Cargando…

Root Transcriptomic Analysis Revealing the Importance of Energy Metabolism to the Development of Deep Roots in Rice (Oryza sativa L.)

Drought is the most serious abiotic stress limiting rice production, and deep root is the key contributor to drought avoidance. However, the genetic mechanism regulating the development of deep roots is largely unknown. In this study, the transcriptomes of 74 root samples from 37 rice varieties, rep...

Descripción completa

Detalles Bibliográficos
Autores principales: Lou, Qiaojun, Chen, Liang, Mei, Hanwei, Xu, Kai, Wei, Haibin, Feng, Fangjun, Li, Tiemei, Pang, Xiaomeng, Shi, Caiping, Luo, Lijun, Zhong, Yang
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2017
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5526896/
https://www.ncbi.nlm.nih.gov/pubmed/28798764
http://dx.doi.org/10.3389/fpls.2017.01314
_version_ 1783252870301220864
author Lou, Qiaojun
Chen, Liang
Mei, Hanwei
Xu, Kai
Wei, Haibin
Feng, Fangjun
Li, Tiemei
Pang, Xiaomeng
Shi, Caiping
Luo, Lijun
Zhong, Yang
author_facet Lou, Qiaojun
Chen, Liang
Mei, Hanwei
Xu, Kai
Wei, Haibin
Feng, Fangjun
Li, Tiemei
Pang, Xiaomeng
Shi, Caiping
Luo, Lijun
Zhong, Yang
author_sort Lou, Qiaojun
collection PubMed
description Drought is the most serious abiotic stress limiting rice production, and deep root is the key contributor to drought avoidance. However, the genetic mechanism regulating the development of deep roots is largely unknown. In this study, the transcriptomes of 74 root samples from 37 rice varieties, representing the extreme genotypes of shallow or deep rooting, were surveyed by RNA-seq. The 13,242 differentially expressed genes (DEGs) between deep rooting and shallow rooting varieties (H vs. L) were enriched in the pathway of genetic information processing and metabolism, while the 1,052 DEGs between the deep roots and shallow roots from each of the plants (D vs. S) were significantly enriched in metabolic pathways especially energy metabolism. Ten quantitative trait transcripts (QTTs) were identified and some were involved in energy metabolism. Forty-nine candidate DEGs were confirmed by qRT-PCR and microarray. Through weighted gene co-expression network analysis (WGCNA), we found 18 hub genes. Surprisingly, all these hub genes expressed higher in deep roots than in shallow roots, furthermore half of them functioned in energy metabolism. We also estimated that the ATP production in the deep roots was faster than shallow roots. Our results provided a lot of reliable candidate genes to improve deep rooting, and firstly highlight the importance of energy metabolism to the development of deep roots.
format Online
Article
Text
id pubmed-5526896
institution National Center for Biotechnology Information
language English
publishDate 2017
publisher Frontiers Media S.A.
record_format MEDLINE/PubMed
spelling pubmed-55268962017-08-10 Root Transcriptomic Analysis Revealing the Importance of Energy Metabolism to the Development of Deep Roots in Rice (Oryza sativa L.) Lou, Qiaojun Chen, Liang Mei, Hanwei Xu, Kai Wei, Haibin Feng, Fangjun Li, Tiemei Pang, Xiaomeng Shi, Caiping Luo, Lijun Zhong, Yang Front Plant Sci Plant Science Drought is the most serious abiotic stress limiting rice production, and deep root is the key contributor to drought avoidance. However, the genetic mechanism regulating the development of deep roots is largely unknown. In this study, the transcriptomes of 74 root samples from 37 rice varieties, representing the extreme genotypes of shallow or deep rooting, were surveyed by RNA-seq. The 13,242 differentially expressed genes (DEGs) between deep rooting and shallow rooting varieties (H vs. L) were enriched in the pathway of genetic information processing and metabolism, while the 1,052 DEGs between the