Genome-wide identification and unveiling the role of MAP kinase cascade genes involved in sugarcane response to abiotic stressors

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Abstract Background The MAP Kinase cascade system is a conserved signaling mechanism essential for plant development, growth, and stress tolerance. Thus far, genes from the MAPK cascade have been identified in several plant species but remain uncharacterized in the polyploid Saccharum spp. Hybrid R570 genome. Results This study identified 89 ScMAPK, 24 ScMAPKK, and 107 ScMAPKKK genes through genome-wide analysis. Phylogenetic classification revealed that four subgroups were present in each ScMAPK and ScMAPKK family, and three sub-families (ZIK-like, RAF-like, and MEKK-like) presented in the ScMAPKKK family. Conserved motif and gene structure analysis supported the evolutionary relationships of the three families inferred from the phylogenetic analysis. All of the ScMAPK, ScMAPKK and ScMAPKKK genes were mapped on four scaffolds (Scaffold_88/89/91/92) and nine chromosomes (1–8, 10). Collinearity and gene duplication analysis identified 169 pairs of allelic and non-allelic segmentally duplicated MAPK cascade genes, contributing to their expansion. Additionally, 13 putative ‘ss-miRNAs’ were predicted to target 87 MAPK cascade genes, with ‘ssp-miR168a’ alone regulating 45 genes. qRT-PCR analysis revealed differential gene expression under abiotic stressors. ScMAPK07, ScMAPK66, and ScRAF43 were down-regulated and acted as negative regulators. Conversely, ScMAPKK13, ScRAF10, and ScZIK18 were up-regulated at specific time points under drought, with ScZIK18 exhibiting strong defense. Under NaCl stress, most genes were down-regulated, except for slight increases in ScZIK18 and ScMAPKK13, suggesting a positive role in salt stress response. Under CaCl2 stress, five genes were significantly down-regulated, while ScRAF43 remained unchanged, reflecting their negative roles in stress adaptation and resource conservation. Conclusion This study provides insights into MAPK cascade gene evolution and function in sugarcane, highlighting distinct regulatory roles in abiotic stress responses. Interestingly, some genes acted as negative regulators, serving as a mechanism to balance stress responses and prevent overactivation. In contrast, others contributed to defense mechanisms, offering potential targets for stress resilience improvement. Clinical Trail Number This study contains no clinical trials. Not applicable.

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