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RNA-Seq and iTRAQ reveal multiple pathways involved in storage root formation and development in sweet potato (Ipomoea batatas L.)

BACKGROUND: Sweet potato (Ipomoea batatas L.) is the sixth most important food crop in the world. The formation and development of storage roots in sweet potato is a highly complicated and genetically programmed process. However, the underlying mechanisms of storage root development have not yet bee...

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Autores principales: Dong, Tingting, Zhu, Mingku, Yu, Jiawen, Han, Rongpeng, Tang, Cheng, Xu, Tao, Liu, Jingran, Li, Zongyun
Formato: Online Artículo Texto
Lenguaje:English
Publicado: BioMed Central 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6458706/
https://www.ncbi.nlm.nih.gov/pubmed/30971210
http://dx.doi.org/10.1186/s12870-019-1731-0
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author Dong, Tingting
Zhu, Mingku
Yu, Jiawen
Han, Rongpeng
Tang, Cheng
Xu, Tao
Liu, Jingran
Li, Zongyun
author_facet Dong, Tingting
Zhu, Mingku
Yu, Jiawen
Han, Rongpeng
Tang, Cheng
Xu, Tao
Liu, Jingran
Li, Zongyun
author_sort Dong, Tingting
collection PubMed
description BACKGROUND: Sweet potato (Ipomoea batatas L.) is the sixth most important food crop in the world. The formation and development of storage roots in sweet potato is a highly complicated and genetically programmed process. However, the underlying mechanisms of storage root development have not yet been elucidated. RESULTS: To better understand the molecular mechanisms involved in storage root development, a combined analysis of the transcriptome and proteome of sweet potato fibrous roots (F) and storage roots at four different stages (D1, D3, D5 and D10) was performed in the present study. A total of 26,273 differentially expressed genes were identified in a comparison between the fibrous root library and four storage root libraries, while 2558 proteins showed a 1.0-fold or greater expression difference as indicated by isobaric tags for relative and absolute quantitation (iTRAQ) analysis. The combination of the transcriptome and proteome analyses and morphological and physiological data revealed several critical pathways involved in storage root formation and development. First, genes/proteins involved in the development of meristems/cambia and starch biosynthesis were all significantly upregulated in storage roots compared with fibrous roots. Second, multiple phytohormones and the genes related to their biosynthesis showed differential expression between fibrous roots and storage roots. Third, a large number of transcription factors were differentially expressed during storage root initiation and development, which suggests the importance of transcription factor regulation in the development of storage roots. Fourth, inconsistent gene expression was found between the transcriptome and proteome data, which indicated posttranscriptional regulatory activity during the development of storage roots. CONCLUSION: Overall, these results reveal multiple events associated with storage root development and provide new insights into the molecular mechanisms underlying the regulatory networks involved in storage root development. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12870-019-1731-0) contains supplementary material, which is available to authorized users.
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spelling pubmed-64587062019-04-19 RNA-Seq and iTRAQ reveal multiple pathways involved in storage root formation and development in sweet potato (Ipomoea batatas L.) Dong, Tingting Zhu, Mingku Yu, Jiawen Han, Rongpeng Tang, Cheng Xu, Tao Liu, Jingran Li, Zongyun BMC Plant Biol Research Article BACKGROUND: Sweet potato (Ipomoea batatas L.) is the sixth most important food crop in the world. The formation and development of storage roots in sweet potato is a highly complicated and genetically programmed process. However, the underlying mechanisms of storage root development have not yet been elucidated. RESULTS: To better understand the molecular mechanisms involved in storage root development, a combined analysis of the transcriptome and proteome of sweet potato fibrous roots (F) and storage roots at four different stages (D1, D3, D5 and D10) was performed in the present study. A total of 26,273 differentially expressed genes were identified in a comparison between the fibrous root library and four storage root libraries, while 2558 proteins showed a 1.0-fold or greater expression difference as indicated by isobaric tags for relative and absolute quantitation (iTRAQ) analysis. The combination of the transcriptome and proteome analyses and morphological and physiological data revealed several critical pathways involved in storage root formation and development. First, genes/proteins involved in the development of meristems/cambia and starch biosynthesis were all significantly upregulated in storage roots compared with fibrous roots. Second, multiple phytohormones and the genes related to their biosynthesis showed differential expression between fibrous roots and storage roots. Third, a large number of transcription factors were differentially expressed during storage root initiation and development, which suggests the importance of transcription factor regulation in the development of storage roots. Fourth, inconsistent gene expression was found between the transcriptome and proteome data, which indicated posttranscriptional regulatory activity during the development of storage roots. CONCLUSION: Overall, these results reveal multiple events associated with storage root development and provide new insights into the molecular mechanisms underlying the regulatory networks involved in storage root development. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (10.1186/s12870-019-1731-0) contains supplementary material, which is available to authorized users. BioMed Central 2019-04-11 /pmc/articles/PMC6458706/ /pubmed/30971210 http://dx.doi.org/10.1186/s12870-019-1731-0 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
Dong, Tingting
Zhu, Mingku
Yu, Jiawen
Han, Rongpeng
Tang, Cheng
Xu, Tao
Liu, Jingran
Li, Zongyun
RNA-Seq and iTRAQ reveal multiple pathways involved in storage root formation and development in sweet potato (Ipomoea batatas L.)
title RNA-Seq and iTRAQ reveal multiple pathways involved in storage root formation and development in sweet potato (Ipomoea batatas L.)
title_full RNA-Seq and iTRAQ reveal multiple pathways involved in storage root formation and development in sweet potato (Ipomoea batatas L.)
title_fullStr RNA-Seq and iTRAQ reveal multiple pathways involved in storage root formation and development in sweet potato (Ipomoea batatas L.)
title_full_unstemmed RNA-Seq and iTRAQ reveal multiple pathways involved in storage root formation and development in sweet potato (Ipomoea batatas L.)
title_short RNA-Seq and iTRAQ reveal multiple pathways involved in storage root formation and development in sweet potato (Ipomoea batatas L.)
title_sort rna-seq and itraq reveal multiple pathways involved in storage root formation and development in sweet potato (ipomoea batatas l.)
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6458706/
https://www.ncbi.nlm.nih.gov/pubmed/30971210
http://dx.doi.org/10.1186/s12870-019-1731-0
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