Comparative Transcriptome Analysis Revealed Candidate Genes Potentially Related to Desiccation Sensitivity of Recalcitrant Quercus variabilis Seeds
Chinese cork oak (Quercus variabilis) is a widely distributed and highly valuable deciduous broadleaf tree from both ecological and economic perspectives. Seeds of this species are recalcitrant, i.e., sensitive to desiccation, which affects their storage and long-term preservation of germplasm. Howe...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2021-09-01
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| Series: | Frontiers in Plant Science |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fpls.2021.717563/full |
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| author | Dongxing Li Yingchao Li Jialian Qian Xiaojuan Liu Huihui Xu Guowei Zhang Junjie Ren Libing Wang Lu Zhang Lu Zhang Lu Zhang Haiyan Yu |
| author_facet | Dongxing Li Yingchao Li Jialian Qian Xiaojuan Liu Huihui Xu Guowei Zhang Junjie Ren Libing Wang Lu Zhang Lu Zhang Lu Zhang Haiyan Yu |
| author_sort | Dongxing Li |
| collection | DOAJ |
| description | Chinese cork oak (Quercus variabilis) is a widely distributed and highly valuable deciduous broadleaf tree from both ecological and economic perspectives. Seeds of this species are recalcitrant, i.e., sensitive to desiccation, which affects their storage and long-term preservation of germplasm. However, little is known about the underlying molecular mechanism of desiccation sensitivity of Q. variabilis seeds. In this study, the seeds were desiccated with silica gel for certain days as different treatments from 0 (Control) to 15 days (T15) with a gradient of 1 day. According to the seed germination percentage, four key stages (Control, T2, T4, and T11) were found. Then the transcriptomic profiles of these four stages were compared. A total of 4,405, 4,441, and 5,907 differentially expressed genes (DEGs) were identified in T2 vs. Control, T4 vs. Control, and T11 vs. Control, respectively. Among them, 2,219 DEGs were overlapped in the three comparison groups. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that these DEGs were enriched into 124 pathways, such as “Plant hormone signal transduction” and “Glycerophospholipid metabolism”. DEGs related to hormone biosynthesis and signal transduction (ZEP, YUC, PYR, ABI5, ERF1B, etc.), stress response proteins (LEA D-29, HSP70, etc.), and phospholipase D (PLD1) were detected during desiccation. These genes and their interactions may determine the desiccation sensitivity of seeds. In addition, group specific DEGs were also identified in T2 vs. Control (PP2C62, UNE12, etc.), T4 vs. Control (WRKY1-like, WAK10, etc.), and T11 vs. Control (IBH1, bZIP44, etc.), respectively. Finally, a possible work model was proposed to show the molecular regulation mechanism of desiccation sensitivity in Q. variabilis seeds. This is the first report on the molecular regulation mechanism of desiccation sensitivity of Q. variabilis seeds using RNA-Seq. The findings could make a great contribution to seed storage and long-term conservation of recalcitrant seeds in the future. |
| first_indexed | 2024-12-14T00:31:34Z |
| format | Article |
| id | doaj.art-d46ad6264d4d4baa97fc4527bc97d1f6 |
| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-12-14T00:31:34Z |
| publishDate | 2021-09-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Plant Science |
| spelling | doaj.art-d46ad6264d4d4baa97fc4527bc97d1f62022-12-21T23:24:49ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2021-09-011210.3389/fpls.2021.717563717563Comparative Transcriptome Analysis Revealed Candidate Genes Potentially Related to Desiccation Sensitivity of Recalcitrant Quercus variabilis SeedsDongxing Li0Yingchao Li1Jialian Qian2Xiaojuan Liu3Huihui Xu4Guowei Zhang5Junjie Ren6Libing Wang7Lu Zhang8Lu Zhang9Lu Zhang10Haiyan Yu11State Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, ChinaState Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, ChinaState Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, ChinaState Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, ChinaState Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, ChinaHongya Mountain State-Owned Forest Farm of Hebei, Yixian, ChinaHongya Mountain State-Owned Forest Farm of Hebei, Yixian, ChinaState Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, ChinaState Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, ChinaCollege