Comparative Transcriptome and Co-Expression Network Analyses Reveal the Molecular Mechanism of Calcium-Deficiency-Triggered Tipburn in Chinese Cabbage (Brassica rapa L. ssp. Pekinensis)

Zhang, Shu; Gao, Hanzhong; Wang, Lixia; Zhang, Yihui; Zhou, Dandan; Anwar, Ali; Li, Jingjuan; Wang, Fengde; Li, Cheng; Zhang, Ye; Gao, Jianwei

doi:10.3390/plants11243555

Open AccessArticle

Comparative Transcriptome and Co-Expression Network Analyses Reveal the Molecular Mechanism of Calcium-Deficiency-Triggered Tipburn in Chinese Cabbage (Brassica rapa L. ssp. Pekinensis)

by

Shu Zhang

^1,†,

Hanzhong Gao

^2,†,

Lixia Wang

¹,

Yihui Zhang

^1,3,

Dandan Zhou

³,

Ali Anwar

¹

,

Jingjuan Li

¹,

Fengde Wang

¹,

Cheng Li

¹,

Ye Zhang

^4,* and

Jianwei Gao

^1,*

¹

Institute of Vegetables, Shandong Key Laboratory of Greenhouse Vegetable Biology, Shandong Branch of National Vegetable Improvement Center, Huanghuai Region Vegetable Scientific Station of Ministry of Agriculture (Shandong), Shandong Academy of Agricultural Sciences, Jinan 250100, China

²

Columbian College of Arts & Sciences, Phillips Hall, The George Washington University, 801 22nd St. NW., Washington, DC 20052, USA

³

College of Life Sciences, Shandong Normal University, Jinan 250061, China

⁴

College of Life Science, Huangshan University, Huangshan 245061, China

^*

Authors to whom correspondence should be addressed.

^†

These authors contributed equally to this work.

Plants 2022, 11(24), 3555; https://doi.org/10.3390/plants11243555

Submission received: 15 November 2022 / Revised: 7 December 2022 / Accepted: 14 December 2022 / Published: 16 December 2022

(This article belongs to the Special Issue Molecular Breeding for Environmental Stress Resistance in Vegetables)

Download

Browse Figures

Review Reports Versions Notes

Abstract

Chinese cabbage tipburn is characterized by the formation of necrotic lesions on the margin of leaves, including on the insides of the leafy head. This physiological disorder is associated with a localized calcium deficiency during leaf development. However, little information is available regarding the molecular mechanisms governing Ca-deficiency-triggered tipburn. This study comprehensively analysed the transcriptomic comparison between control and calcium treatments (CK and 0 mM Ca) in Chinese cabbage to determine its molecular mechanism in tipburn. Our analysis identified that the most enriched gene ontology (GO) categories are photosynthesis, thylakoid and cofactor binding. Moreover, the KEGG pathway was most enriched in photosynthesis, carbon metabolism and carbon fixation. We also analyzed the co-expression network by functional categories and identified ten critical hub differentially expressed genes (DEGs) in each gene regulatory network (GRN). These DEGs might involve abiotic stresses, developmental processes, cell wall metabolism, calcium distribution, transcription factors, plant hormone biosynthesis and signal transduction pathways. Under calcium deficiency, CNX1, calmodulin-binding proteins and CMLs family proteins were downregulated compared to CK. In addition, plant hormones such as GA, JA, BR, Auxin and ABA biosynthesis pathways genes were downregulated under calcium treatment. Likewise, HATs, ARLs and TCP transcription factors were reported as inactive under calcium deficiency, and potentially involved in the developmental process. This work explores the specific DEGs’ significantly different expression levels in 0 mM Ca and the control involved in plant hormones, cell wall developments, a light response such as chlorophylls and photosynthesis, transport metabolism and defence mechanism and redox. Our results provide critical evidence of the potential roles of the calcium signal transduction pathway and candidate genes governing Ca-deficiency-triggered tipburn in Chinese cabbage.

Keywords: Chinese cabbage; calcium deficiency; tipburn; RNA-seq; co-expression analysis

Share and Cite

MDPI and ACS Style

Zhang, S.; Gao, H.; Wang, L.; Zhang, Y.; Zhou, D.; Anwar, A.; Li, J.; Wang, F.; Li, C.; Zhang, Y.; et al. Comparative Transcriptome and Co-Expression Network Analyses Reveal the Molecular Mechanism of Calcium-Deficiency-Triggered Tipburn in Chinese Cabbage (Brassica rapa L. ssp. Pekinensis). Plants 2022, 11, 3555. https://doi.org/10.3390/plants11243555

AMA Style

Zhang S, Gao H, Wang L, Zhang Y, Zhou D, Anwar A, Li J, Wang F, Li C, Zhang Y, et al. Comparative Transcriptome and Co-Expression Network Analyses Reveal the Molecular Mechanism of Calcium-Deficiency-Triggered Tipburn in Chinese Cabbage (Brassica rapa L. ssp. Pekinensis). Plants. 2022; 11(24):3555. https://doi.org/10.3390/plants11243555

Chicago/Turabian Style

Zhang, Shu, Hanzhong Gao, Lixia Wang, Yihui Zhang, Dandan Zhou, Ali Anwar, Jingjuan Li, Fengde Wang, Cheng Li, Ye Zhang, and et al. 2022. "Comparative Transcriptome and Co-Expression Network Analyses Reveal the Molecular Mechanism of Calcium-Deficiency-Triggered Tipburn in Chinese Cabbage (Brassica rapa L. ssp. Pekinensis)" Plants 11, no. 24: 3555. https://doi.org/10.3390/plants11243555

APA Style

Zhang, S., Gao, H., Wang, L., Zhang, Y., Zhou, D., Anwar, A., Li, J., Wang, F., Li, C., Zhang, Y., & Gao, J. (2022). Comparative Transcriptome and Co-Expression Network Analyses Reveal the Molecular Mechanism of Calcium-Deficiency-Triggered Tipburn in Chinese Cabbage (Brassica rapa L. ssp. Pekinensis). Plants, 11(24), 3555. https://doi.org/10.3390/plants11243555

Note that from the first issue of 2016, this journal uses article numbers instead of page numbers. See further details here.

Article Menu

Comparative Transcriptome and Co-Expression Network Analyses Reveal the Molecular Mechanism of Calcium-Deficiency-Triggered Tipburn in Chinese Cabbage (Brassica rapa L. ssp. Pekinensis)

Abstract

Share and Cite

Article Metrics

Article Access Statistics

Further Information

Guidelines

MDPI Initiatives

Follow MDPI