Transcriptome Time-Course Analysis unravels the regulatory networks governing ratooning decline in sugarcane

Sisi Zhang¹Feiyan Zhao¹Zongtao Yang²Ting Yang²Yanye Li²Zhongfu Zhang²Jianming Wu³Jiayong Liu²Jun Deng²Yong Zhao^2*Yuebing Zhang²

• ¹Fujian Agriculture and Forestry University, Fuzhou, China
• ²Yunnan Academy of Agricultural Sciences Yunnan Sugarcane Research Institute, Kaiyuan, China
• ³Sugarcane Research Institute, Guangxi Academy of Agricultural Sciences, Nanning, Nanning, China

Ratooning cultivation is the predominant production mode for sugarcane, yet ratooning decline represents a critical constraint limiting high and stable yields. To elucidate the molecular mechanisms underlying this phenomenon, this study integrated five consecutive years of field yield data (from plant cane to the fourth ratoon, PC–R4) with root time-course transcriptome data from three sugarcane varieties (YT93-159, YZ05-51, and YZ08-1609). Results showed that yields of the three varieties decreased significantly by 14.3%, 12.64%, and 9.45% (P < 0.05), respectively, in R3 (third ratoon) compared to PC (plant cane), indicating the R2-R3 transition as the critical turning point for ratooning decline. Based on this pivotal period, 11,348, 20,638, and 21,977 differentially expressed genes (DEGs) associated with ratooning decline were identified of R3 versus R2 in the three varieties, respectively. Further Mfuzz time-course clustering and WGCNA analyses identified five highly overlapping gene modules with overlap rates ranging from 48% to 100%, from which 25 hub genes were screened. Among these, 15 exhibited peak expression - 删除[张思思]: during R3. Functional enrichment analysis revealed that these hub genes coordinately constitute a regulatory network encompassing energy metabolism, signal transduction, protein homeostasis, and defense responses. Notably, different varieties exhibited specific response pathways within this regulatory network. Transcriptome profiling combined with qRT-PCR validation demonstrated that during the R3 decline phase, YT93-159 specifically upregulated galactinol synthase (GOLS) to enhance osmotic adjustment; YZ05-51 primarily relied on thiosulfate sulfurtransferase (STR) to maintain cellular redox homeostasis; and YZ08-1609 upregulated ubiquitin ligase and proteasome subunit genes to strengthen protein quality control. This study identifies the critical period of ratooning decline and uncovers variety-specific coping mechanisms at the molecular level. The key hub genes revealed here offer valuable molecular targets and genetic resources for the breeding of strong-ratooning sugarcane varieties.