Comprehensive transcriptome analysis reveals heat-responsive genes in flowering Chinese cabbage (Brassica campestris L. ssp. chinensis) using RNA sequencing
Flowering Chinese cabbage (Brassica campestris L. ssp. chinensis var. utilis Tsen et Lee, 2n=20, AA) is a vegetable species in southern parts of China that faces high temperatures in the summer and winter seasons. While heat stress adversely impacts plant productivity and survival, the underlying mo...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2022-12-01
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| Series: | Frontiers in Plant Science |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fpls.2022.1077920/full |
| _version_ | 1797987799500062720 |
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| author | Muhammad Ikram Jingfang Chen Yanshi Xia Ronghua Li Kadambot H. M. Siddique Peiguo Guo |
| author_facet | Muhammad Ikram Jingfang Chen Yanshi Xia Ronghua Li Kadambot H. M. Siddique Peiguo Guo |
| author_sort | Muhammad Ikram |
| collection | DOAJ |
| description | Flowering Chinese cabbage (Brassica campestris L. ssp. chinensis var. utilis Tsen et Lee, 2n=20, AA) is a vegetable species in southern parts of China that faces high temperatures in the summer and winter seasons. While heat stress adversely impacts plant productivity and survival, the underlying molecular and biochemical causes are poorly understood. This study investigated the gene expression profiles of heat-sensitive (HS) ‘3T-6’ and heat-tolerant (HT) ‘Youlu-501’ varieties of flowering Chinese cabbage in response to heat stress using RNA sequencing. Among the 37,958 genes expressed in leaves, 20,680 were differentially expressed genes (DEGs) at 1, 6, and 12 h, with 1,078 simultaneously expressed at all time points in both varieties. Hierarchical clustering analysis identified three clusters comprising 1,958, 556, and 591 down-regulated, up-regulated, and up- and/or down-regulated DEGs (3205 DEGs; 8.44%), which were significantly enriched in MAPK signaling, plant–pathogen interactions, plant hormone signal transduction, and brassinosteroid biosynthesis pathways and involved in stimulus, stress, growth, reproductive, and defense responses. Transcription factors, including MYB (12), NAC (13), WRKY (11), ERF (31), HSF (17), bHLH (16), and regulatory proteins such as PAL, CYP450, and photosystem II, played an essential role as effectors of homeostasis, kinases/phosphatases, and photosynthesis. Among 3205 DEGs, many previously reported genes underlying heat stress were also identified, e.g., BraWRKY25, BraHSP70, BraHSPB27, BraCYP71A23, BraPYL9, and BraA05g032350.3C. The genome-wide comparison of HS and HT provides a solid foundation for understanding the molecular mechanisms of heat tolerance in flowering Chinese cabbage. |
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| id | doaj.art-89d4c1f52ec943fdbfa66c508a9033ce |
| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-04-11T07:53:53Z |
| publishDate | 2022-12-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Plant Science |
| spelling | doaj.art-89d4c1f52ec943fdbfa66c508a9033ce2022-12-22T04:36:00ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2022-12-011310.3389/fpls.2022.10779201077920Comprehensive transcriptome analysis reveals heat-responsive genes in flowering Chinese cabbage (Brassica campestris L. ssp. chinensis) using RNA sequencingMuhammad Ikram0Jingfang Chen1Yanshi Xia2Ronghua Li3Kadambot H. M. Siddique4Peiguo Guo5Guangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, International Crop Research Center for Stress Resistance, School of Life Sciences, Guangzhou University, Guangzhou, ChinaGuangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, International Crop Research Center for Stress Resistance, School of Life Sciences, Guangzhou University, Guangzhou, ChinaGuangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, International Crop Research Center for Stress Resistance, School of Life Sciences, Guangzhou University, Guangzhou, ChinaGuangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, International