Cargando…

Cell Type-Specific Differentiation Between Indica and Japonica Rice Root Tip Responses to Different Environments Based on Single-Cell RNA Sequencing

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 differe...

Descripción completa

Detalles Bibliográficos
Autores principales: Wang, Zhe, Cheng, Daofu, Fan, Chengang, Zhang, Cong, Zhang, Chao, Liu, Zhongmin
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8166412/
https://www.ncbi.nlm.nih.gov/pubmed/34079581
http://dx.doi.org/10.3389/fgene.2021.659500
_version_ 1783701501524312064
author Wang, Zhe
Cheng, Daofu
Fan, Chengang
Zhang, Cong
Zhang, Chao
Liu, Zhongmin
author_facet Wang, Zhe
Cheng, Daofu
Fan, Chengang
Zhang, Cong
Zhang, Chao
Liu, Zhongmin
author_sort Wang, Zhe
collection PubMed
description 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.
format Online
Article
Text
id pubmed-8166412
institution National Center for Biotechnology Information
language English
publishDate 2021
publisher Frontiers Media S.A.
record_format MEDLINE/PubMed
spelling pubmed-81664122021-06-01 Cell Type-Specific Differentiation Between Indica and Japonica Rice Root Tip Responses to Different Environments Based on Single-Cell RNA Sequencing Wang, Zhe Cheng, Daofu Fan, Chengang Zhang, Cong Zhang, Chao Liu, Zhongmin Front Genet Genetics 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. Frontiers Media S.A. 2021-05-17 /pmc/articles/PMC8166412/ /pubmed/34079581 http://dx.doi.org/10.3389/fgene.2021.659500 Text en Copyright © 2021 Wang, Cheng, Fan, Zhang, Zhang and Liu. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Genetics
Wang, Zhe
Cheng, Daofu
Fan, Chengang
Zhang, Cong
Zhang, Chao
Liu, Zhongmin
Cell Type-Specific Differentiation Between Indica and Japonica Rice Root Tip Responses to Different Environments Based on Single-Cell RNA Sequencing
title Cell Type-Specific Differentiation Between Indica and Japonica Rice Root Tip Responses to Different Environments Based on Single-Cell RNA Sequencing
title_full Cell Type-Specific Differentiation Between Indica and Japonica Rice Root Tip Responses to Different Environments Based on Single-Cell RNA Sequencing
title_fullStr Cell Type-Specific Differentiation Between Indica and Japonica Rice Root Tip Responses to Different Environments Based on Single-Cell RNA Sequencing
title_full_unstemmed Cell Type-Specific Differentiation Between Indica and Japonica Rice Root Tip Responses to Different Environments Based on Single-Cell RNA Sequencing
title_short Cell Type-Specific Differentiation Between Indica and Japonica Rice Root Tip Responses to Different Environments Based on Single-Cell RNA Sequencing
title_sort cell type-specific differentiation between indica and japonica rice root tip responses to different environments based on single-cell rna sequencing
topic Genetics
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8166412/
https://www.ncbi.nlm.nih.gov/pubmed/34079581
http://dx.doi.org/10.3389/fgene.2021.659500
work_keys_str_mv AT wangzhe celltypespecificdifferentiationbetweenindicaandjaponicariceroottipresponsestodifferentenvironmentsbasedonsinglecellrnasequencing
AT chengdaofu celltypespecificdifferentiationbetweenindicaandjaponicariceroottipresponsestodifferentenvironmentsbasedonsinglecellrnasequencing
AT fanchengang celltypespecificdifferentiationbetweenindicaandjaponicariceroottipresponsestodifferentenvironmentsbasedonsinglecellrnasequencing
AT zhangcong celltypespecificdifferentiationbetweenindicaandjaponicariceroottipresponsestodifferentenvironmentsbasedonsinglecellrnasequencing
AT zhangchao celltypespecificdifferentiationbetweenindicaandjaponicariceroottipresponsestodifferentenvironmentsbasedonsinglecellrnasequencing
AT liuzhongmin celltypespecificdifferentiationbetweenindicaandjaponicariceroottipresponsestodifferentenvironmentsbasedonsinglecellrnasequencing