Isolation and characterization of microsatellite loci in Acrossocheilus paradoxus (Cyprinidae) using PCR-based isolation of microsatellite arrays (PIMA)

Hsu, Kui‐Ching; Wang, Jiang Ping; Chen, Xiang Lin; Chiang, Tzen‐Yuh

doi:10.1023/b:coge.0000014051.67562.55

Cited by 23 publications

(15 citation statements)

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“…Microsatellite markers in PV were isolated by beginning with a random amplified polymorphic DNA-polymerase chain reaction (RAPD-PCR) enrichment (Hsu et al 2004;Huang et al 2007). This PCR isolation of microsatellite arrays (PIMA) approach was proposed by Lunt et al (1999).…”

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Isolation and characterization of microsatellite loci in Pedicularis verticillata L. using PCR-based isolation of microsatellite arrays (PIMA)

Huang

Chen

et al. 2008

Conserv Genet

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Pedicularis verticillata L. is a highly valuable herb for traditional Chinese medical treatment. In this report, 11 microsatellite loci from P. verticillata were isolated. The simple sequence repeat (SSR) markers were screened in 23 samples of wild populations of P. verticillata, and eight samples from its sister P. ikomai. The number of alleles ranged from 4 to 13, and value of expected (H E ) and observed (H 0 ) heterozygosity was 0.62609-0.89662 and 0-0.95652, respectively. All loci were significantly deviated from Hardy-Weinberg expectations due to the heterozygote deficiency, indicating a dramatic loss of genetic polymorphisms in the restrictedly distributed species. The markers amplified well in the two species are useful for examining genetic diversity and population genetic structure, which, in turn, can provide information for establishing conservation strategy for these endangered species.Keywords Microsatellite Á PIMA Á Pedicularis verticillata L. HeterozygosityThe genus Pedicularis comprises about 500 species all over the world. Pedicularis verticillata L., an annual herb, is restrictedly distributed in the Northern hemisphere, mostly in temperate Asia, and the central part of Taiwan (Prain 1890;Li 1948;Tsoong 1955;Yang et al. 1998). In Taiwan, the plant grows on mountain slopes at high elevations, ca. 2,000-3,500 m alt. above the sea level. Due to the rapid social-economical development, natural habitats for the plants have been severely disturbed, resulting in population fragmentation. Overexploitation is another reason for the quick population decline. Several Pedicularis species have been used as traditional Chinese medicine for treating diuresis, exhaustion, collapse and senility (Su et al. 1997). Recently, pharmacological studies in Pedicularis showed strong scavenging effects on superoxide and anti-oxidation effects (Liu et al. 1991;Jia et al. 1992). For protecting these valuable natural resources, investigating genetic diversity and population structure would provide information for conservation. In the study, we isolated 11 microsatellites from the endangered species.Genomic DNAs were obtained from ground leaf tissue of P. verticillata (PV) using a CTAB methodology (Doyle and Doyle 1987). Microsatellite markers in PV were isolated by beginning with a random amplified polymorphic DNA-polymerase chain reaction (RAPD-PCR) enrichment (Hsu et al. 2004;Huang et al. 2007). This PCR isolation of microsatellite arrays (PIMA) approach was proposed by Lunt et al. (1999). It takes advantage that the RAPD fragments contain microsatellite repeats more frequently than genomic clones (Cifarelli et al. 1995).The RAPD-PCR amplification was performed in a thermal cycler with a reaction mixture (50 ll) containing 20-100 ng DNA, 0.2 mM of each dNTP, 2 mM MgCl 2 , 0.5 U Taq polymerase (Violet), and 5 pmols of one RAPD primer. The PCR program was as follows: initial denaturing 5 min at 94°C for 1 cycles, 35 cycles of 30 s at 94°C, 1 min at 42°C, 2 min at 72°C, followed by 10 min at 72°C for additional extension ste...

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Isolation and characterization of microsatellite loci in Pedicularis verticillata L. using PCR-based isolation of microsatellite arrays (PIMA)

Huang

Chen

et al. 2008

Conserv Genet

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“…DNA was purified with Roche high pure PCR template preparation kit. The isolation of microsatellite markers began with a random amplified polymorphic DNA-polymerase chain reaction (RAPD-PCR) enrichment (Hsu et al 2004;Lin et al 2007;Chiang et al 2008). This PCR isolation of microsatellite arrays (PIMA) approach has been proposed by Lunt et al (1999).…”

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Isolation and characterization of 15 microsatellite loci from Caridina gracilipes (Atyidae, Decapoda)

et al. 2008

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Caridina gracilipes, an atyid shrimp of Taiwan, inhabits the fresh and brackish waters. Its life history can be classified into amphidromous and landlocked types. Recent human's transportation has caused concerns of genetic contamination between these long evolved lineages and ecological instabilities. Molecular markers with high sensitivities are required for detecting the possible introgression due to human disturbance. In the study, we described the development of 15 polymorphic microsatellite loci in C. gracilipes for genetic and ecological studies. These new markers were tested in 20 individuals of three populations. The number of alleles ranged from 6 to 17. Expected (H E ) and observed (H O ) heterozygosities ranged from 0.653 to 0.954, averaged at 0.865, and from 0.000 to 0.4, averaged at 0.146, respectively. All loci are significantly deviated from Hardy-Weinberg expectations due to the heterozygote deficiency. Significant genetic differentiation among populations was detected based on F ST values, which were estimated from 0.82 to 0.88.

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“…DNA was purified by standard phenol:chloroform extraction and ethanol precipitation. The isolation of microsatellite markers began with a random amplified polymorphic DNA-polymerase chain reaction (RAPD-PCR) enrichment (Hsu et al 2004;Huang et al 2008;Lin et al 2007Lin et al , 2008. This PIMA (PCR isolation of microsatellite arrays) approach has been proposed by Lunt et al (1999).…”

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Isolation and characterization of microsatellite loci in the commercially important mudshrimp Austinogebia edulis (Upogebiidae) using PCR-based isolation of microsatellite arrays (PIMA)

et al. 2008

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Populations of mudshrimp, Austinogebia edulis, in the intertidal mud flat of western Taiwan have severely declined due to habitat destruction and overfishing in the past decades. Nine polymorphic microsatellite loci were isolated for this ecologically threatened species by using a polymerase chain reaction-based procedure. The number of alleles per locus ranged from five to 14 in 20 specimens from Central West Taiwan. Observed and expected heterozygosities ranged from 0 to 0.2500 (averaged at 0.0944) and 0.7333 to 0.9385 (averaged at 0.8524), respectively. There were significant departures from Hardy-Weinberg expectations. Significant LD was discovered in most loci. These primers may provide a tool for understanding population structure in A. edulis.

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Isolation and characterization of microsatellite loci in Acrossocheilus paradoxus (Cyprinidae) using PCR-based isolation of microsatellite arrays (PIMA)

Cited by 23 publications

References 7 publications

Isolation and characterization of microsatellite loci in Pedicularis verticillata L. using PCR-based isolation of microsatellite arrays (PIMA)

Isolation and characterization of microsatellite loci in Pedicularis verticillata L. using PCR-based isolation of microsatellite arrays (PIMA)

Isolation and characterization of 15 microsatellite loci from Caridina gracilipes (Atyidae, Decapoda)

Isolation and characterization of microsatellite loci in the commercially important mudshrimp Austinogebia edulis (Upogebiidae) using PCR-based isolation of microsatellite arrays (PIMA)

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