Oryza sativa Transcriptome or Gene expression

Abrupt drought-flood alternation (T1) is a meteorological disaster that frequently occurs during summer in southern China and the Yangtze river basin. Studying the physiological and translational dynamic mechanism of rice yield recovery after abrupt drought-flood alternation has great potential benefits for production application. The main reason for the yield recovery of nitrogen (N) supply after abrupt drought-flood alternation (T1_N) was the increase in effective panicle per plant. N application is achieved by regulating the physiological and biochemical processes such as endogenous hormone balance, N metabolism enzymes, antioxidant enzyme activities, photosynthesis, osmotic adjustment substances, dry matter accumulation and transport, and N absorption and utilization to achieve rapid growth recovery effect after abrupt drought-flood alternation stress in rice. Using ribosome profiling combined with RNA-seq sequencing technology, analysis of the interaction between transcription and translation of N supply recovery after abrupt drought-flood alternation has shown that a small proportion of response genes (14.0% of up-regulated genes and 6.6% of down-regulated genes) were shared between transcription and translation level, which revealed the independence of N supply recovery transcription and translation response after abrupt drought-flood alternation. Further analysis shows that the translation efficiency (TE) of the gene is greatly influenced by its sequence characteristics, including GC content, coding sequence length and normalized minimum free energy. Genome-wide analysis found that 7003 genes contained upstream open reading frames (uORFs). compared with untranslated uORFs, the increased number of translated uORFs promoted the improvement of TE. The TE of uORF in T1_N is lower than that TE of uORF in T1 on a genome-wide basis. This study defines the genome-wide translation regulation pattern of N supply after abrupt drought-flood alternation stress, which is helpful to understand the highly dynamic translation mechanism of rice and provides insights for future field production and breeding.

旱涝急转（Abrupt drought-flood alternation，T1）是我国南方及长江流域夏季频发的气象灾害。解析旱涝急转后水稻产量恢复的生理及翻译调控动态机制，对农业生产应用具有重要潜在价值。旱涝急转后施氮处理（T1_N）下水稻产量恢复的核心原因，在于单株有效穗数的提升。施氮通过调控内源激素平衡、氮代谢酶活性、抗氧化酶活性、光合作用、渗透调节物质、干物质积累与转运以及氮素吸收利用等生理生化过程，帮助水稻在旱涝急转胁迫后快速恢复生长。本研究结合核糖体图谱技术（ribosome profiling）与RNA测序（RNA-seq）技术，对旱涝急转后施氮恢复过程中转录与翻译的互作关系进行分析，结果显示仅有少量响应基因（上调基因中的14.0%、下调基因中的6.6%）在转录与翻译水平上存在共调控，这表明旱涝急转后施氮恢复的转录与翻译响应具有独立性。进一步分析显示，基因的翻译效率（Translation Efficiency，TE）受其序列特征显著影响，包括GC含量、编码区长度以及标准化最小自由能。全基因组分析发现，共有7003个基因包含上游开放阅读框（upstream open reading frames，uORFs）。与未翻译的上游开放阅读框相比，被翻译的上游开放阅读框数量增加可促进翻译效率的提升。全基因组范围内，施氮处理（T1_N）中上游开放阅读框的翻译效率低于旱涝急转处理（T1）。本研究阐明了旱涝急转胁迫下施氮后的全基因组翻译调控模式，有助于解析水稻高度动态的翻译调控机制，为后续田间生产与育种研究提供了新的视角。