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Development and Characterization of 1,827 Expressed Sequence Tag-Derived Simple Sequence Repeat Markers for Ramie (Boehmeria nivea L. Gaud)
Ramie (Boehmeria nivea L. Gaud) is one of the most important natural fiber crops, and improvement of fiber yield and quality is the main goal in efforts to breed superior cultivars. However, efforts aimed at enhancing the understanding of ramie genetics and developing more effective breeding strateg...
Autores principales: | , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Public Library of Science
2013
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3614921/ https://www.ncbi.nlm.nih.gov/pubmed/23565230 http://dx.doi.org/10.1371/journal.pone.0060346 |
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author | Liu, Touming Zhu, Siyuan Fu, Lili Tang, Qingming Yu, Yongting Chen, Ping Luan, Mingbao Wang, Changbiao Tang, Shouwei |
author_facet | Liu, Touming Zhu, Siyuan Fu, Lili Tang, Qingming Yu, Yongting Chen, Ping Luan, Mingbao Wang, Changbiao Tang, Shouwei |
author_sort | Liu, Touming |
collection | PubMed |
description | Ramie (Boehmeria nivea L. Gaud) is one of the most important natural fiber crops, and improvement of fiber yield and quality is the main goal in efforts to breed superior cultivars. However, efforts aimed at enhancing the understanding of ramie genetics and developing more effective breeding strategies have been hampered by the shortage of simple sequence repeat (SSR) markers. In our previous study, we had assembled de novo 43,990 expressed sequence tags (ESTs). In the present study, we searched these previously assembled ESTs for SSRs and identified 1,685 ESTs (3.83%) containing 1,878 SSRs. Next, we designed 1,827 primer pairs complementary to regions flanking these SSRs, and these regions were designated as SSR markers. Among these markers, dinucleotide and trinucleotide repeat motifs were the most abundant types (36.4% and 36.3%, respectively), whereas tetranucleotide, pentanucleotide, and hexanucleotide motifs represented <10% of the markers. The motif AG/CT was the most abundant, accounting for 28.74% of the markers. One hundred EST-SSR markers (97 SSRs located in genes encoding transcription factors and 3 SSRs in genes encoding cellulose synthases) were amplified using polymerase chain reaction for detecting 24 ramie varieties. Of these 100 markers, 98 markers were successfully amplified and 81 markers were polymorphic, with 2–6 alleles among the 24 varieties. Analysis of the genetic diversity of all 24 varieties revealed similarity coefficients that ranged from 0.51 to 0.80. The EST-SSRs developed in this study represent the first large-scale development of SSR markers for ramie. These SSR markers could be used for development of genetic and physical maps, quantitative trait loci mapping, genetic diversity studies, association mapping, and cultivar fingerprinting. |
format | Online Article Text |
id | pubmed-3614921 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2013 |
publisher | Public Library of Science |
record_format | MEDLINE/PubMed |
spelling | pubmed-36149212013-04-05 Development and Characterization of 1,827 Expressed Sequence Tag-Derived Simple Sequence Repeat Markers for Ramie (Boehmeria nivea L. Gaud) Liu, Touming Zhu, Siyuan Fu, Lili Tang, Qingming Yu, Yongting Chen, Ping Luan, Mingbao Wang, Changbiao Tang, Shouwei PLoS One Research Article Ramie (Boehmeria nivea L. Gaud) is one of the most important natural fiber crops, and improvement of fiber yield and quality is the main goal in efforts to breed superior cultivars. However, efforts aimed at enhancing the understanding of ramie genetics and developing more effective breeding strategies have been hampered by the shortage of simple sequence repeat (SSR) markers. In our previous study, we had assembled de novo 43,990 expressed sequence tags (ESTs). In the present study, we searched these previously assembled ESTs for SSRs and identified 1,685 ESTs (3.83%) containing 1,878 SSRs. Next, we designed 1,827 primer pairs complementary to regions flanking these SSRs, and these regions were designated as SSR markers. Among these markers, dinucleotide and trinucleotide repeat motifs were the most abundant types (36.4% and 36.3%, respectively), whereas tetranucleotide, pentanucleotide, and hexanucleotide motifs represented <10% of the markers. The motif AG/CT was the most abundant, accounting for 28.74% of the markers. One hundred EST-SSR markers (97 SSRs located in genes encoding transcription factors and 3 SSRs in genes encoding cellulose synthases) were amplified using polymerase chain reaction for detecting 24 ramie varieties. Of these 100 markers, 98 markers were successfully amplified and 81 markers were polymorphic, with 2–6 alleles among the 24 varieties. Analysis of the genetic diversity of all 24 varieties revealed similarity coefficients that ranged from 0.51 to 0.80. The EST-SSRs developed in this study represent the first large-scale development of SSR markers for ramie. These SSR markers could be used for development of genetic and physical maps, quantitative trait loci mapping, genetic diversity studies, association mapping, and cultivar fingerprinting. Public Library of Science 2013-04-02 /pmc/articles/PMC3614921/ /pubmed/23565230 http://dx.doi.org/10.1371/journal.pone.0060346 Text en © 2013 Liu 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, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are properly credited. |
spellingShingle | Research Article Liu, Touming Zhu, Siyuan Fu, Lili Tang, Qingming Yu, Yongting Chen, Ping Luan, Mingbao Wang, Changbiao Tang, Shouwei Development and Characterization of 1,827 Expressed Sequence Tag-Derived Simple Sequence Repeat Markers for Ramie (Boehmeria nivea L. Gaud) |
title | Development and Characterization of 1,827 Expressed Sequence Tag-Derived Simple Sequence Repeat Markers for Ramie (Boehmeria nivea L. Gaud) |
title_full | Development and Characterization of 1,827 Expressed Sequence Tag-Derived Simple Sequence Repeat Markers for Ramie (Boehmeria nivea L. Gaud) |
title_fullStr | Development and Characterization of 1,827 Expressed Sequence Tag-Derived Simple Sequence Repeat Markers for Ramie (Boehmeria nivea L. Gaud) |
title_full_unstemmed | Development and Characterization of 1,827 Expressed Sequence Tag-Derived Simple Sequence Repeat Markers for Ramie (Boehmeria nivea L. Gaud) |
title_short | Development and Characterization of 1,827 Expressed Sequence Tag-Derived Simple Sequence Repeat Markers for Ramie (Boehmeria nivea L. Gaud) |
title_sort | development and characterization of 1,827 expressed sequence tag-derived simple sequence repeat markers for ramie (boehmeria nivea l. gaud) |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3614921/ https://www.ncbi.nlm.nih.gov/pubmed/23565230 http://dx.doi.org/10.1371/journal.pone.0060346 |
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