Transcriptome Analysis of Rice Seedling Roots in Response to Potassium Deficiency

Xiaoqin Zhang,Hua Jiang,Longbiao Guo,Hua Wang,Jiang Hu,Dawei Xue,Jiahui Wang,Qian Qian,Jun Cui

doi:10.1038/s41598-017-05887-9

Abstract

Rice is one of the most important food crops in the world, and its growth, development, yield, and grain quality are susceptible to a deficiency of the macronutrient potassium (K+). The molecular mechanism for K+ deficiency tolerance remains poorly understood. In this study, K+ deficient conditions were employed to investigate the resulting changes in the transcriptome of rice seedling roots. Using ribonucleic acid sequencing (RNA-Seq) and analysis, a total of 805 differentially expressed genes were obtained, of which 536 genes were upregulated and 269 were downregulated. Gene functional classification showed that the expression of genes involved in nutrient transport, protein kinases, transcription processes, and plant hormones were particularly altered in the roots. Although these changes were significant, the expression of most genes remained constant even in K+-deficient conditions. Interestingly, when our RNA-Seq results were compared to public microarray data, we found that most of the genes that were differentially expressed in low K+ conditions also exhibited changes in expression in other environmental stress conditions.

Highlights

IntroductionThe available potassium increases crop yield and quality. potassium content is abundant in the lithosphere and soil, almost 10 times more so than total nitrogen and total phosphorus, an extremely high proportion (90–98%) of potassium exists in the soil in forms that cannot be directly absorbed or used by plants[4, 5]
In agricultural crops, the available potassium increases crop yield and quality
The present study used Nipponbare rice as source material and Illumina ribonucleic acid sequencing (RNA-Seq) technology combined with real-time fluorescent quantitative PCR (QPCR) to analyze and compare the rice root transcriptome under low and normal potassium conditions, and to identify signal transduction pathways and regulatory networks related to low potassium tolerance

Summary

Introduction

The available potassium increases crop yield and quality. potassium content is abundant in the lithosphere and soil, almost 10 times more so than total nitrogen and total phosphorus, an extremely high proportion (90–98%) of potassium exists in the soil in forms that cannot be directly absorbed or used by plants[4, 5]. Some studies have reported morphological, physiological, and biochemical differences, as well as differences in K+ use efficiency under low K+ stress These studies found there is a significant difference in K+ deficiency tolerance between rice genotypes[9,10,11], further indicating that the potassium nutritional activities of rice are genetically regulated through gene expression that increases its efficient use or tolerance to low potassium. The present study used Nipponbare rice as source material and Illumina RNA-Seq technology combined with real-time fluorescent quantitative PCR (QPCR) to analyze and compare the rice root transcriptome under low and normal potassium conditions, and to identify signal transduction pathways and regulatory networks related to low potassium tolerance

Methods

Results

Discussion

Conclusion