Drought response revealed by chromatin organization variation and transcriptional regulation in cotton

Zhang, Boyang; Long, Yuexuan; Pei, Liuling; Huang, Xianhui; Li, Baoqi; Han, Bei; Zhang, Mengmeng; Lindsey, Keith; Zhang, Xianlong; Wang, Maojun; Yang, Xiyan

Abstract

Background: Cotton is a major world cash crop and an important source of natural fiber, oil, and protein. Drought stress is becoming a restrictive factor affecting cotton production. To facilitate the development of drought-tolerant cotton varieties, it is necessary to study the molecular mechanism of drought stress response by exploring key drought-resistant genes and related regulatory factors. Results: In this study, two cotton varieties, ZY007 (drought-sensitive) and ZY168 (drought-tolerant), showing obvious phenotypic differences under drought stress, were selected. A total of 25,898 drought-induced genes were identified, exhibiting significant enrichment in pathways related to plant stress responses. Under drought induction, At subgenome expression bias was observed at the whole-genome level, which may be due to stronger inhibition of Dt subgenome expression. A gene co-expression module that was significantly associated with drought resistance was identified. About 90% of topologically associating domain (TAD) boundaries were stable, and 6613 TAD variation events were identified between the two varieties under drought. We identified 92 genes in ZY007 and 98 in ZY168 related to chromatin 3D structural variation and induced by drought stress. These genes are closely linked to the cotton response to drought stress through canonical hormone-responsive pathways, modulation of kinase and phosphatase activities, facilitation of calcium ion transport, and other related molecular mechanisms. Conclusions: These results lay a foundation for elucidating the molecular mechanism of the cotton drought response and provide important regulatory locus and gene resources for the future molecular breeding of drought-resistant cotton varieties.

Citation

Zhang, B., Long, Y., Pei, L., Huang, X., Li, B., Han, B., …Yang, X. (2024). Drought response revealed by chromatin organization variation and transcriptional regulation in cotton. BMC Biology, 22(1), Article 114. https://doi.org/10.1186/s12915-024-01906-0

• Journal Article Type: Article
• Acceptance Date: Apr 29, 2024
• Online Publication Date: May 20, 2024
• Publication Date: May 20, 2024
• Deposit Date: May 28, 2024
• Publicly Available Date: May 28, 2024
• Journal: BMC Biology
• Publisher: BioMed Central
• Peer Reviewed: Peer Reviewed
• Volume: 22
• Issue: 1
• Article Number: 114
• DOI: https://doi.org/10.1186/s12915-024-01906-0
• Keywords: Cotton, Drought stress response, Gene expression, TAD, Subgenomic expression bias
• Public URL: https://durham-repository.worktribe.com/output/2465890