Comparative Transcriptome Analysis Revealed Genes Commonly Responsive to Varied Nitrate Stress in Leaves of Tibetan Hulless Barley

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.

Genomic and Genetic Studies of Abiotic Stress Tolerance in Barley

“…However, these gains are not sufficient to alleviate concerns over rising fertilizer costs and increasing environmental regulations of fertilizer application. Variation in NUE has been identified in adapted barley varieties (Anbessa et al 2009;Anbessa et al 2010;Beatty et al 2010); however, variation in the transcriptomic responses of contrasting Tibetan wild barley lines to low N or K barley lines suggests that this collection may be a source of greater variation in NUE and component traits (Quan et al 2016;Wei et al 2016;Zeng et al 2014). To assess the potential of exotic germplasm to be a source of superior NUE more fully will require its incorporation into more advanced populations such as the nested association mapping (NAM) or multi-parent advanced generation inter-cross (MAGIC) populations (Nice et al 2016;Sannemann et al 2015) to reduce the 'wildness' of the material, which can create artefacts in data due to issues such as phenology (Karley et al 2011).…”

Variable Levels of Tolerance to Water Stress (Drought) and Associated Biochemical Markers in Tunisian Barley Landraces

“…Munns et al [ 1 ] highlighted that barley is the most salt tolerant cereal, and its tolerance to drought or biotic stresses such as fungal disease is well-known [ 2 ]. There is a plethora of information on barley’s responses to abiotic stress, including recent studies and review articles on physiological, biochemical [ 2 , 3 , 4 , 5 ], metabolomics [ 6 , 7 ] and transcriptomics [ 8 , 9 , 10 , 11 ] aspects. Being an annual diploid plant species, with a small number of chromosomes (2 n = 14) and a huge range of genetic variability that accounts for different levels of stress tolerance, barley is a model species among crops for deciphering stress tolerance mechanisms, and hence has been subjected to many genetic studies in relation to stress tolerance, ranging from genetic variability analysis [ 12 , 13 ] to marker assisted selection in conjunction with the use of quantitative trait loci (QTLs) [ 14 , 15 ].…”

Improved high-quality genome assembly and annotation of Tibetan hulless barley

“…Although the publication of the Tibetan hulless barley genome has attracted a new upsurge in Tibetan hulless barley genetics research[15, 16], due to the current poor genome assembly, such as the particularly short contig, the very low contig N50, and the poor genome annotation, the functional genome studying of Tibetan hulless barley has caused some vital problems. In addition, with the development of single-molecule sequencing platforms, such as those by Pacific Biosciences and Oxford Nanopore Technologies, have become available to researchers and are currently being increasingly applied in de novo genome assembly and genome update, and other scaffolding techniques(such as BioNano optical mapping, Chicago, Hi-C and 10X genomics)[17-19], it provides a new opportunity for improving Tibetan hulless barley genome assembly.…”