Development of 15 nuclear microsatellite markers in the genus Dyckia (Pitcairnioideae; Bromeliaceae) using 454 pyrosequencing

Wöhrmann, Tina; Pinangé, Diego Sotero de Barros; Krapp, Florian; Benko‐Iseppon, Ana Maria; Huettel, Bruno; Weising, Kurt

doi:10.1007/s12686-012-9738-y

Cited by 10 publications

(7 citation statements)

References 10 publications

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“…A popular use of NGS data is the discovery of large numbers of molecular markers for population genetic studies (Pashley, 2006 ; Wöhrmann et al, 2012 ; Lopez et al, 2015 ; Tanwar et al, 2017 ). The accurate assessment of genetic variation within and across species is pivotal in studies addressing topics like evolution, phylogeny and/or conservation and the larger the marker data set used, the more accurate the results and extrapolations are.…”

Section: Introductionmentioning

confidence: 99%

Molecular Resources from Transcriptomes in the Brassicaceae Family

et al. 2017

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The rapidly falling costs and the increasing availability of large DNA sequence data sets facilitate the fast and affordable mining of large molecular markers data sets for comprehensive evolutionary studies. The Brassicaceae (mustards) are an important species-rich family in the plant kingdom with taxa distributed worldwide and a complex evolutionary history. We performed Simple Sequence Repeats (SSRs) mining using de novo assembled transcriptomes from 19 species across the Brassicaceae in order to study SSR evolution and provide comprehensive sets of molecular markers for genetic studies within the family. Moreover, we selected the genus Cochlearia to test the transferability and polymorphism of these markers among species. Additionally, we annotated Cochlearia pyrenaica transcriptome in order to identify the position of each of the mined SSRs. While we introduce a new set of tools that will further enable evolutionary studies across the Brassicaceae, we also discuss some broader aspects of SSR evolution. Overall, we developed 2012 ready-to-use SSR markers with their respective primers in 19 Brassicaceae species and a high quality annotated transcriptome for C. pyrenaica. As indicated by our transferability test with the genus Cochlearia these SSRs are transferable to species within the genus increasing exponentially the number of targeted species. Also, our polymorphism results showed substantial levels of variability for these markers. Finally, despite its complex evolutionary history, SSR evolution across the Brassicaceae family is highly conserved and we found no deviation from patterns reported in other Angiosperms.

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Section: Introductionmentioning

confidence: 99%

Molecular Resources from Transcriptomes in the Brassicaceae Family

et al. 2017

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“…Previous studies involving the development and crossamplification of SSRs markers in Bromeliaceae have primarily focused on species of the Tillandsioideae (Boneh et al 2003;Palma-Silva et al 2007;Lavor et al 2013;Neri et al 2015) and Pitcairnioideae subfamilies (Sarthou et al 2003;Paggi et al 2008;Krapp et al 2012;Miranda et al 2012;Wöhrmann et al 2012Wöhrmann et al , 2013Zanella et al 2012;Hmeljevski et al 2013). Few studies have focused on the species in the subfamily Bromelioideae (Goetze et al 2013;Krapp et al 2013;Aoki-Gonçalves et al 2014).…”

Section: Introductionmentioning

confidence: 99%

Cross-amplification of nuclear microsatellite markers in two species of Cryptanthus Otto & A. Dietr. (Bromeliaceae)

et al. 2017

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Thirty-eight nuclear microsatellite loci originally developed for Aechmea caudata Lindm., Orthophytum ophiuroides Louzada & Wand., Pitcairnia albiflos Herb., Vriesea gigantea (Gaud.) and V. simplex (Vell.) Beer were tested in Cryptanthus burle-marxii Leme and C. zonatus (Vis.) Vis. Of the 38 loci tested, 13 were polymorphic. Ten polymorphic microsatellite loci were selected to be amplified and genotyped in one population each of C. burle-marxii and C. zonatus. The observed and expected heterozygosity per locus in the C. burle-marxii population ranged from 0.050 to 0.850 and 0.050 to 0.770, respectively. In C. zonatus, the observed and expected heterozygosity per locus ranged from 0.167 to 0.846 and 0.290 to 0.692, respectively. The O. ophiuroides locus Op52 for the C. zonatus population and P. albiflos locus PaC05 for the two species showed significant departure from HWE. These ten polymorphic loci tested will be used to assess the genetic diversity and structure of the two species of Cryptanthus.

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“…The majority of the microsatellite markers developed for Bromeliaceae focus on rock-outcrop species (i.e. Pitcairnia - Sarthou et al, 2003;Paggi et al, 2008;Alcantarea -Palma-Silva et al, 2007;Dyckia -Zanella et al, 2012;Wohrmann et al, 2013;Fosterella -Wohrmann et al, 2012;Encholirium -Hmeljevski et al, 2013;Orthophytum -Aoki-Gonçalves et al, 2014). At present, only 10 microsatellite loci are available for the genus Vriesea (PalmaSilva et al, 2007).…”

Section: Introductionmentioning

confidence: 99%

Development and characterization of microsatellite markers for Vriesea simplex (Bromeliaceae) and cross-amplification in other species of Bromeliaceae

Neri

Nazareno

Wendt

et al. 2015

Biochemical Systematics and Ecology

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a b s t r a c tTen polymorphic microsatellite loci were isolated and characterized for Vriesea simplex epiphytic and endemic species from the Brazilian Atlantic Rainforest. The number of alleles per locus ranged from 2 to 16. The observed and expected heterozygosity ranged from 0.000 to 0.414 and 0.068 to 0.795, respectively. All loci departed significantly from HardyeWeinberg equilibrium. Linkage disequilibrium was not detected in any pair of loci. Transferability of 10 loci was positive across ten other Bromeliaceae species. The loci will be used for studying population genetic structure, mating system variation, and the origin and maintenance of reproductive barriers to gene exchange among sympatric Vriesea species.

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Development of 15 nuclear microsatellite markers in the genus Dyckia (Pitcairnioideae; Bromeliaceae) using 454 pyrosequencing

Cited by 10 publications

References 10 publications

Molecular Resources from Transcriptomes in the Brassicaceae Family

Molecular Resources from Transcriptomes in the Brassicaceae Family

Cross-amplification of nuclear microsatellite markers in two species of Cryptanthus Otto & A. Dietr. (Bromeliaceae)

Development and characterization of microsatellite markers for Vriesea simplex (Bromeliaceae) and cross-amplification in other species of Bromeliaceae

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