Molecular mechanism analysis of natural leaf abscission in sugarcane based on multi-omics and mining of key genes in ABA pathway

Abstract

Poor leaf abscission in sugarcane significantly increases harvesting costs and constrains mechanized efficiency, yet its molecular basis remains poorly understood. Here, we performed an integrated hormone-targeted metabolomics and transcriptomics analysis in three sugarcane cultivars (GT47, LZ02-169, and ROC22) with contrasting abscission phenotypes. A total of 37 differentially accumulated metabolites and 3109 differentially expressed genes (DEGs) were identified. Integrated analysis revealed extensive reprogramming of phytohormone-related pathways, particularly those associated with auxin, jasmonic acid, abscisic acid (ABA), salicylic acid, gibberellin, and cytokinin. Notably, comparisons involving LZ02-169 and GT47 showed a higher enrichment of hormone-related DEGs, indicating dynamic hormonal regulation underlying phenotypic divergence. Focusing on ABA biosynthesis, two key genes, zeaxanthin epoxidase (ZEP) and β-carotene hydroxylase (BCH), were consistently upregulated in abscission-prone cultivars. Metabolomic data further supported increased accumulation of ABA precursors, including zeaxanthin, suggesting activation of the carotenoid-derived ABA biosynthetic pathway. Correlation analysis indicated a strong association between ZEP/BCH expression and ABA accumulation. Importantly, Upregulation of ZEP and BCH is associated with increased ABA accumulation in the leaf abscission zone, suggesting a potential role for this carotenoid-derived pathway in modulating cell separation during natural abscission. This coordinated transcriptional–metabolic regulation suggests that ABA is a potential key correlate of natural leaf abscission in sugarcane. Collectively, this study provides a multi-omics correlative framework linking carotenoid metabolism to hormone signaling and identifies ZEP and BCH as promising targets for improving sugarcane harvesting efficiency.