Identification of functional pathways and hub genes associated with the heterochronic development of sugarcane axillary buds and sett roots through multi-omics analysis

Jiabao Zheng ¹ Xiaoyu Huang ¹ Yanli Wei ¹ Wenyan Li ¹ Baoshan Chen ^1,2* Wenlan Li ^1,2*

• ¹ State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources, Guangxi University, Nanning, China
• ² Key Laboratory for Sugarcane Biology, Guangxi University, Nanning, Guangxi Zhuang Region, China

Sugarcane is primarily propagated for large-scale agricultural production through vegetative reproduction by planting stem cuttings. The selection of sprouting strategy for these cuttings establishes the foundation for sugarcane growth and sugar accumulation. Therefore, investigating the developmental patterns of stem cuttings is essential. We observed asynchronous development during the sprouting of stem cuttings in two sugarcane cultivars with the same genetic background: the axillary buds of cultivar ZZ2 (ZZ2B) sprout earlier, while the sett roots of ZZ9 (ZZ9R) emerge sooner. Paraffin section cross-sections of sett roots on the 12th day indicated that ZZ9 has a lower root cortex thickness ratio and a higher vascular cylinder thickness ratio, which suggests that earlier root emergence enhances water uptake capacity in sugarcane. We also identified significant differences in the levels of soluble sugars, 3-Indolebutyric acid (IBA), N6-isopentenyladenosine (IPA), cis-Zeatin (cZ), Abscisic Acid (ABA), Gibberellin A3 (GA3), Gibberellin A7 (GA7), (±)-Jasmonic acid (JA), and N-((-)-jasmonoyl)-S-isoleucine (JA-Ile) between these cultivars using physiological and biochemical assays and ultra-high performance liquid chromatography-MS/MS (UHPLC-MS/MS). These differences play a crucial role in determining the selection of distinct sprouting strategies in sugarcane stem cuttings. In addition, we identified differentially expressed genes through transcriptomic analysis and discovered, via GO and KEGG enrichment analyses, that negative regulation of external stimulus response is key to the preference of ZZ2 for early bud sprouting. Meanwhile the Twin-arginine translocation complex (Tat) significantly influences the preference of ZZ9's root emergence. Furthermore, weighted gene co-expression network analysis (WGCNA) revealed that specific metabolic processes in seed coat mucilage uniquely determine the asynchronous development of sett roots and axillary buds. Our findings provide a theoretical foundation and new research perspective for understand asynchronous development in sugarcane agricultural production, offering novel insights for breeding high-quality varieties.