Niu Yuan, Fan Song, Cheng Baoshan, Li Henan, Wu Jiang, Zhao Hongliang, Huang Zhiwei, Yan Feiyu, Qi Bo, Zhang Linqing, Zhang Guoliang
School of Life Science and Food Engineering, Huaiyin Institute of Technology, Huai'an, 223003, China.
Huaiyin Institute of Agricultural Science in Xuhuai Region of Jiangsu Province, Huai'an, 223001, China.
Plant Cell Rep. 2023 Apr;42(4):707-722. doi: 10.1007/s00299-023-02984-0. Epub 2023 Feb 1.
The resistance of Huaidao5 results from the high constitutive expression of tolerance genes, while that of Huaidao9 is due to the cold-induced resistance in flag leaves and panicles. The regulation mechanism of rice seedlings' cold tolerance is relatively clear, and knowledge of its underlying mechanisms at the reproductive stage is limited. We performed differential expression and co-expression network analyses to transcriptomes from panicle and flag leaf tissues of a cold-tolerant cultivar (Huaidao5), and a sensitive cultivar (Huaidao9), under reproductive-stage cold stress. The results revealed that the expression levels of genes in stress-related pathways such as MAPK signaling pathway, diterpenoid biosynthesis, glutathione metabolism, plant-pathogen interaction and plant hormone signal transduction were constitutively highly expressed in Huaidao5, especially in panicles. Moreover, the Hudaidao5's panicle sample-specific (under cold) module contained some genes related to rice yield, such as GW5L, GGC2, SG1 and CTPS1. However, the resistance of Huaidao9 was derived from the induced resistance to cold in flag leaves and panicles. In the flag leaves, the responses included a series of stress response and signal transduction, while in the panicles nitrogen metabolism was severely affected, especially 66 endosperm-specific genes. Through integrating differential expression with co-expression networks, we predicted 161 candidate genes (79 cold-responsive genes common to both cultivars and 82 cold-tolerance genes associated with differences in cold tolerance between cultivars) potentially affecting cold response/tolerance, among which 85 (52.80%) were known to be cold-related genes. Moreover, 52 (65.82%) cold-responsive genes (e.g., TIFY11C, LSK1 and LPA) could be confirmed by previous transcriptome studies and 72 (87.80%) cold-tolerance genes (e.g., APX5, OsFbox17 and OsSTA109) were located within QTLs associated with cold tolerance. This study provides an efficient strategy for further discovery of mechanisms of cold tolerance in rice.
淮稻5号的抗性源于耐受基因的高组成型表达，而淮稻9号的抗性则归因于剑叶和穗部的冷诱导抗性。水稻幼苗耐冷性的调控机制相对明确，但其在生殖阶段潜在机制的了解有限。我们对耐冷品种（淮稻5号）和敏感品种（淮稻9号）在生殖阶段冷胁迫下的穗部和剑叶组织转录组进行了差异表达和共表达网络分析。结果表明，与胁迫相关途径（如丝裂原活化蛋白激酶信号通路、二萜生物合成、谷胱甘肽代谢、植物-病原体相互作用和植物激素信号转导）中的基因表达水平在淮稻5号中组成型高表达，尤其是在穗部。此外，淮稻5号穗部样本特异性（低温下）模块包含一些与水稻产量相关的基因，如GW5L、GGC2、SG1和CTPS1。然而，淮稻9号的抗性源于剑叶和穗部对冷的诱导抗性。在剑叶中，响应包括一系列应激反应和信号转导，而在穗部，氮代谢受到严重影响，尤其是66个胚乳特异性基因。通过将差异表达与共表达网络相结合，我们预测了161个可能影响冷响应/耐受性的候选基因（79个两个品种共有的冷响应基因和82个与品种间耐冷性差异相关的耐冷基因），其中85个（52.80%）已知为冷相关基因。此外，52个（65.82%）冷响应基因（如TIFY11C、LSK1和LPA）可通过先前的转录组研究得到证实，72个（87.80%）耐冷基因（如APX5、OsFbox17和OsSTA109）位于与耐冷性相关的数量性状位点内。本研究为进一步揭示水稻耐冷机制提供了有效策略。
