Isolation and Characterization of Microsatellite Primers for the Critically Endangered Shrub Styphelia longissima (Ericaceae)

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Abstract

Premise of the study: Microsatellite markers were developed for population genetic analysis in the rare shrub Styphelia longissima (Ericaceae). Methods and Results: We generated ca. 2.5 million sequence reads using a Personal Genome Machine semiconductor sequencer. Using the QDD pipeline, we designed primers for >12,000 sequences with PCR product lengths of 80-480 bp. From these, 30 primer pairs were selected and screened using PCR; of these, 16 loci were found to be polymorphic, four loci were monomorphic, and 10 loci did not amplify reliably for S. longissima. For a sample of 57 plants from the only known population, the number of alleles observed for these 16 loci ranged from two to 21 and expected heterozygosity ranged from 0.49 to 0.91. These markers were also amplified in Astroloma xerophyllum, a closely related species. Conclusions: These markers will be used to characterize population genetic variation, spatial genetic structure, mating system parameters, and dispersal to aid in the management and conservation of the rare shrub S. longissima.

Original languageEnglish
Article number1700108
JournalApplications in Plant Sciences
Volume5
Issue number11
DOIs
Publication statusPublished - 1 Nov 2017

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Styphelia
Ericaceae
shrub
shrubs
microsatellite repeats
population genetics
loci
genetic analysis
semiconductors
reproductive strategy
heterozygosity
genetic structure
genetic variation
aid
allele
genome
mating systems
genetic techniques and protocols
alleles
marker

Cite this

@article{a073e1ab4edc4757a258a8a94add684c,
title = "Isolation and Characterization of Microsatellite Primers for the Critically Endangered Shrub Styphelia longissima (Ericaceae)",
abstract = "Premise of the study: Microsatellite markers were developed for population genetic analysis in the rare shrub Styphelia longissima (Ericaceae). Methods and Results: We generated ca. 2.5 million sequence reads using a Personal Genome Machine semiconductor sequencer. Using the QDD pipeline, we designed primers for >12,000 sequences with PCR product lengths of 80-480 bp. From these, 30 primer pairs were selected and screened using PCR; of these, 16 loci were found to be polymorphic, four loci were monomorphic, and 10 loci did not amplify reliably for S. longissima. For a sample of 57 plants from the only known population, the number of alleles observed for these 16 loci ranged from two to 21 and expected heterozygosity ranged from 0.49 to 0.91. These markers were also amplified in Astroloma xerophyllum, a closely related species. Conclusions: These markers will be used to characterize population genetic variation, spatial genetic structure, mating system parameters, and dispersal to aid in the management and conservation of the rare shrub S. longissima.",
keywords = "Astroloma xerophyllum, Ericaceae, Microsatellite primers, Shotgun sequencing, Styphelia longissima",
author = "Anthony, {Janet M.} and Allcock, {Richard J.N.} and Dobrowolski, {Mark P.} and Krauss, {Siegfried L.}",
year = "2017",
month = "11",
day = "1",
doi = "10.3732/apps.1700108",
language = "English",
volume = "5",
journal = "Applications in Plant Sciences",
issn = "2168-0450",
publisher = "John Wiley & Sons",
number = "11",

}

TY - JOUR

T1 - Isolation and Characterization of Microsatellite Primers for the Critically Endangered Shrub Styphelia longissima (Ericaceae)

AU - Anthony, Janet M.

AU - Allcock, Richard J.N.

AU - Dobrowolski, Mark P.

AU - Krauss, Siegfried L.

PY - 2017/11/1

Y1 - 2017/11/1

N2 - Premise of the study: Microsatellite markers were developed for population genetic analysis in the rare shrub Styphelia longissima (Ericaceae). Methods and Results: We generated ca. 2.5 million sequence reads using a Personal Genome Machine semiconductor sequencer. Using the QDD pipeline, we designed primers for >12,000 sequences with PCR product lengths of 80-480 bp. From these, 30 primer pairs were selected and screened using PCR; of these, 16 loci were found to be polymorphic, four loci were monomorphic, and 10 loci did not amplify reliably for S. longissima. For a sample of 57 plants from the only known population, the number of alleles observed for these 16 loci ranged from two to 21 and expected heterozygosity ranged from 0.49 to 0.91. These markers were also amplified in Astroloma xerophyllum, a closely related species. Conclusions: These markers will be used to characterize population genetic variation, spatial genetic structure, mating system parameters, and dispersal to aid in the management and conservation of the rare shrub S. longissima.

AB - Premise of the study: Microsatellite markers were developed for population genetic analysis in the rare shrub Styphelia longissima (Ericaceae). Methods and Results: We generated ca. 2.5 million sequence reads using a Personal Genome Machine semiconductor sequencer. Using the QDD pipeline, we designed primers for >12,000 sequences with PCR product lengths of 80-480 bp. From these, 30 primer pairs were selected and screened using PCR; of these, 16 loci were found to be polymorphic, four loci were monomorphic, and 10 loci did not amplify reliably for S. longissima. For a sample of 57 plants from the only known population, the number of alleles observed for these 16 loci ranged from two to 21 and expected heterozygosity ranged from 0.49 to 0.91. These markers were also amplified in Astroloma xerophyllum, a closely related species. Conclusions: These markers will be used to characterize population genetic variation, spatial genetic structure, mating system parameters, and dispersal to aid in the management and conservation of the rare shrub S. longissima.

KW - Astroloma xerophyllum

KW - Ericaceae

KW - Microsatellite primers

KW - Shotgun sequencing

KW - Styphelia longissima

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U2 - 10.3732/apps.1700108

DO - 10.3732/apps.1700108

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JO - Applications in Plant Sciences

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SN - 2168-0450

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