Wang Zhe, Cheng Daofu, Fan Chengang, Zhang Cong, Zhang Chao, Liu Zhongmin
Shanghai Key Laboratory of Signaling and Disease Research, Translational Medical Center for Stem Cell Therapy and Institute for Regenerative Medicine, Frontier Science Center for Stem Cell Research, School of Life Sciences and Technology, Shanghai East Hospital, Tongji University, Shanghai, China.
Department of Cardiac Surgery, School of Medicine, Shanghai East Hospital, Tongji University, Shanghai, China.
Front Genet. 2021 May 17;12:659500. doi: 10.3389/fgene.2021.659500. eCollection 2021.
As ssp. and ssp. 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 and 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. We analyzed a published single-cell RNA sequencing dataset to explore the differentially expressed genes between and 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 . We found differentially expressed genes between and 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, _, _, _, and _ may be potential markers of quiescent center cells in rice root tips. These results identified cell type-specific differentially expressed genes between - 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.
由于粳稻和籼稻是亚洲栽培稻的两个主要亚种，这些品种在不同环境中的适应性进化是理论和实践研究中的一个重要课题。然而，关于粳稻和籼稻品种在不同栖息地环境下的细胞类型特异性分化，这有助于在细胞水平上理解水稻亚种间分化和环境适应的遗传基础，目前所知甚少。我们分析了一个已发表的单细胞RNA测序数据集，以探索粳稻和籼稻品种在每种细胞类型中的差异表达基因。为了估计细胞类型特异性分化与环境适应之间的关系，我们重点关注了与非生物胁迫反应密切相关的WRKY、NAC和BZIP转录因子家族中的基因。此外，在本研究中，我们整合了在包括寒冷、干旱和盐度等非生物胁迫条件下获得的五个大量RNA测序数据集。此外，我们基于粳稻中的直系同源标记分析了水稻根尖的静止中心细胞。我们发现粳稻和籼稻品种之间具有细胞类型特异性模式的差异表达基因，这些基因在与根系发育和胁迫反应相关的途径中富集。其中一些基因是WRKY、NAC和BZIP转录因子家族的成员，并且在寒冷、干旱或盐度胁迫下差异表达。此外，、、_和_可能是水稻根尖静止中心细胞的潜在标记。这些结果确定了粳稻-籼稻品种之间与各种环境胁迫相关的细胞类型特异性差异表达基因，并提供了静止中心细胞的推定标记。这项研究为理解植物在适应性分化过程中的发育和生理提供了新线索，此外还为水稻育种应用中提高胁迫耐受性确定了潜在的靶基因。
