Transcriptome profiling analysis for two Tibetan wild barley genotypes in responses to low nitrogen

BACKGROUND: Nitrogen (N) is the most common limiting factor for crop productivity worldwide. An effective approach to solve N deficiency is to develop low N (LN) tolerant crop cultivars. Tibetan annual wild barley is well-known for its wide genetic diversity and high tolerance to poor soil fertility. Up to date, no study has been done to illustrate the mechanism of LN tolerance underlying the wild barley at transcriptional level. RESULTS: In this study, we employed Illumina RNA-Sequencing to determine the genotypic difference in transcriptome profile using two Tibetan wild barley genotypes differing in LN tolerance (XZ149, tolerant and XZ56, sensitive). A total of 1469 differentially expressed genes (DEGs) were identified in the two genotypes at 6 h and 48 h after LN treatment. Genetic difference existed in DEGs between XZ149 and XZ56, including transporters, transcription factors (TFs), kinases, antioxidant stress and hormone signaling related genes. Meanwhile, 695 LN tolerance-associated DEGs were mainly mapped to amino acid metabolism, starch and sucrose metabolism and secondary metabolism, and involved in transporter activity, antioxidant activities, and other gene ontology (GO). XZ149 had a higher capability of N absorption and use efficiency under LN stress than XZ56. The higher expression of nitrate transporters and energy-saving assimilation pattern could be attributed to its more N uptake and higher LN tolerance. In addition, auxin (IAA) and ethylene (ETH) response pathways may be also related to the genotypic difference in LN tolerance. CONCLUSION: The responses of XZ149 and XZ56 to LN stress differed dramatically at transcriptional level. The identified candidate genes related to LN tolerance may provide new insights into comprehensive understanding of the genotypic difference in N utilization and LN tolerance. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1186/s12870-016-0721-8) contains supplementary material, which is available to authorized users.