Development of 20 novel microsatellite markers in the Hong Kong oyster, Crassostrea hongkongensis

Xiao, Shijun; Ma, Haitao; Zhou, Yu

doi:10.1007/s12686-010-9368-1

Cited by 10 publications

(5 citation statements)

References 11 publications

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“…The deficiencies were frequently explained by inbreeding, null alleles, population substructure, bottleneck effects, Wahlund effects, or low gene flow (Zouros, 1987;Charbonnel et al, 2002;Fauvelot et al, 2009). However, in many mollusks, the null allele was the most likely reason for heterozygote deficiency (Kennington et al, 2008;Nicot et al, 2009;Xiao et al, 2011). Large allele dropout and evidence of stuttering were absent, but using Bonferroni's confidence interval, we determined that null alleles were present in most loci, except TXH66 and TXH113, in the studied population (Van Oosterhout et al, 2004).…”

Section: Resultsmentioning

confidence: 95%

Development of 18 microsatellite loci for the freshwater snail Bellamya aeruginosa (Mollusca, Gastropoda)

Bx²,

Zhu³

et al. 2012

Genet. Mol. Res.

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ABSTRACT. Although it is a major freshwater gastropod species, genetic diversity of Bellamya aeruginosa was completely unknown. Eighteen microsatellite loci were isolated and characterized from (AC) 15 -enriched genomic libraries of the freshwater snail B. aeruginosa. Most of the 18 loci were successfully amplified and high polymorphic information content values were found, ranging from 0.244 to 0.792 (mean 0.541). The number of alleles per locus ranged from 5 to 13 (mean 8.8), the expected heterozygosity varied from 0.347 to 0.950 (mean 0.815) and the observed heterozygosity varied from 0.087 to 0.782 (mean 0.431). Eight loci showed significant deviation from Hardy-Weinberg equilibrium after Bonferroni's correction and no significant genotypic linkage disequilibrium was detected between most locus pairs, except for TXH79-TXH97 and TXH113-TXH121. These 18 polymorphic microsatellite loci should be useful for population genetics analysis and species identification of Bellamya.

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Section: Resultsmentioning

confidence: 95%

Development of 18 microsatellite loci for the freshwater snail Bellamya aeruginosa (Mollusca, Gastropoda)

Bx²,

Zhu³

et al. 2012

Genet. Mol. Res.

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“…The study of microsatellite presence and its distribution in mammalian genomes has gained much attention, compared with the Ostreidae family. Although several attempts were made to investigate and characterize microsatellite markers for oyster stock and genetic analysis, still a comprehensive analysis is missing (Xiao, Ma et al 2011, Ma, Zhang et al 2021, Monteiro, Galvão et al 2023). Thus, the objectives of this study aims, were 1) genome-wide analysis of abundance and frequency of simple and compound microsatellites within five important oyster genomes, 2) Analysis of microsatellites through chromosomes level and its correlation with length, incidence, abundance, density and GC content, 3) development of cSSR in C. hongkongenesis followed by diversity analysis and cross-species amplification.…”

Section: Introductionmentioning

confidence: 99%

Genome-wide and chromosomal microsatellite marker landscape analysis within the genus Crassostrea

Sahu,

Fazil,

Panda

et al. 2023

Preprint

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Microsatellite is a classical codominant marker frequently used to study genetics and evolution of living entities as well as molecular breeding in commercially important species. Although it has a tremendous application in oyster aquaculture, the lack of knowledge about its type, distribution pattern, and comparative analysis is limited. Thus, in this study, we conducted a genome-wide as well as chromosomal microsatellite landscape analysis within the genus Crassostrea. The genome-wide microsatellites number varied from 169432-212368, with relative abundance (RA) and relative density (RD) ranging from 310.18-336.5 loci/Mb and 7553.4-8793.42 bp/Mb, respectively. About 14.99-16.75% of total microsatellites were considered compound microsatellites having cRA and cRD, 21.78-25.5 loci/Mb, and 1332.81-1694.54 bp/Mb, respectively. The mononucleotide microsatellites were predominant followed by di and tetranucleotide. The RA and RD of the SSRs revealed no correlation with genome size but a significant correlation with GC content. However, the number of SSRs showed a significant relationship with the genome size but no relation with GC content. In contrast, the incidence of cSSR was positively associated with genome size and GC content. Finally, 29 cSSR loci were developed and validated inC. hongkonensisusing one wild population followed by its cross-species amplification. The allele number (Ne), observed heterozygosity (Ho), expected heterozygosity (He), inbreeding co-efficient (Fis), the polymorphic information content (PIC), ranged from 2-10, 0.092-0.897, 0.0001-1, 0.088-0.828, respectively. The present study elucidated microsatellite evolution within the Crassostrea genome and the loci developed can be utilized for brood stock analysis, parentage assignment, and construction of linkage map of the respective species.

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“…Microsatellite markers are useful for the applications mentioned above (McGoldrick et al, 2000;Liu and Cordes, 2004). However, few microsatellite loci have been reported in this species (Xia et al, 2009;Li and Yu, 2010;Xiao et al, 2011;Zhao et al, 2015) and more loci are required to enable further work such as genetic mapping and trait improvement studies. Here, we described the development and characterization of 40 new polymorphic microsatellite loci for C. hongkongensis, which will be a useful tool in future studies of this species.…”

Section: Introductionmentioning

confidence: 99%

Polymorphic microsatellite loci developed from the Hong Kong oyster (Crassostrea hongkongensis)

Xiao

Zhang

et al. 2016

Genet. Mol. Res.

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Forty polymorphic microsatellite loci were developed from Crassostrea hongkongensis using an enriched partial genomic library with magnetic beads. The polymorphism of these loci was assessed in 30 individuals from a wild population. The allele number of the polymorphic markers ranged from 2 to 13, with an average of 5.8 per locus. The polymorphism information content ranged from 0.032 to 0.891 and 37 loci presented a medium or high level of polymorphism. The observed and expected heterozygosity values ranged from 0.033 to 1.000 and 0.033 to 0.931, respectively. Of the 40 loci, 28 were found to conform to Hardy-Weinberg equilibrium (HWE), whereas the remaining 12 showed a significant departure from HWE. The availability of these markers will aid future genetic studies in C. hongkongensis.

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Development of 20 novel microsatellite markers in the Hong Kong oyster, Crassostrea hongkongensis

Cited by 10 publications

References 11 publications

Development of 18 microsatellite loci for the freshwater snail Bellamya aeruginosa (Mollusca, Gastropoda)

Development of 18 microsatellite loci for the freshwater snail Bellamya aeruginosa (Mollusca, Gastropoda)

Genome-wide and chromosomal microsatellite marker landscape analysis within the genus Crassostrea

Polymorphic microsatellite loci developed from the Hong Kong oyster (Crassostrea hongkongensis)

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