Abstract
Rice (Oryza sativa) is a tropical cereal crop that is severely affected by chilling stress at the seedling stage, although glutinous rice 89-1 (Gr89-1) in Chongqing, China, shows tolerance to low temperatures and overwintering ability. However, little research has been conducted on the mechanisms regulating chilling stress in Gr89-1. In this study, a comprehensive of transcriptional profiles of Gr89-1 seedlings at the three-leaf stage was conducted after a 4 °C treatment for 2, 6, 12, 24, or 48 h. Overall, 2993 differentially expressed genes were detected in Gr89-1 seedlings upon cold exposure. Gene Ontology testing and pathway analysis revealed differentially expressed genes involved in transcriptional regulation, carbohydrate metabolism, plant hormone signal, and cell wall composition. A total of 243 transcription factors were differentially expressed during the cold treatment; in particular, the AP2/EREBP, bHLH, NAC, WRKY, C2H2, and TIFY families were generally upregulated after cold treatment, whereas the mTERF and GNAT families were downregulated. Chilling stress changed the starch and sucrose metabolism, coupled with the accumulation of sucrose and trehalose level, and increases in jasmonic acid level in Gr89-1 seedlings. Furthermore, a number of the cell wall-related genes identified in the present study were also differentially expressed during the cold treatment. The genes and pathways identified in the current study increase our understanding of the mechanisms underlying cold resistance in rice seedlings.
Highlights
Chilling (0–15 °C) stress severely affects rice growth and development in temperate and sub-tropical areas
After 48 h, the ratio was almost zero in WH86, versus 0.456 in Glutinous rice 89-1 (Gr89-1) (Fig. 1c). These results demonstrate that Gr89-1 adapted more rapidly than WH86 in response to the low temperature treatment
82 genes were involved in different plant hormone biosynthetic and signal transduction pathways during chilling stress, including jasmonic acid(JA), brassinosteroids (BRs), gibberellins (GAs), ABA, cytokinin (CK), ethylene (ET), salicylic acid (SA), and auxin (Figs. 5 and 6, Supplementary Table S5). These data indicated that a collaboration between phytohormone biosynthesis and signal transduction might be involved in the Gr89-1 seedlings during chilling tolerance
Summary
Chilling (0–15 °C) stress severely affects rice growth and development in temperate and sub-tropical areas. Rice seedlings during early spring in such areas are often subjected to low temperatures, leading to poor growth and reduced yield (Baruah et al 2009). The C-repeat binding factor/dehydration-responsive element-binding protein 1 (CBF/ DREB1; DREB1A, DREB1B, and DREB1C)-dependent response pathway plays a vital role in cold tolerance during cold acclimation (Chinnusamy et al 2007; Kim 2007; Shinozaki et al 2003). CBFs mediate cold-responsive genes with various functions, including transcription, osmoprotectant biosynthesis, and signal transduction events (e.g., plant hormone signaling), among many others (Krasensky et al 2012; Lissarre et al 2010). Many studies have found that soluble carbohydrate, sucrose, trehalose, and stachyose drastically accumulated in plants under low temperatures (Krasensky and Jonak 2012). Jasmonic acid (JA) represents an important class of lipidderived plant hormones involved in the cold response (Peleg and Blumwald 2011). The integrative regulatory effects of JA in rice subject to cold are poorly understood
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