Dataset Information

Development of polymorphic simple sequence repeat markers in Huperzia serrata (Lycopodiaceae).

ABSTRACT: Premise:The natural population size of Huperzia serrata (Lycopodiaceae) has dramatically decreased and the species has become endangered due to overexploitation. Here, we developed simple sequence repeat (SSR) markers for H. serrata to survey both its genetic diversity and population structure. Methods and Results:Based on 177 individuals, 120 SSR primer pairs were developed and optimized from five regions of the H. serrata transcriptomic data. Of these primer pairs, 20 were successfully amplified and 10 showed obvious polymorphism. These polymorphic loci were investigated to study the genetic diversity of H. serrata. Two to 11 alleles per locus were identified, the level of observed heterozygosity ranged from 0.00 to 1.00, and the level of expected heterozygosity ranged from 0.19 to 0.79. All loci were successfully amplified in H. crispata, H. sutchueniana, and H. selago. Conclusions:The 10 polymorphic primer pairs developed here will be valuable for studies of the endangered H. serrata and other related species.

SUBMITTER: Guo B

PROVIDER: S-EPMC6636615 | biostudies-literature | 2019 Jul

REPOSITORIES: biostudies-literature

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Development of polymorphic simple sequence repeat markers in <i>Huperzia serrata</i> (Lycopodiaceae).

Guo Bin B Ren Jing-Yu JY He Mei-Na MN Yao Kai K Wang Tian-Shu TS Wang Li-Qing LQ Liu Xin X He Wei W Fu Yan-Ping YP Wang De-Li DL Wei Ya-Hui YH

Applications in plant sciences 20190712 7

<h4>Premise</h4>The natural population size of <i>Huperzia serrata</i> (Lycopodiaceae) has dramatically decreased and the species has become endangered due to overexploitation. Here, we developed simple sequence repeat (SSR) markers for <i>H. serrata</i> to survey both its genetic diversity and population structure.<h4>Methods and results</h4>Based on 177 individuals, 120 SSR primer pairs were developed and optimized from five regions of the <i>H. serrata</i> transcriptomic data. Of these primer ...[more]

PMID: 31346505

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Project description:BackgroundVicia bungei is an economically important forage crop in South Korea and China. Although detailed genetic and genomic data can improve population genetic studies, conservation efforts, and improved breeding of crops, few such data are available for Vicia species in general and none at all for V. bungei. Therefore, the main objectives of this study were to sequence, assemble, and annotate V. bungei chloroplast genome and to identify simple sequence repeats (SSRs) as polymorphic genetic markers.ResultsThe whole-genome sequence of V. bungei was generated using an Illumina MiSeq platform. De novo assembly of complete chloroplast genome sequences was performed for the low-coverage sequence using CLC Genome Assembler with a 200-600-bp overlap size. Vicia bungei chloroplast genome was 130,796-bp long. The genome lacked an inverted repeat unit and thus resembled those of species in the inverted repeat-lacking clade within Fabaceae. Genome annotation using Dual OrganellarGenoMe Annotator (DOGMA) identified 107 genes, comprising 75 protein-coding, 28 transfer RNA, and 4 ribosomal RNA genes. In total, 432 SSRs were detected in V. bungei chloroplast genome, including 64 mononucleotides, 14 dinucleotides, 5 trinucleotides, 4 tetranucleotides, 233 pentanucleotides, 90 hexanucleotides, and 14 complex repeated motifs. These were used to develop 232 novel chloroplast SSR markers, 39 of which were chosen at random to test amplification and genetic diversity in Vicia species (20 accessions from seven species). The unweighted pair group method with arithmetic mean cluster analysis identified seven clusters at the interspecies level and intraspecific differences within clusters.ConclusionThe complete chloroplast genome sequence of V. bungei was determined. This reference genome should facilitate chloroplast resequencing and future searches for additional genetic markers using population samples. The novel chloroplast genome resources and SSR markers will greatly contribute to the conservation of the genus Vicia and facilitate genetic and evolutionary studies of this genus and of other higher plants.

Dataset Information

Development of polymorphic simple sequence repeat markers in Huperzia serrata (Lycopodiaceae).

Publications

Development of polymorphic simple sequence repeat markers in <i>Huperzia serrata</i> (Lycopodiaceae).

Similar Datasets

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