Nitrite Promotes the Growth and Decreases the Lignin Content of indica Rice Calli: A Comprehensive Transcriptome Analysis of Nitrite-Responsive Genes during In Vitro Culture of Rice

As both major macronutrients and signal molecules, nitrogen metabolites, such as nitrate and nitrite, play an important role in plant growth and development. In this study, the callus growth of indica rice cv. 9311 was significantly enhanced by nitrite, whereas the soluble protein content remained unchanged. The deep RNA sequencing technology (RNA-seq) showed that the transcriptional profiles of cv. 9311 calli were significantly changed after adding nitrite to the nitrate-free medium, and these nitrite-responsive genes were involved in a wide range of plant processes, particularly in the secondary metabolite pathways. Interestingly, most of the genes involved in phenylpropanoid-related pathways were coordinately down-regulated by nitrite, such as four cinnamoyl-CoA reductase, and these in turn resulted in the decrease of lignin content of indica calli. Furthermore, several candidate genes related to cell growth or stress responses were identified, such as genes coding for expansins, SMALL AUXIN UP RNA (SAUR) and HSP20s, and these suggested that nitrite could probably serve as a transcriptome signal to enhance the indica calli growth by regulation of various downstream genes expression. This study contributes to a better understanding of the function of nitrite during the process of plant tissue culture and could aid in the application of this technology to improved indica genetic transformation efficiency.氮代谢物（nitrogen metabolites）作为一类重要的大量营养素与信号分子，诸如硝酸盐（nitrate）与亚硝酸盐（nitrite），在植物生长发育进程中发挥关键调控作用。本研究发现，亚硝酸盐可显著促进籼稻（indica rice）品种9311愈伤组织的生长，但其可溶性蛋白含量未发生明显变化。深度RNA测序技术（RNA-seq）结果显示，在无硝酸盐培养基中添加亚硝酸盐后，籼稻9311愈伤组织的转录组图谱发生显著改变；这些亚硝酸盐响应基因参与了众多植物生理过程，尤其富集于次生代谢物通路中。有趣的是，参与苯丙烷类相关通路的多数基因可被亚硝酸盐协同下调，例如4个肉桂酰辅酶A还原酶（cinnamoyl-CoA reductase）编码基因，这一变化继而导致籼稻愈伤组织的木质素含量降低。此外，本研究还鉴定出若干与细胞生长或胁迫响应相关的候选基因，包括膨胀素（expansins）、生长素上调小RNA（SAUR）以及热休克蛋白20家族（HSP20s）编码基因；这表明亚硝酸盐或可作为一种转录组信号，通过调控诸多下游基因的表达，进而促进籼稻愈伤组织的生长。本研究有助于更深入地理解亚硝酸盐在植物组织培养过程中的功能，同时可为该技术应用于提升籼稻遗传转化效率提供理论支撑。