Dataset Information

Development of highly variable microsatellite markers for the tetraploid Silene stellata (Caryophyllaceae).

ABSTRACT: PREMISE OF THE STUDY:We designed and tested microsatellite markers for the North American native species Silene stellata (Caryophyllaceae) to investigate its population genetic structure and identify selection on floral design through male reproductive success. METHODS AND RESULTS:A total of 153 candidate microsatellite loci were isolated based on next-generation sequencing. We identified 18 polymorphic microsatellite loci in three populations of S. stellata, with di- or trinucleotide repeats. Genotyping results showed the number of alleles per locus ranged from six to 45 and expected heterozygosity ranged from 0.511 to 0.951. Five of these loci were successfully amplified in S. virginica and S. caroliniana and were also polymorphic. CONCLUSIONS:The microsatellite markers reported here provide a valuable tool for paternity analysis in S. stellata. They will also be useful for investigating the population genetic structures of S. stellata and related species.

SUBMITTER: Zhou J

PROVIDER: S-EPMC5238704 | biostudies-literature | 2016 Dec

REPOSITORIES: biostudies-literature

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Development of highly variable microsatellite markers for the tetraploid <i>Silene stellata</i> (Caryophyllaceae).

Zhou Juannan J Dudash Michele R MR Fenster Charles B CB Zimmer Elizabeth A EA

Applications in plant sciences 20161208 12

<h4>Premise of the study</h4>We designed and tested microsatellite markers for the North American native species <i>Silene stellata</i> (Caryophyllaceae) to investigate its population genetic structure and identify selection on floral design through male reproductive success.<h4>Methods and results</h4>A total of 153 candidate microsatellite loci were isolated based on next-generation sequencing. We identified 18 polymorphic microsatellite loci in three populations of <i>S. stellata</i>, with di ...[more]

PMID: 28101439

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Project description:BACKGROUND:Lychnis kiusiana Makino is an endangered perennial herb native to wetland areas in Korea and Japan. Despite its conservational and evolutionary significance, population genetic resources are lacking for this species. Next-generation sequencing has been accepted as a rapid and cost-effective solution for the identification of microsatellite markers in nonmodel plants. RESULTS:Using Illumina HiSeq 2000 sequencing technology, we assembled 67,498,600 reads into 91,900 contigs and identified 11,403 microsatellite repeat motifs in 9563 contigs. A total of 4510 microsatellite-containing transcripts had Gene Ontology (GO) annotations, and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis identified 124 pathways with significant scores. Many microsatellites in the L. kiusiana leaf transcriptome were linked to genes involved in the plant response to light intensity, salt stress, temperature stimulus, and nutrient and water deprivation. A total of 12,486 single-nucleotide polymorphisms (SNPs) were identified on transcripts harboring microsatellites. The analysis of nucleotide substitution rates for 2389 unigenes indicated that 39 genes were under strong positive selection. The primers of 6911 microsatellites were designed, and 40 of 50 selected primer pairs were consistently and successfully amplified from 51 individuals. Twenty-five of these were polymorphic, and the average number of alleles per SSR locus was 6.96, with a range from 2 to 15. The observed and expected heterozygosities ranged from 0.137 to 0.902 and 0.131 to 0.827, respectively, and locus-specific FIS estimates ranged from -?0.116 to 0.290. Eleven of the 25 primer pairs were successfully amplified in three additional species of Lychnis: 56% in L. wilfordii, 64% in L. cognata and 80% in L. fulgens. CONCLUSIONS:The transcriptomic SSR markers of Lychnis kiusiana provide a valuable resource for understanding the population genetics, evolutionary history, and effective conservation management of this species. Furthermore, the identified microsatellite loci linked to the annotated genes should be useful for developing functional markers of L. kiusiana. The developed markers represent a potentially valuable source of transcriptomic SSR markers for population genetic analyses with moderate levels of cross-taxon portability.

Dataset Information

Development of highly variable microsatellite markers for the tetraploid Silene stellata (Caryophyllaceae).

Publications

Development of highly variable microsatellite markers for the tetraploid <i>Silene stellata</i> (Caryophyllaceae).

Similar Datasets

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