Dataset Information

Development, characterization, and transferability of SSR markers for Vriesea carinata (Bromeliaceae) based on RNA sequencing.

ABSTRACT: Premise of the Study:Expressed sequence tag-simple sequence repeat (EST-SSR) markers were isolated for Vriesea carinata, an endemic bromeliad from the Brazilian Atlantic Forest. These SSR loci may be used to investigate the genetic diversity and population structure of this species and related bromeliads. Methods and Results:Based on the transcriptome data of V. carinata, 30 primer pairs were designed and selected for initial validation. Of these primer pairs, 16 generated suitable SSR loci in 69 individuals. The number of alleles per locus ranged from one to 13; the levels of observed and expected heterozygosity per locus ranged from 0.000 to 1.000 and from 0.000 to 0.935, respectively. All loci produced heterologous amplification. Transferability of the loci was tested in 15 species belonging to three Bromeliaceae subfamilies. Conclusions:The developed EST-SSR markers revealed polymorphism in the four studied populations and could be useful to investigate the genetic diversity of V. carinata and related species. The markers may also be suitable for novel gene annotation and discovery.

SUBMITTER: Todeschini CC

PROVIDER: S-EPMC6201730 | biostudies-literature | 2018 Oct

REPOSITORIES: biostudies-literature

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Development, characterization, and transferability of SSR markers for <i>Vriesea carinata</i> (Bromeliaceae) based on RNA sequencing.

Todeschini Cristina C CC Parizotto José L B JLB Guzman Frank F Zanella Camila M CM Margis Rogério R Goetze Márcia M Paggi Gecele M GM Santana Costa Laís M LM de Aguiar Melo Camila C Hirsch Luiza D LD Bered Fernanda F

Applications in plant sciences 20181016 10

<h4>Premise of the study</h4>Expressed sequence tag-simple sequence repeat (EST-SSR) markers were isolated for <i>Vriesea carinata</i>, an endemic bromeliad from the Brazilian Atlantic Forest. These SSR loci may be used to investigate the genetic diversity and population structure of this species and related bromeliads.<h4>Methods and results</h4>Based on the transcriptome data of <i>V. carinata</i>, 30 primer pairs were designed and selected for initial validation. Of these primer pairs, 16 gen ...[more]

PMID: 30386710

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Project description:BackgroundCarex L. is one of the largest genera in the Cyperaceae family and an important vascular plant in the ecosystem. However, the genetic background of Carex is complex and the classification is not clear. In order to investigate the gene function annotation of Carex, RNA-sequencing analysis was performed. Simple sequence repeats (SSRs) were generated based on the Illumina data and then were utilized to investigate the genetic characteristics of the 79 Carex germplasms.ResultsIn this study, 36,403 unigenes with a total length of 41,724,615 bp were obtained and annotated based on GO, KOG, KEGG, NR databases. The results provide a theoretical basis for gene function exploration. Out of 8776 SSRs, 96 pairs of primers were randomly selected. One hundred eighty polymorphic bands were amplified with a polymorphism rate of 100% based on 42 pairs of primers with higher polymorphism levels. The average band number was 4.3 per primer, the average distance value was 0.548, and the polymorphic information content was ranged from 0.133 to 0.494. The number of observed alleles (Na), effective alleles (Ne), Nei's (1973) gene diversity (H), and the Shannon information index (I) were 2.000, 1.376, 0.243, and 0.391, respectively. NJ clustering divided into three groups and the accessions from New Zealand showed a similar genetic attribute and clustered into one group. UPGMA and PCoA analysis also revealed the same result. The analysis of molecular variance (AMOVA) revealed a superior genetic diversity within accessions than between accessions based on geographic origin cluster and NJ cluster. What's more, the fingerprints of 79 Carex species are established in this study. Different combinations of primer pairs can be used to identify multiple Carex at one time, which overcomes the difficulties of traditional identification methods.ConclusionsThe transcriptomic analysis shed new light on the function categories from the annotated genes and will facilitate future gene functional studies. The genetic characteristics analysis indicated that gene flow was extensive among 79 Carex species. These markers can be used to investigate the evolutionary history of Carex and related species, as well as to serve as a guide in future breeding projects.

Dataset Information

Development, characterization, and transferability of SSR markers for Vriesea carinata (Bromeliaceae) based on RNA sequencing.

Publications

Development, characterization, and transferability of SSR markers for <i>Vriesea carinata</i> (Bromeliaceae) based on RNA sequencing.

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