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Global Transcriptome and Co-Expression Network Analysis Reveal Contrasting Response of Japonica and Indica Rice Cultivar to γ Radiation

Japonica and indica are two important subspecies in cultivated Asian rice. Irradiation is a classical approach to induce mutations and create novel germplasm. However, little is known about the differential response between japonica and indica rice after γ radiation. Here, we utilized the RNA sequen...

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Autores principales: Zhang, Xiaoxiang, Huang, Niansheng, Mo, Lanjing, Lv, Minjia, Gao, Yingbo, Wang, Junpeng, Liu, Chang, Yin, Shuangyi, Zhou, Juan, Xiao, Ning, Pan, Cunhong, Xu, Yabin, Dong, Guichun, Yang, Zefeng, Li, Aihong, Huang, Jianye, Wang, Yulong, Yao, Youli
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2019
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6769861/
https://www.ncbi.nlm.nih.gov/pubmed/31491955
http://dx.doi.org/10.3390/ijms20184358
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author Zhang, Xiaoxiang
Huang, Niansheng
Mo, Lanjing
Lv, Minjia
Gao, Yingbo
Wang, Junpeng
Liu, Chang
Yin, Shuangyi
Zhou, Juan
Xiao, Ning
Pan, Cunhong
Xu, Yabin
Dong, Guichun
Yang, Zefeng
Li, Aihong
Huang, Jianye
Wang, Yulong
Yao, Youli
author_facet Zhang, Xiaoxiang
Huang, Niansheng
Mo, Lanjing
Lv, Minjia
Gao, Yingbo
Wang, Junpeng
Liu, Chang
Yin, Shuangyi
Zhou, Juan
Xiao, Ning
Pan, Cunhong
Xu, Yabin
Dong, Guichun
Yang, Zefeng
Li, Aihong
Huang, Jianye
Wang, Yulong
Yao, Youli
author_sort Zhang, Xiaoxiang
collection PubMed
description Japonica and indica are two important subspecies in cultivated Asian rice. Irradiation is a classical approach to induce mutations and create novel germplasm. However, little is known about the differential response between japonica and indica rice after γ radiation. Here, we utilized the RNA sequencing and Weighted Gene Co-expression Network Analysis (WGCNA) to compare the transcriptome differences between japonica Nipponbare (NPB) and indica Yangdao6 (YD6) in response to irradiation. Japonica subspecies are more sensitive to irradiation than the indica subspecies. Indica showed a higher seedling survival rate than japonica. Irradiation caused more extensive DNA damage in shoots than in roots, and the severity was higher in NPB than in YD6. GO and KEGG pathway analyses indicate that the core genes related to DNA repair and replication and cell proliferation are similarly regulated between the varieties, however the universal stress responsive genes show contrasting differential response patterns in japonica and indica. WGCNA identifies 37 co-expressing gene modules and ten candidate hub genes for each module. This provides novel evidence indicating that certain peripheral pathways may dominate the molecular networks in irradiation survival and suggests more potential target genes in breeding for universal stress tolerance in rice.
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spelling pubmed-67698612019-10-30 Global Transcriptome and Co-Expression Network Analysis Reveal Contrasting Response of Japonica and Indica Rice Cultivar to γ Radiation Zhang, Xiaoxiang Huang, Niansheng Mo, Lanjing Lv, Minjia Gao, Yingbo Wang, Junpeng Liu, Chang Yin, Shuangyi Zhou, Juan Xiao, Ning Pan, Cunhong Xu, Yabin Dong, Guichun Yang, Zefeng Li, Aihong Huang, Jianye Wang, Yulong Yao, Youli Int J Mol Sci Article Japonica and indica are two important subspecies in cultivated Asian rice. Irradiation is a classical approach to induce mutations and create novel germplasm. However, little is known about the differential response between japonica and indica rice after γ radiation. Here, we utilized the RNA sequencing and Weighted Gene Co-expression Network Analysis (WGCNA) to compare the transcriptome differences between japonica Nipponbare (NPB) and indica Yangdao6 (YD6) in response to irradiation. Japonica subspecies are more sensitive to irradiation than the indica subspecies. Indica showed a higher seedling survival rate than japonica. Irradiation caused more extensive DNA damage in shoots than in roots, and the severity was higher in NPB than in YD6. GO and KEGG pathway analyses indicate that the core genes related to DNA repair and replication and cell proliferation are similarly regulated between the varieties, however the universal stress responsive genes show contrasting differential response patterns in japonica and indica. WGCNA identifies 37 co-expressing gene modules and ten candidate hub genes for each module. This provides novel evidence indicating that certain peripheral pathways may dominate the molecular networks in irradiation survival and suggests more potential target genes in breeding for universal stress tolerance in rice. MDPI 2019-09-05 /pmc/articles/PMC6769861/ /pubmed/31491955 http://dx.doi.org/10.3390/ijms20184358 Text en © 2019 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Zhang, Xiaoxiang
Huang, Niansheng
Mo, Lanjing
Lv, Minjia
Gao, Yingbo
Wang, Junpeng
Liu, Chang
Yin, Shuangyi
Zhou, Juan
Xiao, Ning
Pan, Cunhong
Xu, Yabin
Dong, Guichun
Yang, Zefeng
Li, Aihong
Huang, Jianye
Wang, Yulong
Yao, Youli
Global Transcriptome and Co-Expression Network Analysis Reveal Contrasting Response of Japonica and Indica Rice Cultivar to γ Radiation
title Global Transcriptome and Co-Expression Network Analysis Reveal Contrasting Response of Japonica and Indica Rice Cultivar to γ Radiation
title_full Global Transcriptome and Co-Expression Network Analysis Reveal Contrasting Response of Japonica and Indica Rice Cultivar to γ Radiation
title_fullStr Global Transcriptome and Co-Expression Network Analysis Reveal Contrasting Response of Japonica and Indica Rice Cultivar to γ Radiation
title_full_unstemmed Global Transcriptome and Co-Expression Network Analysis Reveal Contrasting Response of Japonica and Indica Rice Cultivar to γ Radiation
title_short Global Transcriptome and Co-Expression Network Analysis Reveal Contrasting Response of Japonica and Indica Rice Cultivar to γ Radiation
title_sort global transcriptome and co-expression network analysis reveal contrasting response of japonica and indica rice cultivar to γ radiation
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6769861/
https://www.ncbi.nlm.nih.gov/pubmed/31491955
http://dx.doi.org/10.3390/ijms20184358
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