deep roots and shallow roots from each of the plants (D vs. S) were significantly enriched in metabolic pathways especially energy metabolism. Ten quantitative trait transcripts (QTTs) were identified and some were involved in energy metabolism. Forty-nine candidate DEGs were confirmed by qRT-PCR and microarray. Through weighted gene co-expression network analysis (WGCNA), we found 18 hub genes. Surprisingly, all these hub genes expressed higher in deep roots than in shallow roots, furthermore half of them functioned in energy metabolism. We also estimated that the ATP production in the deep roots was faster than shallow roots. Our results provided a lot of reliable candidate genes to improve deep rooting, and firstly highlight the importance of energy metabolism to the development of deep roots. Frontiers Media S.A. 2017-07-26 /pmc/articles/PMC5526896/ /pubmed/28798764 http://dx.doi.org/10.3389/fpls.2017.01314 Text en Copyright © 2017 Lou, Chen, Mei, Xu, Wei, Feng, Li, Pang, Shi, Luo and Zhong. http://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Plant Science
Lou, Qiaojun
Chen, Liang
Mei, Hanwei
Xu, Kai
Wei, Haibin
Feng, Fangjun
Li, Tiemei
Pang, Xiaomeng
Shi, Caiping
Luo, Lijun
Zhong, Yang
Root Transcriptomic Analysis Revealing the Importance of Energy Metabolism to the Development of Deep Roots in Rice (Oryza sativa L.)
title Root Transcriptomic Analysis Revealing the Importance of Energy Metabolism to the Development of Deep Roots in Rice (Oryza sativa L.)
title_full Root Transcriptomic Analysis Revealing the Importance of Energy Metabolism to the Development of Deep Roots in Rice (Oryza sativa L.)
title_fullStr Root Transcriptomic Analysis Revealing the Importance of Energy Metabolism to the Development of Deep Roots in Rice (Oryza sativa L.)
title_full_unstemmed Root Transcriptomic Analysis Revealing the Importance of Energy Metabolism to the Development of Deep Roots in Rice (Oryza sativa L.)
title_short Root Transcriptomic Analysis Revealing the Importance of Energy Metabolism to the Development of Deep Roots in Rice (Oryza sativa L.)
title_sort root transcriptomic analysis revealing the importance of energy metabolism to the development of deep roots in rice (oryza sativa l.)
topic Plant Science
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5526896/
https://www.ncbi.nlm.nih.gov/pubmed/28798764
http://dx.doi.org/10.3389/fpls.2017.01314
work_keys_str_mv AT louqiaojun roottranscriptomicanalysisrevealingtheimportanceofenergymetabolismtothedevelopmentofdeeprootsinriceoryzasatival
AT chenliang roottranscriptomicanalysisrevealingtheimportanceofenergymetabolismtothedevelopmentofdeeprootsinriceoryzasatival
AT meihanwei roottranscriptomicanalysisrevealingtheimportanceofenergymetabolismtothedevelopmentofdeeprootsinriceoryzasatival
AT xukai roottranscriptomicanalysisrevealingtheimportanceofenergymetabolismtothedevelopmentofdeeprootsinriceoryzasatival
AT weihaibin roottranscriptomicanalysisrevealingtheimportanceofenergymetabolismtothedevelopmentofdeeprootsinriceoryzasatival
AT fengfangjun roottranscriptomicanalysisrevealingtheimportanceofenergymetabolismtothedevelopmentofdeeprootsinriceoryzasatival
AT litiemei roottranscriptomicanalysisrevealingtheimportanceofenergymetabolismtothedevelopmentofdeeprootsinriceoryzasatival
AT pangxiaomeng roottranscriptomicanalysisrevealingtheimportanceofenergymetabolismtothedevelopmentofdeeprootsinriceoryzasatival
AT shicaiping roottranscriptomicanalysisrevealingtheimportanceofenergymetabolismtothedevelopmentofdeeprootsinriceoryzasatival
AT luolijun roottranscriptomicanalysisrevealingtheimportanceofenergymetabolismtothedevelopmentofdeeprootsinriceoryzasatival
AT zhongyang roottranscriptomicanalysisrevealingtheimportanceofenergymetabolismtothedevelopmentofdeeprootsinriceoryzasatival