Spatiotemporal Transcriptomic Analysis of Saccharum robustum Reveals Developmental Dynamics and Key Role of 4CL Genes in Lignin Biosynthesis and Stress Response

Abstract

Saccharum robustum, a pivotal wild relative within the Saccharum, serves as a crucial reservoir of genetic diversity for improving lodging resistance in sugarcane breeding. However, the developmental dynamics and transcriptomic mechanisms underpinning its lodging resistance remain largely unexplored. Here, we conducted a spatiotemporal transcriptomic analysis of roots, leaves, and stem segments (basal, middle, and apical) in S. robustum, which revealed greater transcriptome complexity in underground tissues compared to above-ground organs. Tissue-specific enrichment analysis revealed that leaf-specific transcripts were predominantly associated with photosynthesis, whereas root-specific transcripts were enriched for defence responses and lignification pathways. Gene regulatory network inference identified key transcription factors governing tissue development. Genes involved in cellulose biosynthesis were highly expressed in stems, while lignin biosynthesis genes were upregulated in both roots and stems. We further investigated 4-Coumarate: CoA ligase (4CL), a key branch-point enzyme in the phenylpropanoid pathway. We identified 17 Ss4CL and 38 So4CL members from AP85-441 (S. spontaneum) and LA-purple (S. officinarum), respectively. Promoter analysis revealed enrichment of cis-regulatory elements responsive to plant hormones and abiotic stresses. Evolutionary analysis indicated that the 4CL gene family has primarily undergone purifying selection. Notably, Ss4CL1/4/6 exhibited high expression in roots and stems. qRT-PCR validation showed that their expression levels were significantly lower in smut-resistant varieties (ZZ1, ZZ6, ZZ9) compared to smut-susceptible ones (GT42, ROC22, FN41), suggesting that these genes respond to smut disease. In summary, this study provides comprehensive insights into the transcriptional regulation of S. robustum development and pinpoints candidate genes for optimizing lignin biosynthesis and disease resistance in cultivated sugarcane.