Transcriptome analysis of Populus × canadensis ‘Zhongliao1’ in response to low temperature stress
Abstract Background Low temperatures are known to limit the growth and geographical distribution of poplars. Although some transcriptomic studies have been conducted to explore the response of poplar leaves to cold stress, only a few have comprehensively analyzed the effects of low temperature on th...
| Main Authors: | , , , |
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| Format: | Article |
| Language: | English |
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BMC
2023-02-01
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| Series: | BMC Genomics |
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| Online Access: | https://doi.org/10.1186/s12864-023-09187-7 |
| _version_ | 1797865491802357760 |
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| author | Chengchao Yang Xiaoyu Li Yan Zhang Hua Jin |
| author_facet | Chengchao Yang Xiaoyu Li Yan Zhang Hua Jin |
| author_sort | Chengchao Yang |
| collection | DOAJ |
| description | Abstract Background Low temperatures are known to limit the growth and geographical distribution of poplars. Although some transcriptomic studies have been conducted to explore the response of poplar leaves to cold stress, only a few have comprehensively analyzed the effects of low temperature on the transcriptome of poplars and identified genes related to cold stress response and repair of freeze–thaw injury. Results We exposed the Euramerican poplar Zhongliao1 to low temperatures; after stems were exposed to − 40℃, 4℃, and 20℃, the mixture of phloem and cambium was collected for transcriptome sequencing and bioinformatics analysis. A total of 29,060 genes were detected, including 28,739 known genes and 321 novel genes. Several differentially expressed genes (n = 36) were found to be involved in the Ca2+ signaling pathway, starch–sucrose metabolism pathway, abscisic acid signaling pathway, and DNA repair. They were functionally annotated; glucan endo-1,3-beta-glucosidase and UDP-glucuronosyltransferase genes, for instance, showed a close relationship with cold resistance. The expression of 11 differentially expressed genes was verified by qRT-PCR; RNA-Seq and qRT-PCR data were found to be consistent, which validated the robustness of our RNA-Seq findings. Finally, multiple sequence alignment and evolutionary analysis were performed, the results of which suggested a close association between several novel genes and cold resistance in Zhongliao1. Conclusion We believe that the cold resistance and freeze–thaw injury repair genes identified in this study are of great significance for cold tolerance breeding. |
| first_indexed | 2024-04-09T23:09:11Z |
| format | Article |
| id | doaj.art-b50af8f7592a478c8c0f87d1bb96b04c |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-04-09T23:09:11Z |
| publishDate | 2023-02-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Genomics |
| spelling | doaj.art-b50af8f7592a478c8c0f87d1bb96b04c2023-03-22T10:30:51ZengBMCBMC Genomics1471-21642023-02-0124111210.1186/s12864-023-09187-7Transcriptome analysis of Populus × canadensis ‘Zhongliao1’ in response to low temperature stressChengchao Yang0Xiaoyu Li1Yan Zhang2Hua Jin3Liaoning Provincial Institute of PoplarLiaoning Provincial Institute of PoplarLiaoning Provincial Institute of PoplarCollege of Environment and Bioresources, Dalian Minzu UniversityAbstract Background Low temperatures are known to limit the growth and geographical distribution of poplars. Although some transcriptomic studies have been conducted to explore the response of poplar leaves to cold stress, only a few have comprehensively analyzed the effects of low temperature on the transcriptome of poplars and identified genes related to cold stress response and repair of freeze–thaw injury. Results We exposed the Euramerican poplar Zhongliao1 to low temperatures; after stems were exposed to − 40℃, 4℃, and 20℃, the mixture of phloem and cambium was collected for transcriptome sequencing and bioinformatics analysis. A total of 29,060 genes were detected, including 28,739 known genes and 321 novel genes. Several differentially expressed genes (n = 36) were found to be involved in the Ca2+ signaling pathway, starch–sucrose metabolism pathway, abscisic acid signaling pathway, and DNA repair. They were functionally annotated; glucan endo-1,3-beta-glucosidase and UDP-glucuronosyltransferase genes, for instance, showed a close relationship with cold resistance. The expression of 11 differentially expressed genes was verified by qRT-PCR; RNA-Seq and qRT-PCR data were found to be consistent, which validated the robustness of our RNA-Seq findings. Finally, multiple sequence alignment and evolutionary analysis were performed, the results of which suggested a close association between several novel genes and cold resistance in Zhongliao1. Conclusion We believe that the cold resistance and freeze–thaw injury repair genes identified in this study are of great significance for cold tolerance breeding.https://doi.org/10.1186/s12864-023-09187-7PoplarFreeze–thaw injuryOverwinteringLow temperature stressCold stress response |
| spellingShingle | Chengchao Yang Xiaoyu Li Yan Zhang Hua Jin Transcriptome analysis of Populus × canadensis ‘Zhongliao1’ in response to low temperature stress BMC Genomics Poplar Freeze–thaw injury Overwintering Low temperature stress Cold stress response |
| title | Transcriptome analysis of Populus × canadensis ‘Zhongliao1’ in response to low temperature stress |
| title_full | Transcriptome analysis of Populus × canadensis ‘Zhongliao1’ in response to low temperature stress |
| title_fullStr | Transcriptome analysis of Populus × canadensis ‘Zhongliao1’ in response to low temperature stress |
| title_full_unstemmed | Transcriptome analysis of Populus × canadensis ‘Zhongliao1’ in response to low temperature stress |
| title_short | Transcriptome analysis of Populus × canadensis ‘Zhongliao1’ in response to low temperature stress |
| title_sort | transcriptome analysis of populus canadensis zhongliao1 in response to low temperature stress |
| topic | Poplar Freeze–thaw injury Overwintering Low temperature stress Cold stress response |
| url | https://doi.org/10.1186/s12864-023-09187-7 |
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