Cold tolerance in rice plants is partially controlled by root responses. Cold tolerance in rice plants is partially controlled by root responses

Purpose: Rice (Oryza sativa) ssp. indica is the most cultivated species in the South of Brazil. However, these plants face low temperature stress from September to November, which is the period of early sowing, affecting plant development during the initial stages of growth, and reducing rice productivity. This study aimed to characterize the roots of two rice genotypes (CT, cold-tolerant; and CS, cold-sensitive) in response to low temperature stress during the early vegetative stage. Results: RNAseq analysis revealed that contrasting genotypes present a completely different molecular response to cold stress. The number of over-represented functional categories was lower in CT than CS under cold condition, suggesting that CS genotype is more impacted by low temperature stress than CT. Several genes that might contribute to rice cold tolerance, including the ones related with cell wall remodeling (glycosyl hydrolase, cellulose synthase, glycosyl transferase, wall-associated kinase, glycine-rich cell wall structural protein), cytoskeleton and growth (microtubule-associated protein 70, kinesin motor domain containing protein, growth regulating factor protein, auxin-independent growth promoter protein, RopGEF7), signaling (receptor-like protein kinase, Rapid Alkalinization Factor 21)), antioxidant system (glutathione peroxidase, metallothionein), lipid metabolism (fatty acid desaturase and phosphatidylinositol transfer protein), and stress response (Tetratricopeptide Repeat-Containing Protein). On the other hand, high expression of the genes SRC2 (defense), root architecture associated 1 (growth), ACC oxidase, ethylene-responsive transcription factor, and cytokinin-O-glucosyltransferase 2 (hormone-related) seems to be related with cold sensibility. Even though these two genotypes have a similar genetic background (sister lines), some of these genes can probably be involved with cold tolerance or sensitivity and could be used in future biotechnological approaches aiming to increase rice tolerance to low temperature. Overall design: Identify and characterize novel genes and metabolic pathways in roots of two indica rice genotypes (CT, cold-tolerant; and CS, cold-sensitive) in response to low temperature stress (10°C for up to 10 days) during the early vegetative stage (three-leaf stage, approximately 30 days).

研究目的：籼稻（Oryza sativa ssp. indica）是巴西南部种植面积最广的水稻品种。但这类作物在9月至11月的早播期会遭遇低温胁迫，影响其生长早期的发育进程，进而降低水稻总产量。本研究旨在表征两个籼稻基因型（CT：耐冷型；CS：冷敏感型）在营养生长早期响应低温胁迫的根系特征。

研究结果：RNA测序（RNAseq）分析显示，两个基因型对低温胁迫的分子响应模式截然不同。低温条件下，CT中富集的功能类别数量少于CS，提示CS基因型比CT受到低温胁迫的影响更为显著。本研究鉴定出多个可能参与水稻冷耐受性调控的基因，涵盖以下类别：细胞壁重塑相关基因（糖基水解酶、纤维素合酶、糖基转移酶、细胞壁相关激酶、富含甘氨酸的细胞壁结构蛋白）、细胞骨架与生长调控相关基因（微管相关蛋白70、含驱动蛋白马达结构域蛋白、生长调节因子蛋白、非生长素依赖型生长启动子蛋白、RopGEF7）、信号通路相关基因（类受体蛋白激酶、快速碱化因子21（Rapid Alkalinization Factor 21））、抗氧化系统相关基因（谷胱甘肽过氧化物酶、金属硫蛋白）、脂质代谢相关基因（脂肪酸去饱和酶与磷脂酰肌醇转运蛋白）以及胁迫响应相关基因（含四肽重复结构域蛋白）。此外，SRC2（防御相关）、根系结构相关1（生长相关）、ACC氧化酶、乙烯响应转录因子以及细胞分裂素-O-葡萄糖基转移酶2（激素相关）等基因的高表达，似乎与冷敏感性密切相关。尽管两个基因型具有相似的遗传背景（姊妹系），但上述部分基因极有可能参与调控水稻的冷耐受性或冷敏感性，可作为未来提升水稻低温耐受性的生物技术研究靶点。

整体实验设计：在营养生长早期（三叶期，约30日龄），对两个籼稻基因型（CT：耐冷型；CS：冷敏感型）的根系施加低温胁迫处理（10℃，持续最长10天），以鉴定并表征其响应低温胁迫的新型基因与代谢通路。