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De novo transcriptome assembly and identification of genes related to seed size in common buckwheat (Fagopyrum esculentum M.)
Common buckwheat (Fagopyrum esculentum M.) belongs to the eudicot family Polygonaceae, Fagopyrum Mill, and its seeds have high nutritional value. The mechanism of seed development of common buckwheat remains unclear at the molecular level and no genes related to seed size have been identified. In th...
Autores principales: | , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Japanese Society of Breeding
2019
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6776140/ https://www.ncbi.nlm.nih.gov/pubmed/31598082 http://dx.doi.org/10.1270/jsbbs.18194 |
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author | Fang, Xiaomei Zhang, Yuanli Zhang, Yuke Huang, Kehui Yang, Wenjuan Li, Xiaoyu Zhang, Zhiyong Wu, Kanghong Xu, Xin Ruan, Renwu Yuan, Xiaohui Zhang, Zhengsheng Yi, Zelin |
author_facet | Fang, Xiaomei Zhang, Yuanli Zhang, Yuke Huang, Kehui Yang, Wenjuan Li, Xiaoyu Zhang, Zhiyong Wu, Kanghong Xu, Xin Ruan, Renwu Yuan, Xiaohui Zhang, Zhengsheng Yi, Zelin |
author_sort | Fang, Xiaomei |
collection | PubMed |
description | Common buckwheat (Fagopyrum esculentum M.) belongs to the eudicot family Polygonaceae, Fagopyrum Mill, and its seeds have high nutritional value. The mechanism of seed development of common buckwheat remains unclear at the molecular level and no genes related to seed size have been identified. In this study, we performed genome-wide transcriptome sequencing and analysis using common buckwheat seeds at 5 days post anthesis (DPA) and 10 DPA from two cultivars (large-seeded and small-seeded). A total of 259,895 transcripts were assembled, resulting in 187,034 unigenes with average length of 1097 bp and N50 of 1538 bp. Based on gene expression profiles, 9127 differentially expressed genes (DEGs) were identified and analyzed in GO enrichment and KEGG analysis. In addition, genes related to seed size in the IKU pathway, ubiquitin–proteasome pathway, MAPK signaling pathway, TFs and phytohormones were identified and analyzed. AP2 and bZIP transcription factors, BR-signal and ABA were considered to be important regulators of seed size. This study provides a valuable genetic resource for future identification and functional analysis of candidate genes regulating seed size in common buckwheat and will be useful for improving seed yield in common buckwheat through molecular breeding in the future. |
format | Online Article Text |
id | pubmed-6776140 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2019 |
publisher | Japanese Society of Breeding |
record_format | MEDLINE/PubMed |
spelling | pubmed-67761402019-10-09 De novo transcriptome assembly and identification of genes related to seed size in common buckwheat (Fagopyrum esculentum M.) Fang, Xiaomei Zhang, Yuanli Zhang, Yuke Huang, Kehui Yang, Wenjuan Li, Xiaoyu Zhang, Zhiyong Wu, Kanghong Xu, Xin Ruan, Renwu Yuan, Xiaohui Zhang, Zhengsheng Yi, Zelin Breed Sci Research Paper Common buckwheat (Fagopyrum esculentum M.) belongs to the eudicot family Polygonaceae, Fagopyrum Mill, and its seeds have high nutritional value. The mechanism of seed development of common buckwheat remains unclear at the molecular level and no genes related to seed size have been identified. In this study, we performed genome-wide transcriptome sequencing and analysis using common buckwheat seeds at 5 days post anthesis (DPA) and 10 DPA from two cultivars (large-seeded and small-seeded). A total of 259,895 transcripts were assembled, resulting in 187,034 unigenes with average length of 1097 bp and N50 of 1538 bp. Based on gene expression profiles, 9127 differentially expressed genes (DEGs) were identified and analyzed in GO enrichment and KEGG analysis. In addition, genes related to seed size in the IKU pathway, ubiquitin–proteasome pathway, MAPK signaling pathway, TFs and phytohormones were identified and analyzed. AP2 and bZIP transcription factors, BR-signal and ABA were considered to be important regulators of seed size. This study provides a valuable genetic resource for future identification and functional analysis of candidate genes regulating seed size in common buckwheat and will be useful for improving seed yield in common buckwheat through molecular breeding in the future. Japanese Society of Breeding 2019-09 2019-08-02 /pmc/articles/PMC6776140/ /pubmed/31598082 http://dx.doi.org/10.1270/jsbbs.18194 Text en Copyright © 2019 by JAPANESE SOCIETY OF BREEDING http://creativecommons.org/licenses/by-nc-nd/3.0 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 work is properly cited. |
spellingShingle | Research Paper Fang, Xiaomei Zhang, Yuanli Zhang, Yuke Huang, Kehui Yang, Wenjuan Li, Xiaoyu Zhang, Zhiyong Wu, Kanghong Xu, Xin Ruan, Renwu Yuan, Xiaohui Zhang, Zhengsheng Yi, Zelin De novo transcriptome assembly and identification of genes related to seed size in common buckwheat (Fagopyrum esculentum M.) |
title | De novo transcriptome assembly and identification of genes related to seed size in common buckwheat (Fagopyrum esculentum M.) |
title_full | De novo transcriptome assembly and identification of genes related to seed size in common buckwheat (Fagopyrum esculentum M.) |
title_fullStr | De novo transcriptome assembly and identification of genes related to seed size in common buckwheat (Fagopyrum esculentum M.) |
title_full_unstemmed | De novo transcriptome assembly and identification of genes related to seed size in common buckwheat (Fagopyrum esculentum M.) |
title_short | De novo transcriptome assembly and identification of genes related to seed size in common buckwheat (Fagopyrum esculentum M.) |
title_sort | de novo transcriptome assembly and identification of genes related to seed size in common buckwheat (fagopyrum esculentum m.) |
topic | Research Paper |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6776140/ https://www.ncbi.nlm.nih.gov/pubmed/31598082 http://dx.doi.org/10.1270/jsbbs.18194 |
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