Co-expression gene network analysis identifies key regulators of root development in contrasting gamma...

Sugarcane is a global cash and bioenergy crop whose highly water-intensive cultivation poses a risk for sustainable production, especially given the progressively worsening drought stress scenario. This necessitates the development and use of high-yielding sugarcane varieties with improved water use efficiency and drought tolerance to meet current and future production goals. Given the crucial role of root system architecture (RSA) in lodging resistance, water uptake, nutrient absorption, and stress tolerance in sugarcane, understanding the genetic regulation of root development is essential for breeding high-yielding drought-tolerant varieties. Using gamma ray-induced in vitro mutagenesis of a popular sugarcane variety Co 99004, we have developed two sugarcane mutant lines- super shoot-root mutant (SRM) and rootless mutant (RLM). While SRM exhibited highly differentiating meristematic cells and accelerated root development, RLM was devoid of a proper root meristematic layer and root system. Using a tissue-specific transcriptome profiling, we have demonstrated that an auxin-centric transcriptional network of cell wall development-associated genes is responsible for the divergent root system architecture (RSA) exhibited by the mutant lines. Higher root growth in SRM was associated with the activation of coordinated network of auxin, histone, peroxidases and cell-wall remodelling hub genes. By contrast, HY5-mediated upregulation of light and photosynthesis-related gene expression contributed towards poor root development in RLM. The key hub genes identified by WGCNA are promising candidates for genetic improvement of RSA and drought tolerance in sugarcane. Finally, SRM, with its accelerated root development and vigorous RSA, holds potential agronomic relevance in present and future climatic scenario.