Dynamic changes in the transcriptome of tropical regionoriginated king grasses in response to cold stress

Xianjun Lai ¹ Junfeng Yan ² Zihan Chen ¹ Yizheng Zhang ^3,4 Fan Luo ¹ Guangze Cai ¹ Lang Yan ^1*

• ¹ Xichang College, Xichang, China
• ² Chengdu Ke’an Technology Co., Ltd., Chengdu, Sichuan Province, China
• ³ Sichuan University, Chengdu, Sichuan Province, China
• ⁴ Mianyang Youxian Innovation Technology and Industrial Technology Research Institute, Mianyang, China

The mechanism underlying cold acclimatization in tropical region-originated plants is complicated, involving the reprogramming of gene expression to adapt to constantly changing temperatures. The molecular mechanism and related gene networks involved in the regulation of cold tolerance in king grass are largely unknown.Here, we established a full-length reference transcriptome of king grass that significantly improved the assemble quality and conducted multiple time-point transcriptomic analyses after cold treatment at 4°C. Our results demonstrated that the expression profiles of the king grass genes exhibited progressive expression dynamics as a cold accumulation process, which could be classified as early (before 3 h), middle (6~24 h) and late responses (48 and 72 h). A total of 13,056 DEGs were identified and classified into nine clusters through cluster analysis (k-means). The DEGs associated with crucial, basic biological processes were most significantly enriched. The early responsive genes were enriched in glycolipid metabolism and photosynthesis, the genes responsive to the middle-stage stress were mainly enriched in carbohydrate metabolism, and the genes exhibiting constant upregulation in late-stage response were related to response to cold stress, osmotic stress, and acid chemical and endogenous stimulus. We in further identified the differentially expressed genes (DEGs) and transcription factors (TFs) that were critical for the later-stage response to cold stress, including 13 positive and negative regulators of the ICE-CBF-COR signaling module. The co-expression regulatory network constructed based on the gene expression patterns after exposure to cold stress showed the mutual regulatory relationship between these ICE-CBF-COR signaling module genes. Our findings provided an improved understanding of the cold tolerance of king grass, laying the foundation for the genetic modification of cold stress regulators, which is of great significance to the study of low-temperature adaptive mechanisms in tropical region-originated plants.