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Elymus nutans genes for seed shattering and candidate gene-derived EST-SSR markers for germplasm evaluation
BACKGROUND: Elymus nutans and E. sibiricus are two important forage grasses of the genus Elymus. But they are difficult to grow for commercial seed production due to serious seed shattering. We conducted a comparative transcriptome analysis of abscission zone to find possible transcription changes a...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2019
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6416926/ https://www.ncbi.nlm.nih.gov/pubmed/30866819 http://dx.doi.org/10.1186/s12870-019-1691-4 |
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author | Zhao, Yongqiang Zhang, Junchao Zhang, Zongyu Xie, Wengang |
author_facet | Zhao, Yongqiang Zhang, Junchao Zhang, Zongyu Xie, Wengang |
author_sort | Zhao, Yongqiang |
collection | PubMed |
description | BACKGROUND: Elymus nutans and E. sibiricus are two important forage grasses of the genus Elymus. But they are difficult to grow for commercial seed production due to serious seed shattering. We conducted a comparative transcriptome analysis of abscission zone to find possible transcription changes associated with seed shattering, explore candidate genes involved in seed shattering and identify candidate gene-based EST-SSR markers for germplasm evaluation. RESULTS: cDNA libraries from abscission zone (AZ) and non-abscission zone (NAZ) tissues of E. nutans were constructed and sequenced. A total of 111,667 unigenes were annotated and 7644 differentially expressed transcripts (DETs) were predicted, corresponding to 6936 up-regulated in AZ and 708 down-regulated in NAZ. We identified 489 candidate genes related to transcription factor, cell wall hydrolysis or modification, hydrolase activity, phytohormone signaling and response, lignin biosynthesis, and signal transduction or protein turnover. Eleven similar candidate genes involved in polygalacturonase activity, hydrolase activity, and mitogen-activated protein kinase were up-regulated in the abscission zone of the two Elymus species, suggesting these genes may have specific function for abscission zone development and seed shattering. A total of 67 polymorphic EST-SSR markers were developed and characterized based on the sequences of these candidate genes. Fourteen polymorphic EST-SSR primers were finally used to study genetic diversity in 48 E. nutans genotypes with contrasting seed shattering habit. The dendrogram based on molecular data showed that most accessions with similar seed shattering degree tended to group together. CONCLUSIONS: The expression data generated from this study provides an important resource for future molecular biological research. Many DETs were associated with abscission zone development, and EST-SSR loci related to candidate genes may have potential application in identifying trait-associated markers in E. nutans in the future. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12870-019-1691-4) contains supplementary material, which is available to authorized users. |
format | Online Article Text |
id | pubmed-6416926 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-64169262019-03-25 Elymus nutans genes for seed shattering and candidate gene-derived EST-SSR markers for germplasm evaluation Zhao, Yongqiang Zhang, Junchao Zhang, Zongyu Xie, Wengang BMC Plant Biol Research Article BACKGROUND: Elymus nutans and E. sibiricus are two important forage grasses of the genus Elymus. But they are difficult to grow for commercial seed production due to serious seed shattering. We conducted a comparative transcriptome analysis of abscission zone to find possible transcription changes associated with seed shattering, explore candidate genes involved in seed shattering and identify candidate gene-based EST-SSR markers for germplasm evaluation. RESULTS: cDNA libraries from abscission zone (AZ) and non-abscission zone (NAZ) tissues of E. nutans were constructed and sequenced. A total of 111,667 unigenes were annotated and 7644 differentially expressed transcripts (DETs) were predicted, corresponding to 6936 up-regulated in AZ and 708 down-regulated in NAZ. We identified 489 candidate genes related to transcription factor, cell wall hydrolysis or modification, hydrolase activity, phytohormone signaling and response, lignin biosynthesis, and signal transduction or protein turnover. Eleven similar candidate genes involved in polygalacturonase activity, hydrolase activity, and mitogen-activated protein kinase were up-regulated in the abscission zone of the two Elymus species, suggesting these genes may have specific function for abscission zone development and seed shattering. A total of 67 polymorphic EST-SSR markers were developed and characterized based on the sequences of these candidate genes. Fourteen polymorphic EST-SSR primers were finally used to study genetic diversity in 48 E. nutans genotypes with contrasting seed shattering habit. The dendrogram based on molecular data showed that most accessions with similar seed shattering degree tended to group together. CONCLUSIONS: The expression data generated from this study provides an important resource for future molecular biological research. Many DETs were associated with abscission zone development, and EST-SSR loci related to candidate genes may have potential application in identifying trait-associated markers in E. nutans in the future. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12870-019-1691-4) contains supplementary material, which is available to authorized users. BioMed Central 2019-03-13 /pmc/articles/PMC6416926/ /pubmed/30866819 http://dx.doi.org/10.1186/s12870-019-1691-4 Text en © The Author(s). 2019 Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. |
spellingShingle | Research Article Zhao, Yongqiang Zhang, Junchao Zhang, Zongyu Xie, Wengang Elymus nutans genes for seed shattering and candidate gene-derived EST-SSR markers for germplasm evaluation |
title | Elymus nutans genes for seed shattering and candidate gene-derived EST-SSR markers for germplasm evaluation |
title_full | Elymus nutans genes for seed shattering and candidate gene-derived EST-SSR markers for germplasm evaluation |
title_fullStr | Elymus nutans genes for seed shattering and candidate gene-derived EST-SSR markers for germplasm evaluation |
title_full_unstemmed | Elymus nutans genes for seed shattering and candidate gene-derived EST-SSR markers for germplasm evaluation |
title_short | Elymus nutans genes for seed shattering and candidate gene-derived EST-SSR markers for germplasm evaluation |
title_sort | elymus nutans genes for seed shattering and candidate gene-derived est-ssr markers for germplasm evaluation |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6416926/ https://www.ncbi.nlm.nih.gov/pubmed/30866819 http://dx.doi.org/10.1186/s12870-019-1691-4 |
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