Transcriptome Analysis Reveals Differences in Key Genes and Pathways Regulating Carbon and Nitrogen Metabolism in Cotton Genotypes under N Starvation and Resupply.

Asif Iqbal,Meizhen Song,Xiangru Wang,Hengheng Zhang,Xiling Zhang,Huiping Gui,Qiang Dong

doi:10.3390/ijms21041500

Abstract

Nitrogen (N) is the most important limiting factor for cotton production worldwide. Genotype-dependent ability to cope with N shortage has been only partially explored in cotton, and in this context, the comparison of molecular responses of cotton genotypes with different nitrogen use efficiency (NUE) is of particular interest to dissect the key molecular mechanisms underlying NUE. In this study, we employed Illumina RNA-Sequencing to determine the genotypic difference in transcriptome profile using two cotton genotypes differing in NUE (CCRI-69, N-efficient, and XLZ-30, N-inefficient) under N starvation and resupply treatments. The results showed that a large genetic variation existed in differentially expressed genes (DEGs) related to amino acid, carbon, and nitrogen metabolism between CCRI-69 and XLZ-30. Further analysis of metabolic changes in cotton genotypes under N resupply showed that nitrogen metabolism and aromatic amino acid metabolism pathways were mainly enriched in CCRI-69 by regulating carbon metabolism pathways such as starch and sucrose metabolism, glycolysis/gluconeogenesis, and pentose phosphate pathway. Additionally, we performed an expression network analysis of genes related to amino acid, carbon, and nitrogen metabolism. In total, 75 and 33 genes were identified as hub genes in shoots and roots of cotton genotypes, respectively. In summary, the identified hub genes may provide new insights into coordinating carbon and nitrogen metabolism and improving NUE in cotton.

Highlights

Nitrogen (N) is one of the most important and limiting factors for plant growth and productivity [1] and serves as a constituent of many important macromolecules, including proteins, enzymes, metabolites, signaling compounds, and several plant hormones [2]
The discussion section will focus on which key genes/pathways play an important role in improving amino acid, carbon and nitrogen metabolism in cotton genotypes, which can be further used for improving nitrogen use efficiency (NUE)
The identification of differentially expressed genes (DEGs) transcripts in plants would reveal the genetic mechanism of NUE

Summary

Introduction

Nitrogen (N) is one of the most important and limiting factors for plant growth and productivity [1] and serves as a constituent of many important macromolecules, including proteins, enzymes, metabolites, signaling compounds, and several plant hormones [2]. The application of N fertilizer has significantly increased crop production and as a result, reduced the pressure of population growth [1]. A large amount of N fertilizers is being used to improve growth and productivity [5,6], and the application may increase by threefold in the future [7] due to increasingly-declined soil fertility and widely planted high-yield crop cultivars. To compensate for that reduction, improved crop genotypes must be sought with higher nitrogen use efficiency (NUE) [11,12,13], as it is a basic and the most efficient approach for coping with low N availability in the soil and insufficient N fertilizer supply. It may be assumed that N-efficient cotton genotypes contain some unique mechanisms of nitrogen and carbon metabolism

Methods

Results

Discussion

Conclusion