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...
Autores principales: | , , , , , , , , , , |
---|---|
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 |