Genome-wide analysis of the sugarcane PTP family combined with yeast cDNA library screening identifies key cold-responsive genes

Sugarcane ( Saccharum spp.) is an important industrial crop. Its sucrose accumulation and overall biomass utilization for bioethanol production are highly vulnerable to environmental stresses, particularly cold stress. Protein tyrosine phosphatases (PTP) have been reported to participate in cold stress signaling in other plant species, but their roles in sugarcane remain largely unknown. To identify and investigate the mechanisms by which PTP regulate cold tolerance in sugarcane, we performed a genome-wide analysis of the PTP gene family. Gene structure analysis revealed conserved exon-intron patterns within each subfamily, while promoter analysis indicated that most PTP genes harbor cis -regulatory elements (CREs) associated with Abscisic Acid (ABA) and stress responses. A further yeast cDNA library screening under cold stress conditions identified 23 ScPTP candidates responsive to low temperature, among which Saccharum dual specificity phosphatase 2 ( ScDSP2 ) was selected for further functional characterization. Transgenic Arabidopsis assays demonstrated that ScDSP2 significantly enhanced plant tolerance to cold stress. Transcriptome profiling further revealed that ScDSP2 regulates circadian rhythm and integrates multiple phytohormone signaling pathways to optimize energy allocation under cold conditions. Overall, this work provides the first comprehensive genome-wide analysis of the sugarcane PTP family and identifies key regulators of cold signaling, offering a valuable gene resource for improving cold tolerance in sugarcane. • A total of 117 PTP (protein tyrosine phosphatases) genes were identified and classified into seven subfamilies in sugarcane. • Twenty-three ScPTP genes were responsive to cold stress from yeast library screening. • Overexpression of ScDSP2 ( Saccharum dual specificity phosphatase 2) enhanced cold tolerance in transgenic Arabidopsis. • The ScDSP2 ( Saccharum dual specificity phosphatase 2) protein integrates circadian and hormone pathways under cold stress.