Abstract
Nitrogen (N) deprivation or excess can lead to dramatic phenotype change, disrupt important biological processes, and ultimately limit plant productivity. To explore genes in Tibetan hulless barley responsive to varied N stress, we utilized a comparative transcriptomics method to investigate gene expression patterns under three nitrate treatments. The transcriptome of the control (optimal-nitrate, ON) sample was compared with that of free-nitrate (FN), low-nitrate (LN), and high-nitrate (HN) treatment samples, identifying 2428, 1274, and 1861 genes, respectively, that exhibited significant differences in transcript abundance. Among these, 9 genes encoding ribulose bisphosphate carboxylases exhibited up-regulated expression under varied N stress. We further compared FN vs. ON and LN vs. ON to investigate the impact of stress degree on gene expression. With the aggravation of stress, more genes were differentially expressed and thus possibly involved in the response to nitrogen deficiency. Cluster and functional enrichment analysis indicated that the differentially expressed genes (DEGs) in FN were highly enriched in response to stress, defense response, and gene expression regulation. Comprehensive comparison analysis further suggested that Tibetan hulless barley could respond to varied N stress by regulating multiple common biological processes and pathways such as nitrogen metabolism, carbon metabolism, and photosynthesis. A large number of specific DEGs involved in diverse biological processes were also detected, implying differences in the potential regulatory patterns of low- and high-N stress response. Notably, we also identified some NIN-like proteins and other transcription factors significantly modulated by these stresses, suggesting the involvement of these transcription factors in N stress response. To our knowledge, this study is the first investigation of the Tibetan hulless barley transcriptome under N stress. The identified N-stress-related genes may provide resources for genetic improvement and promote N use efficiency.
Highlights
Nitrogen (N), a necessary factor for life, plays crucial roles in plant growth and development, and represents the essential constituent of most macromolecules and many secondary and signaling compounds such as proteins, nucleic acids, and hormones (Krapp, 2015)
The results of data quality assessment showed that clean reads exhibited good quality scores with Q20 percentages of all samples over 95%, whereas the uncalled base (“N”) percentages were lower than 0.01% (Table S2)
We identified 809 common differentially expressed genes (DEGs) among the three N stress-treated groups as compared to the ON group that were associated with multiple biological processes including “cellular aldehyde metabolic process,” “cellular amino acid metabolic process,” and “photosynthesis” (Figure 3)
Summary
Nitrogen (N), a necessary factor for life, plays crucial roles in plant growth and development, and represents the essential constituent of most macromolecules and many secondary and signaling compounds such as proteins, nucleic acids, and hormones (Krapp, 2015). N has both positive and negative effects on plant development and growth. Increasing evidence demonstrates that excess N can negatively affect plant growth (Tian et al, 2008; Saiz-Fernández et al, 2015). Significant negative effects of high N doses include the restriction of root growth, leaf expansion, and whole plant development (Zhang et al, 1999; Saiz-Fernández et al, 2015). Changes in plant hormone levels were shown to play a relevant role in this inhibitory effect (Kiba et al, 2011; Saiz-Fernández et al, 2015)
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