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Mining of simple sequence repeats (SSRs) loci and development of novel transferability-across EST-SSR markers from de novo transcriptome assembly of Angelica dahurica

Angelica dahurica is a widely grown plant species with multiple uses, especially in the medical field. However, the frequent introduction of A. dahurica to new areas has made it difficult to distinguish between varieties. Simple sequence repeats (SSRs) detected based on transcriptome analyses are ve...

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Autores principales: Chen, Chen, Chen, Youjun, Huang, Wenjuan, Jiang, Yijie, Zhang, Huihui, Wu, Wei
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6706007/
https://www.ncbi.nlm.nih.gov/pubmed/31437239
http://dx.doi.org/10.1371/journal.pone.0221040
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author Chen, Chen
Chen, Youjun
Huang, Wenjuan
Jiang, Yijie
Zhang, Huihui
Wu, Wei
author_facet Chen, Chen
Chen, Youjun
Huang, Wenjuan
Jiang, Yijie
Zhang, Huihui
Wu, Wei
author_sort Chen, Chen
collection PubMed
description Angelica dahurica is a widely grown plant species with multiple uses, especially in the medical field. However, the frequent introduction of A. dahurica to new areas has made it difficult to distinguish between varieties. Simple sequence repeats (SSRs) detected based on transcriptome analyses are very useful for constructing genetic maps and analyzing genetic diversity. They are also relevant for the molecular marker-assisted breeding of A. dahurica. We identified 33,724 genic SSR loci based on transcriptome sequencing data. A total of 114 primer pairs were designed for the SSR loci and were tested for their specificity and diversity. Ten SSR loci in untranslated regions were ultimately selected. Subsequently, 56 A. dahurica ecotypes collected from different regions were analyzed. The SSR loci comprised 2–8 alleles, with a mean of 5.2 alleles per locus. The polymorphic information content value and Shannon’s information index were 0.6274–0.2702 (average of 0.4091) and 1.3040–0.5618 (average of 0.8475), respectively. Thus, the 10 novel SSRs identified in this study were almost in accordance with Harvey-Weinberg equilibrium and will be useful for analyzing A. dahurica genetic relationships. The results of this study confirm the potential value of transcriptome databases for the development of new SSR markers.
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spelling pubmed-67060072019-09-04 Mining of simple sequence repeats (SSRs) loci and development of novel transferability-across EST-SSR markers from de novo transcriptome assembly of Angelica dahurica Chen, Chen Chen, Youjun Huang, Wenjuan Jiang, Yijie Zhang, Huihui Wu, Wei PLoS One Research Article Angelica dahurica is a widely grown plant species with multiple uses, especially in the medical field. However, the frequent introduction of A. dahurica to new areas has made it difficult to distinguish between varieties. Simple sequence repeats (SSRs) detected based on transcriptome analyses are very useful for constructing genetic maps and analyzing genetic diversity. They are also relevant for the molecular marker-assisted breeding of A. dahurica. We identified 33,724 genic SSR loci based on transcriptome sequencing data. A total of 114 primer pairs were designed for the SSR loci and were tested for their specificity and diversity. Ten SSR loci in untranslated regions were ultimately selected. Subsequently, 56 A. dahurica ecotypes collected from different regions were analyzed. The SSR loci comprised 2–8 alleles, with a mean of 5.2 alleles per locus. The polymorphic information content value and Shannon’s information index were 0.6274–0.2702 (average of 0.4091) and 1.3040–0.5618 (average of 0.8475), respectively. Thus, the 10 novel SSRs identified in this study were almost in accordance with Harvey-Weinberg equilibrium and will be useful for analyzing A. dahurica genetic relationships. The results of this study confirm the potential value of transcriptome databases for the development of new SSR markers. Public Library of Science 2019-08-22 /pmc/articles/PMC6706007/ /pubmed/31437239 http://dx.doi.org/10.1371/journal.pone.0221040 Text en © 2019 Chen et al http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Article
Chen, Chen
Chen, Youjun
Huang, Wenjuan
Jiang, Yijie
Zhang, Huihui
Wu, Wei
Mining of simple sequence repeats (SSRs) loci and development of novel transferability-across EST-SSR markers from de novo transcriptome assembly of Angelica dahurica
title Mining of simple sequence repeats (SSRs) loci and development of novel transferability-across EST-SSR markers from de novo transcriptome assembly of Angelica dahurica
title_full Mining of simple sequence repeats (SSRs) loci and development of novel transferability-across EST-SSR markers from de novo transcriptome assembly of Angelica dahurica
title_fullStr Mining of simple sequence repeats (SSRs) loci and development of novel transferability-across EST-SSR markers from de novo transcriptome assembly of Angelica dahurica
title_full_unstemmed Mining of simple sequence repeats (SSRs) loci and development of novel transferability-across EST-SSR markers from de novo transcriptome assembly of Angelica dahurica
title_short Mining of simple sequence repeats (SSRs) loci and development of novel transferability-across EST-SSR markers from de novo transcriptome assembly of Angelica dahurica
title_sort mining of simple sequence repeats (ssrs) loci and development of novel transferability-across est-ssr markers from de novo transcriptome assembly of angelica dahurica
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6706007/
https://www.ncbi.nlm.nih.gov/pubmed/31437239
http://dx.doi.org/10.1371/journal.pone.0221040
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