Submergence Stress Alters the Expression of Clock Genes and Configures New Zeniths and Expression of Outputs in Brachypodium distachyon

• Published in: International journal of molecular sciences Vol. 24; no. 10; p. 8555
• Main Authors: Medina-Chávez, Lucisabel, Camacho, Christian, Martínez-Rodríguez, Jorge Arturo, Barrera-Figueroa, Blanca Estela, Nagel, Dawn H, Juntawong, Piyada, Peña-Castro, Julián Mario
• Format: Journal Article
• Language: English
• Published: Switzerland MDPI AG 10.05.2023; MDPI
• Subjects: Amplitudes; Arabidopsis - genetics; Arabidopsis Proteins - genetics; Brachypodium - genetics; Brachypodium - metabolism; Brachypodium distachyon; Carbohydrates; chronoculture; Circadian rhythm; Circadian Rhythm - genetics; Clustering; Diurnal; diurnal expression; Diurnal variations; Drought; Ecotypes; Floods; Gene expression; Gene Expression Regulation, Plant; Genes; Hypoxia; Leaves; Metabolism; Mitochondria; Photosynthesis; Rhythms; RNA-seq; Submergence; Suppressors; Transcriptome; Transcriptomes; submergence; hypoxia; chronoculture; RNA-seq; circadian rhythm; diurnal expression; abiotic stress
• ISSN: 1422-0067; 1661-6596; 1422-0067
• DOI: 10.3390/ijms24108555

Plant networks of oscillating genes coordinate internal processes with external cues, contributing to increased fitness. We hypothesized that the response to submergence stress may dynamically change during different times of the day. In this work, we determined the transcriptome (RNA sequencing) of the model monocotyledonous plant, , during a day of submergence stress, low light, and normal growth. Two ecotypes of differential tolerance, Bd21 (sensitive) and Bd21-3 (tolerant), were included. We submerged 15-day-old plants under a long-day diurnal cycle (16 h light/8 h dark) and collected samples after 8 h of submergence at ZT0 (dawn), ZT8 (midday), ZT16 (dusk), ZT20 (midnight), and ZT24 (dawn). Rhythmic processes were enriched both with up- and down-regulated genes, and clustering highlighted that the morning and daytime oscillator components ( ) show peak expression in the night, and a decrease in the amplitude of the clock genes ( , , ) was observed. Outputs included photosynthesis-related genes losing their known rhythmic expression. Up-regulated genes included oscillating suppressors of growth, hormone-related genes with new late zeniths (e.g., , ), and mitochondrial and carbohydrate signaling genes with shifted zeniths. The results highlighted genes up-regulated in the tolerant ecotype such as and . Finally, we show by luciferase assays that clock genes are also altered by submergence changing their amplitude and phase. This study can guide the research of chronocultural strategies and diurnal-associated tolerance mechanisms.