Integrated transcriptomics and metabolomics analyses reveal key response mechanisms underlying ratoon growth in sugarcane

Sugarcane ( Saccharum spp.) is a globally important crop for both sugar production and bioenergy. Ratooning ability is a key agronomic trait that determines its regenerative capacity and economic efficiency. Abscisic acid (ABA) plays an important role in regulating ratoon performance in sugarcane; however, the molecular mechanisms underlying its regulatory effects remain poorly understood. In this study, two-year-old plants of Zhongtang 1 (ZT1) and Xintaitang 22 (XTT22) were subjected to root irrigation with the ABA biosynthesis inhibitor sodium tungstate (ST). The results showed that the ratoon growth decreased with increasing concentrations of ST in XTT22. In ZT1, the ratoon growth also reduced at high concentrations, but remained higher than that of XTT22, whereas under control conditions, ZT1 had less ratoon growth than XTT22. Integrated transcriptomics and metabolomics analyses revealed that ABA content in XTT22 decreased as ST concentration increased, while in ZT1, it increased. Gene set enrichment analysis (GSEA) further indicated that JA-related and nitrogen metabolism pathways were significantly suppressed in ZT1, whereas in XTT22, JA-related pathways were significantly activated and nitrogen metabolism pathways were significantly downregulated. Collectively, these results suggested that under ST stress, ZT1 activated downstream ABA and JA signaling to maintain hormonal homeostasis while reducing its nitrogen assimilation capacity to sustain ratoon ability. This study provides valuable data and theoretical support for understanding the ABA-mediated regulation of ratooning ability in sugarcane and offers a scientific basis for the breeding of strong-ratooning cultivars.