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Transcriptome Analysis of Rice Embryo and Endosperm during Seed Germination
Seed germination is a complex, multistage developmental process that is an important step in plant development. In this study, RNA-Seq was conducted in the embryo and endosperm of unshelled germinating rice seeds. A total of 14,391 differentially expressed genes (DEGs) were identified between the dr...
Autores principales: | , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
MDPI
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10218590/ https://www.ncbi.nlm.nih.gov/pubmed/37240056 http://dx.doi.org/10.3390/ijms24108710 |
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author | Zhang, Heng Chen, Guang Xu, Heng Jing, Sasa Jiang, Yingying Liu, Ziwen Zhang, Hua Wang, Fulin Hu, Xiangyang Zhu, Ying |
author_facet | Zhang, Heng Chen, Guang Xu, Heng Jing, Sasa Jiang, Yingying Liu, Ziwen Zhang, Hua Wang, Fulin Hu, Xiangyang Zhu, Ying |
author_sort | Zhang, Heng |
collection | PubMed |
description | Seed germination is a complex, multistage developmental process that is an important step in plant development. In this study, RNA-Seq was conducted in the embryo and endosperm of unshelled germinating rice seeds. A total of 14,391 differentially expressed genes (DEGs) were identified between the dry seeds and the germinating seeds. Of these DEGs, 7109 were identified in both the embryo and endosperm, 3953 were embryo specific, and 3329 were endosperm specific. The embryo-specific DEGs were enriched in the plant-hormone signal-transduction pathway, while the endosperm-specific DEGs were enriched in phenylalanine, tyrosine, and tryptophan biosynthesis. We categorized these DEGs into early-, intermediate-, and late-stage genes, as well as consistently responsive genes, which can be enriched in various pathways related to seed germination. Transcription-factor (TF) analysis showed that 643 TFs from 48 families were differentially expressed during seed germination. Moreover, 12 unfolded protein response (UPR) pathway genes were induced by seed germination, and the knockout of OsBiP2 resulted in reduced germination rates compared to the wild type. This study enhances our understanding of gene responses in the embryo and endosperm during seed germination and provides insight into the effects of UPR on seed germination in rice. |
format | Online Article Text |
id | pubmed-10218590 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | MDPI |
record_format | MEDLINE/PubMed |
spelling | pubmed-102185902023-05-27 Transcriptome Analysis of Rice Embryo and Endosperm during Seed Germination Zhang, Heng Chen, Guang Xu, Heng Jing, Sasa Jiang, Yingying Liu, Ziwen Zhang, Hua Wang, Fulin Hu, Xiangyang Zhu, Ying Int J Mol Sci Article Seed germination is a complex, multistage developmental process that is an important step in plant development. In this study, RNA-Seq was conducted in the embryo and endosperm of unshelled germinating rice seeds. A total of 14,391 differentially expressed genes (DEGs) were identified between the dry seeds and the germinating seeds. Of these DEGs, 7109 were identified in both the embryo and endosperm, 3953 were embryo specific, and 3329 were endosperm specific. The embryo-specific DEGs were enriched in the plant-hormone signal-transduction pathway, while the endosperm-specific DEGs were enriched in phenylalanine, tyrosine, and tryptophan biosynthesis. We categorized these DEGs into early-, intermediate-, and late-stage genes, as well as consistently responsive genes, which can be enriched in various pathways related to seed germination. Transcription-factor (TF) analysis showed that 643 TFs from 48 families were differentially expressed during seed germination. Moreover, 12 unfolded protein response (UPR) pathway genes were induced by seed germination, and the knockout of OsBiP2 resulted in reduced germination rates compared to the wild type. This study enhances our understanding of gene responses in the embryo and endosperm during seed germination and provides insight into the effects of UPR on seed germination in rice. MDPI 2023-05-13 /pmc/articles/PMC10218590/ /pubmed/37240056 http://dx.doi.org/10.3390/ijms24108710 Text en © 2023 by the authors. https://creativecommons.org/licenses/by/4.0/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 (https://creativecommons.org/licenses/by/4.0/). |
spellingShingle | Article Zhang, Heng Chen, Guang Xu, Heng Jing, Sasa Jiang, Yingying Liu, Ziwen Zhang, Hua Wang, Fulin Hu, Xiangyang Zhu, Ying Transcriptome Analysis of Rice Embryo and Endosperm during Seed Germination |
title | Transcriptome Analysis of Rice Embryo and Endosperm during Seed Germination |
title_full | Transcriptome Analysis of Rice Embryo and Endosperm during Seed Germination |
title_fullStr | Transcriptome Analysis of Rice Embryo and Endosperm during Seed Germination |
title_full_unstemmed | Transcriptome Analysis of Rice Embryo and Endosperm during Seed Germination |
title_short | Transcriptome Analysis of Rice Embryo and Endosperm during Seed Germination |
title_sort | transcriptome analysis of rice embryo and endosperm during seed germination |
topic | Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10218590/ https://www.ncbi.nlm.nih.gov/pubmed/37240056 http://dx.doi.org/10.3390/ijms24108710 |
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