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

Caiping Shi,Haibin Wei,Kai Xu,Tiemei Li,Liang Chen,Fangjun Feng,Lijun Luo,Qiaojun Lou,Hanwei Mei,Xiaomeng Pang,Yang Zhong

doi:10.3389/fpls.2017.01314

Caiping Shi, Haibin Wei + Show 9 more

Open Access

https://doi.org/10.3389/fpls.2017.01314

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Abstract

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.

Highlights

Drought stress is one of the most pressing issues inhibiting global agriculture today (Osakabe et al, 2014)
All the deep rooting samples were clustered into one group (Cluster 1), while all the shallow rooting samples were clustered into another group (Cluster 2)
In China, agriculture used about 70% of the total water consumption of the country, 70% of which was used for rice production alone (Zhang, 2007)

Summary

Introduction

Drought stress is one of the most pressing issues inhibiting global agriculture today (Osakabe et al, 2014). Rice (Oryza sativa L.) is the main food for more than half of the world’s population. Water deficit may reduce rice production seriously and threaten world food security (Serraj et al, 2009; Luo, 2010; Ahmadi et al, 2014). There is an urgent need to understand the underlying physiological and molecular mechanisms of drought resistance to sustain rice production in water-limiting areas (Nguyen et al, 1997; Lanceras et al, 2004; Rabello et al, 2008; Bernier et al, 2009; Serraj et al, 2011). As the main organ to uptake water in soil, root is the key contributor of plants’ drought resistance (Kato et al, 2006; Henry et al, 2012). Recently root has become a hot area of research to improve drought resistance (Coudert et al, 2014)

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