Crop Research Center for Stress Resistance, School of Life Sciences, Guangzhou University, Guangzhou, ChinaThe UWA Institute of Agriculture, UWA School of Agriculture & Environment, The University of Western Australia, Perth, WA, AustraliaGuangdong Provincial Key Laboratory of Plant Adaptation and Molecular Design, International Crop Research Center for Stress Resistance, School of Life Sciences, Guangzhou University, Guangzhou, ChinaFlowering Chinese cabbage (Brassica campestris L. ssp. chinensis var. utilis Tsen et Lee, 2n=20, AA) is a vegetable species in southern parts of China that faces high temperatures in the summer and winter seasons. While heat stress adversely impacts plant productivity and survival, the underlying molecular and biochemical causes are poorly understood. This study investigated the gene expression profiles of heat-sensitive (HS) ‘3T-6’ and heat-tolerant (HT) ‘Youlu-501’ varieties of flowering Chinese cabbage in response to heat stress using RNA sequencing. Among the 37,958 genes expressed in leaves, 20,680 were differentially expressed genes (DEGs) at 1, 6, and 12 h, with 1,078 simultaneously expressed at all time points in both varieties. Hierarchical clustering analysis identified three clusters comprising 1,958, 556, and 591 down-regulated, up-regulated, and up- and/or down-regulated DEGs (3205 DEGs; 8.44%), which were significantly enriched in MAPK signaling, plant–pathogen interactions, plant hormone signal transduction, and brassinosteroid biosynthesis pathways and involved in stimulus, stress, growth, reproductive, and defense responses. Transcription factors, including MYB (12), NAC (13), WRKY (11), ERF (31), HSF (17), bHLH (16), and regulatory proteins such as PAL, CYP450, and photosystem II, played an essential role as effectors of homeostasis, kinases/phosphatases, and photosynthesis. Among 3205 DEGs, many previously reported genes underlying heat stress were also identified, e.g., BraWRKY25, BraHSP70, BraHSPB27, BraCYP71A23, BraPYL9, and BraA05g032350.3C. The genome-wide comparison of HS and HT provides a solid foundation for understanding the molecular mechanisms of heat tolerance in flowering Chinese cabbage.https://www.frontiersin.org/articles/10.3389/fpls.2022.1077920/fullheat stresstranscriptomedifferentially expressed genescluster analysisflowering chinese cabbageRT-qPCR |
| spellingShingle | Muhammad Ikram Jingfang Chen Yanshi Xia Ronghua Li Kadambot H. M. Siddique Peiguo Guo Comprehensive transcriptome analysis reveals heat-responsive genes in flowering Chinese cabbage (Brassica campestris L. ssp. chinensis) using RNA sequencing Frontiers in Plant Science heat stress transcriptome differentially expressed genes cluster analysis flowering chinese cabbage RT-qPCR |
| title | Comprehensive transcriptome analysis reveals heat-responsive genes in flowering Chinese cabbage (Brassica campestris L. ssp. chinensis) using RNA sequencing |
| title_full | Comprehensive transcriptome analysis reveals heat-responsive genes in flowering Chinese cabbage (Brassica campestris L. ssp. chinensis) using RNA sequencing |
| title_fullStr | Comprehensive transcriptome analysis reveals heat-responsive genes in flowering Chinese cabbage (Brassica campestris L. ssp. chinensis) using RNA sequencing |
| title_full_unstemmed | Comprehensive transcriptome analysis reveals heat-responsive genes in flowering Chinese cabbage (Brassica campestris L. ssp. chinensis) using RNA sequencing |
| title_short | Comprehensive transcriptome analysis reveals heat-responsive genes in flowering Chinese cabbage (Brassica campestris L. ssp. chinensis) using RNA sequencing |
| title_sort | comprehensive transcriptome analysis reveals heat responsive genes in flowering chinese cabbage brassica campestris l ssp chinensis using rna sequencing |
| topic | heat stress transcriptome differentially expressed genes cluster analysis flowering chinese cabbage RT-qPCR |
| url | https://www.frontiersin.org/articles/10.3389/fpls.2022.1077920/full |
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