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Open Access Research article

Identification of differentially expressed genes between sorghum genotypes with contrasting nitrogen stress tolerance by genome-wide transcriptional profiling

Malleswari Gelli1, Yongchao Duo23, Anji Reddy Konda4, Chi Zhang23, David Holding13 and Ismail Dweikat1*

Author Affiliations

1 Department of Agronomy and Horticulture, University of Nebraska, Lincoln, NE 68588, USA

2 School of Biological Sciences, University of Nebraska, Lincoln, NE 68588, USA

3 Center for Plant Science Innovation, University of Nebraska, Lincoln, NE 68588, USA

4 Department of Biochemistry, University of Nebraska, Lincoln, NE 68588, USA

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BMC Genomics 2014, 15:179  doi:10.1186/1471-2164-15-179

Published: 5 March 2014

Abstract

Background

Sorghum is an important cereal crop, which requires large quantities of nitrogen fertilizer for achieving commercial yields. Identification of the genes responsible for low-N tolerance in sorghum will facilitate understanding of the molecular mechanisms of low-N tolerance, and also facilitate the genetic improvement of sorghum through marker-assisted selection or gene transformation. In this study we compared the transcriptomes of root tissues from seven sorghum genotypes having differential response to low-N stress.

Results

Illumina RNA-sequencing detected several common differentially expressed genes (DEGs) between four low-N tolerant sorghum genotypes (San Chi San, China17, KS78 and high-NUE bulk) and three sensitive genotypes (CK60, BTx623 and low-NUE bulk). In sensitive genotypes, N-stress increased the abundance of DEG transcripts associated with stress responses including oxidative stress and stimuli were abundant. The tolerant genotypes adapt to N deficiency by producing greater root mass for efficient uptake of nutrients. In tolerant genotypes, higher abundance of transcripts related to high affinity nitrate transporters (NRT2.2, NRT2.3, NRT2.5, and NRT2.6) and lysine histidine transporter 1 (LHT1), may suggest an improved uptake efficiency of inorganic and organic forms of nitrogen. Higher abundance of SEC14 cytosolic factor family protein transcript in tolerant genotypes could lead to increased membrane stability and tolerance to N-stress.

Conclusions

Comparison of transcriptomes between N-stress tolerant and sensitive genotypes revealed several common DEG transcripts. Some of these DEGs were evaluated further by comparing the transcriptomes of genotypes grown under full N. The DEG transcripts showed higher expression in tolerant genotypes could be used for transgenic over-expression in sensitive genotypes of sorghum and related crops for increased tolerance to N-stress, which results in increased nitrogen use efficiency for sustainable agriculture.

Keywords:
N-stress; Sorghum; Nitrogen use efficiency; Transcriptome; RNA-seq; Genotypes; Differentially expressed genes