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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...

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Autores principales: 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
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Japanese Society of Breeding 2019
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.
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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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