Microsatellite analysis of genetic diversity and population structure of Chinese mitten crab (Eriocheir sinensis)

Chang, Yumei; Liang, Liqun; Ma, Haitao; He, Jianguo; Sun, Xiaowen

doi:10.1016/s1673-8527(08)60023-5

Cited by 24 publications

(18 citation statements)

References 9 publications

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“…Adjusting for null alleles, the mean number of alleles per locus, H E and H O are 7.4, 0.800 and 0.689 respectively, demonstrating a relatively high genetic diversity within crab individuals. This is similar to reports from studies in other locations [21,23,24,38,39]; however, four microsatellite loci exhibited drastic departures from HWE as shown by the fact that H E was apparently higher than H O (Table 2). In this study, heterozygote deficiency at the four loci seems to be strong evidence for the deviations of HWE .…”

Section: Discussionsupporting

confidence: 89%

Large-Scale Isolation of Microsatellites from Chinese Mitten Crab Eriocheir sinensis via a Solexa Genomic Survey

Xiong

Wang

Qiu

2012

IJMS

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Microsatellites are simple sequence repeats with a high degree of polymorphism in the genome; they are used as DNA markers in many molecular genetic studies. Using traditional methods such as the magnetic beads enrichment method, only a few microsatellite markers have been isolated from the Chinese mitten crab Eriocheir sinensis, as the crab genome sequence information is unavailable. Here, we have identified a large number of microsatellites from the Chinese mitten crab by taking advantage of Solexa genomic surveying. A total of 141,737 SSR (simple sequence repeats) motifs were identified via analysis of 883 Mb of the crab genomic DNA information, including mono-, di-, tri-, tetra-, penta- and hexa-nucleotide repeat motifs. The number of di-nucleotide repeat motifs was 82,979, making this the most abundant type of repeat motif (58.54%); the second most abundant were the tri-nucleotide repeats (42,657, 30.11%). Among di-nucleotide repeats, the most frequent repeats were AC motifs, accounting for 67.55% of the total number. AGG motifs were the most frequent (59.32%) of the tri-nucleotide motifs. A total of 15,125 microsatellite loci had a flanking sequence suitable for setting the primer of a polymerase chain reaction (PCR). To verify the identified SSRs, a subset of 100 primer pairs was randomly selected for PCR. Eighty two primer sets (82%) produced strong PCR products matching expected sizes, and 78% were polymorphic. In an analysis of 30 wild individuals from the Yangtze River with 20 primer sets, the number of alleles per locus ranged from 2–14 and the mean allelic richness was 7.4. No linkage disequilibrium was found between any pair of loci, indicating that the markers were independent. The Hardy-Weinberg equilibrium test showed significant deviation in four of the 20 microsatellite loci after sequential Bonferroni corrections. This method is cost- and time-effective in comparison to traditional approaches for the isolation of microsatellites.

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Section: Discussionsupporting

confidence: 89%

Large-Scale Isolation of Microsatellites from Chinese Mitten Crab Eriocheir sinensis via a Solexa Genomic Survey

Xiong

Wang

Qiu

2012

IJMS

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“…Chinese mitten crab, Eriocheir sinensis is an important aquaculture species in China and has a higher food commercial value than any other species of Eriocheir (Chang et al, 2008). Recently, increased numbers of small mature individuals have been observed in E. sinensis, which devalues commercial production (Li et al, 2005).…”

Section: Introductionmentioning

confidence: 99%

Expression characteristics of the SUMOylation genes SUMO-1 and Ubc9 in the developing testis and ovary of Chinese mitten crab, Eriocheir sinensis

Wang

Chen

et al. 2012

Gene

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“…Heterozygote deficiency at all loci seems to be the strong evidence for the deviations of HWE. The presence of null alleles and samplings (such as inbreeding individuals) could cause significant heterozygote deficit (Chang et al 2008). Meanwhile, an exact P value test for genotypic linkage disequilibrium discovered three pairs of loci showed remarkable linkage (HLJDH137-HLJDH186, HLJDH185-HLJDH186 and HLJDH137-HLJDH107) (P \ 0.001), which indicated these markers should be used selectively.…”

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confidence: 99%

Isolation and characterization of 11 microsatellite markers for the large yellow croaker, Pseudosciaena crocea

et al. 2008

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A new set of 11 microsatellite markers was isolated and characterized in the large yellow croaker (Pseudosciaena crocea Richardson) from a CA-enriched genomic library. Of 35 microsatellite markers screened, 11 microsatellite markers are highly polymorphic in one hatchery stock which contained 58 individuals. The high genetic variability was represented mainly by the number of alleles, which ranged from 7 to 16, and the observed heterozygosity, which ranged from 0.43 to 0.79. These newly isolated markers increase the available molecular resources that can be used to analyze genetic diversity and population structure of large yellow croaker.

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Microsatellite analysis of genetic diversity and population structure of Chinese mitten crab (Eriocheir sinensis)

Cited by 24 publications

References 9 publications

Large-Scale Isolation of Microsatellites from Chinese Mitten Crab Eriocheir sinensis via a Solexa Genomic Survey

Large-Scale Isolation of Microsatellites from Chinese Mitten Crab Eriocheir sinensis via a Solexa Genomic Survey

Expression characteristics of the SUMOylation genes SUMO-1 and Ubc9 in the developing testis and ovary of Chinese mitten crab, Eriocheir sinensis

Isolation and characterization of 11 microsatellite markers for the large yellow croaker, Pseudosciaena crocea

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