

References 2 publications

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“…The mean overall observed heterozygosity found in this study, 0.286 for A. opercularis and 0.275 for M. varia , is within the range described in scallops after the analysis of allozyme loci, 0.016 for Lyropecten nodosa (Coronado et al 1991) and 0.321 for Chlamys distorta (Beaumont and Beveridge 1984), but lower than the values inferred from the high polymorphic microsatellite loci which usually exceed 0.80 (Gjetvaj et al 1997; Kenchington et al 2006; Zhan et al 2007). The level of genetic diversity reported here for the two scallops was similar, contrasting with the data provided by allozyme loci (Beaumont and Beveridge 1984) and mtDNA (Fernández‐Moreno et al 2008) that revealed higher levels in M. varia than in A. opercularis .…”

Section: Discussionsupporting

confidence: 76%

Intron characterization and their potential as molecular markers for population studies in the scallopsAequipecten opercularisandMimachlamys varia

et al. 2009

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Exon-primed intron-crossing PCR was used on the European commercial scallops Aequipecten opercularis and Mimachlamys varia to characterize introns of four nuclear genes and to identify DNA markers useful for population studies. The primers used yielded the expected product, except those for the lysozyme gene that failed to work in M. varia and amplified a fragment of a proteasome subunit gene (APSM) in A. opercularis. According to the sequences characterized, A. opercularis has at least four calmodulin genes, one of arginine kinase and two of beta-tubulin, and M. varia five, one and one, respectively. Length polymorphism or/and restriction fragment length polymorphism was detected at two loci of A. opercularis (arginine kinase and APSM) and four of M. varia (calmodulin and beta-tubulin), distinguishing in each case two or three alleles. The polymorphic loci were not closely linked. The population survey included four localities from Spain and one from Northern Ireland for A. opercularis and two Spanish localities for M. varia. Observed heterozygosity (H(o)) per locus was 0.276 and 0.296 in A. opercularis. The Northern Ireland sample had the lowest H(o) value (0.200) and the Mediterranean Spanish sample the highest (0.350). In M. varia, H(o) per locus ranged from 0.172 to 0.391 and the two localities showed similar H(o) values (0.255 and 0.293). All population-locus combinations were in agreement with Hardy-Weinberg equilibrium, except two loci of M. varia that showed a strong heterozygote deficit in the two localities examined. Evidence for genetic differentiation among samples was not found.

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Section: Discussionsupporting

confidence: 76%

Intron characterization and their potential as molecular markers for population studies in the scallopsAequipecten opercularisandMimachlamys varia

et al. 2009

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“…The number of polymorphic microsatellite loci obtained with respect to the total sequences examined in A. opercularis (6.0%) is higher than that yielded by enriched libraries constructed in the scallop Mizuhopecten yessoensis (4.6%, An et al 2005), the oyster Crassostrea virginica (2.4%, Reece et al 2004) or the pearl oyster Pinctada maxima (0.2%, Evans et al 2006), and lower than that obtained in other scallops, Chlamys farreri (12.5%, Zhan et al 2007), Pecten maximus (15.8%, Watts et al 2005) and C. nobilis (27.5%, Ma and Yu 2009) or the oyster C. gigas (19.6%, Li et al 2003). The efficiency of the isolation of microsatellites as usable markers might be affected by both biological and technical factors.…”

Section: Discussionmentioning

confidence: 61%

Isolation and characterization of microsatellite markers in the queen scallopAequipecten opercularisand their application to a population genetic study

Arias

Freire

Méndez

et al. 2010

Aquat. Living Resour.

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-Microsatellites are one of the most popular markers in genetic studies but typically they need to be isolated and characterized de novo for each species. In this work, a genomic library enriched for a trinucleotide motif was constructed to identify polymorphic microsatellite loci in Aequipecten opercularis, a scallop species commercially fished in Europe, and to examine the level of genetic variation and genetic differentiation in samples from Spain and Northern Ireland. Sequencing of 83 clones led to the identification of 30 microsatellite-containing sequences which showed often other repeated sequences. Five microsatellite loci were successfully amplified and found polymorphic. The number of alleles and the expected heterozygosity per locus ranged from 9 to 86 and 0.341 to 0.927, respectively, all localities showing similar levels of genetic variation (allelic richness, 13.164-15.487; expected heterozygosity, 0.527-0.638). Discrepancies in genotype proportions from Hardy-Weinberg equilibrium were observed in 11 out of 25 locality-locus combinations, a heterozygote deficiency occurring in all cases probably due to null alleles. Significant genetic differentiation was detected among A. opercularis from Northern Ireland, Fuengirola (southern Spain) and the homogeneous samples from northwest Spain. Isolation by distance was the most likely hypothesis to explain the differentiation detected. (richesse allélique : 13,164-15,487 ; hétérozygosité attendue : 0,527-0,638). Des différences dans les proportions de génotype sont observées par rapport à l'équilibre de Hardy-Weinberg dans 11 des 25 combinaisons « sites géographiques-locus », une déficience hétérozygote est détectée dans tous les cas, probablement due aux allèles nuls. Une différentiation génétique significative est détectée parmi les échantillons de A. opercularis provenant d'Irlande du Nord, de Fuengirola (sud de l'Espagne), et des échantillons homogènes du nord-ouest de l'Espagne. L'isolation due à la distance est l'hypothèse la plus probable pour expliquer ces différences détectées.

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“…In this study, we used Zhikong scallop (Chlamys farreri) as a target species to compare the efficiency of five popular methods derived from the above three strategies. Microsatellite markers in Zhikong scallop show several unique characteristics such as wide spread of null alleles (Zhan et al, 2007a(Zhan et al, , 2007b and poor transferability among scallop species (Zhan et al, 2005). If the strategies work efficiently in Zhikong scallop, they are also expected to be robust candidates for other species.…”

Section: Introductionmentioning

confidence: 98%

Methods comparison for microsatellite marker development: Different isolation methods, different yield efficiency

Zhan

Bao

et al. 2009

J. Ocean Univ. China

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Microsatellite markers have become one kind of the most important molecular tools used in various researches. A large number of microsatellite markers are required for the whole genome survey in the fields of molecular ecology, quantitative genetics and genomics. Therefore, it is extremely necessary to select several versatile, low-cost, efficient and time-and labor-saving methods to develop a large panel of microsatellite markers. In this study, we used Zhikong scallop (Chlamys farreri) as the target species to compare the efficiency of the five methods derived from three strategies for microsatellite marker development. The results showed that the strategy of constructing small insert genomic DNA library resulted in poor efficiency, while the microsatellite-enriched strategy highly improved the isolation efficiency. Although the mining public database strategy is time-and cost-saving, it is difficult to obtain a large number of microsatellite markers, mainly due to the limited sequence data of non-model species deposited in public databases. Based on the results in this study, we recommend two methods, microsatellite-enriched library construction method and FIASCO-colony hybridization method, for large-scale microsatellite marker development. Both methods were derived from the microsatellite-enriched strategy. The experimental results obtained from Zhikong scallop also provide the reference for microsatellite marker development in other species with large genomes.

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Isolation and characterization of 150 novel microsatellite markers for Zhikong scallop (Chlamys farreri)

Cited by 31 publications

References 2 publications

Intron characterization and their potential as molecular markers for population studies in the scallopsAequipecten opercularisandMimachlamys varia

Intron characterization and their potential as molecular markers for population studies in the scallopsAequipecten opercularisandMimachlamys varia

Isolation and characterization of microsatellite markers in the queen scallopAequipecten opercularisand their application to a population genetic study

Methods comparison for microsatellite marker development: Different isolation methods, different yield efficiency

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