of Landscape and Architecture, Zhejiang Agriculture and Forestry University, Hangzhou, ChinaZhejiang Provincial Key Laboratory of Germplasm Innovation and Utilization for Garden Plants, Zhejiang Agriculture and Forestry University, Hangzhou, ChinaState Key Laboratory of Tree Genetics and Breeding, Research Institute of Forestry, Chinese Academy of Forestry, Beijing, ChinaChinese cork oak (Quercus variabilis) is a widely distributed and highly valuable deciduous broadleaf tree from both ecological and economic perspectives. Seeds of this species are recalcitrant, i.e., sensitive to desiccation, which affects their storage and long-term preservation of germplasm. However, little is known about the underlying molecular mechanism of desiccation sensitivity of Q. variabilis seeds. In this study, the seeds were desiccated with silica gel for certain days as different treatments from 0 (Control) to 15 days (T15) with a gradient of 1 day. According to the seed germination percentage, four key stages (Control, T2, T4, and T11) were found. Then the transcriptomic profiles of these four stages were compared. A total of 4,405, 4,441, and 5,907 differentially expressed genes (DEGs) were identified in T2 vs. Control, T4 vs. Control, and T11 vs. Control, respectively. Among them, 2,219 DEGs were overlapped in the three comparison groups. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that these DEGs were enriched into 124 pathways, such as “Plant hormone signal transduction” and “Glycerophospholipid metabolism”. DEGs related to hormone biosynthesis and signal transduction (ZEP, YUC, PYR, ABI5, ERF1B, etc.), stress response proteins (LEA D-29, HSP70, etc.), and phospholipase D (PLD1) were detected during desiccation. These genes and their interactions may determine the desiccation sensitivity of seeds. In addition, group specific DEGs were also identified in T2 vs. Control (PP2C62, UNE12, etc.), T4 vs. Control (WRKY1-like, WAK10, etc.), and T11 vs. Control (IBH1, bZIP44, etc.), respectively. Finally, a possible work model was proposed to show the molecular regulation mechanism of desiccation sensitivity in Q. variabilis seeds. This is the first report on the molecular regulation mechanism of desiccation sensitivity of Q. variabilis seeds using RNA-Seq. The findings could make a great contribution to seed storage and long-term conservation of recalcitrant seeds in the future.https://www.frontiersin.org/articles/10.3389/fpls.2021.717563/fullQuercus variabilisrecalcitrant seedsdesiccation sensitivitytranscriptomedifferentially expressed genesplant hormone signaling |
| spellingShingle | Dongxing Li Yingchao Li Jialian Qian Xiaojuan Liu Huihui Xu Guowei Zhang Junjie Ren Libing Wang Lu Zhang Lu Zhang Lu Zhang Haiyan Yu Comparative Transcriptome Analysis Revealed Candidate Genes Potentially Related to Desiccation Sensitivity of Recalcitrant Quercus variabilis Seeds Frontiers in Plant Science Quercus variabilis recalcitrant seeds desiccation sensitivity transcriptome differentially expressed genes plant hormone signaling |
| title | Comparative Transcriptome Analysis Revealed Candidate Genes Potentially Related to Desiccation Sensitivity of Recalcitrant Quercus variabilis Seeds |
| title_full | Comparative Transcriptome Analysis Revealed Candidate Genes Potentially Related to Desiccation Sensitivity of Recalcitrant Quercus variabilis Seeds |
| title_fullStr | Comparative Transcriptome Analysis Revealed Candidate Genes Potentially Related to Desiccation Sensitivity of Recalcitrant Quercus variabilis Seeds |
| title_full_unstemmed | Comparative Transcriptome Analysis Revealed Candidate Genes Potentially Related to Desiccation Sensitivity of Recalcitrant Quercus variabilis Seeds |
| title_short | Comparative Transcriptome Analysis Revealed Candidate Genes Potentially Related to Desiccation Sensitivity of Recalcitrant Quercus variabilis Seeds |
| title_sort | comparative transcriptome analysis revealed candidate genes potentially related to desiccation sensitivity of recalcitrant quercus variabilis seeds |
| topic | Quercus variabilis recalcitrant seeds desiccation sensitivity transcriptome differentially expressed genes plant hormone signaling |
| url | https://www.frontiersin.org/articles/10.3389/fpls.2021.717563/full |
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