Background: As Oryza sativa ssp. indica and Oryza sativa ssp. japonica are the two major subspecies of Asian cultivated rice, the adaptative evolution of these varieties in divergent environments is an important topic in both theoretical and practical studies. However, the cell type-specific differentiation between indica and japonica rice varieties in response to divergent habitat environments, which facilitates an understanding of the genetic basis underlying differentiation and environmental adaptation between rice subspecies at the cellular level, is little known.Methods: We analyzed a published single-cell RNA sequencing dataset to explore the differentially expressed genes between indica and japonica rice varieties in each cell type. To estimate the relationship between cell type-specific differentiation and environmental adaptation, we focused on genes in the WRKY, NAC, and BZIP transcription factor families, which are closely related to abiotic stress responses. In addition, we integrated five bulk RNA sequencing datasets obtained under conditions of abiotic stress, including cold, drought and salinity, in this study. Furthermore, we analyzed quiescent center cells in rice root tips based on orthologous markers in Arabidopsis.Results: We found differentially expressed genes between indica and japonica rice varieties with cell type-specific patterns, which were enriched in the pathways related to root development and stress reposes. Some of these genes were members of the WRKY, NAC, and BZIP transcription factor families and were differentially expressed under cold, drought or salinity stress. In addition, LOC_Os01g16810, LOC_Os01g18670, LOC_Os04g52960, and LOC_Os08g09350 may be potential markers of quiescent center cells in rice root tips.Conclusion: These results identified cell type-specific differentially expressed genes between indica-japonica rice varieties that were related to various environmental stresses and provided putative markers of quiescent center cells. This study provides new clues for understanding the development and physiology of plants during the process of adaptative divergence, in addition to identifying potential target genes for the improvement of stress tolerance in rice breeding applications.
Glandular trichomes, a specialized multicellular structure, are considered as biofactories due to their capability to synthesize and secrete a large amount of secondary metabolites. Tobacco leaves have a high density of glandular trichomes that produce huge amounts of secondary metabolites, which can be used as important industrial raw materials. However, molecular mechanism controling glandular trichome development in tobacco still remains largely unknown. In the present study, we found that NbGL3, an HD-Zip IV family gene from Nicotiana benthamiana, was highly expressed in mature leaves, and ethylene or auxin application could increase the expression of NbGL3. Virus induced gene silencing NbGL3 resulted in a decreased glandular trichome density on leaves. Putative downstream genes, such as micro trichome, cyclin B2, and wax inducer 1 like were down regulated in NbGL3 silenced plants. Our results demonstrate that NbGL3 could positively regulate initiation of glandular trichomes in tobacco.
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