Genome-Wide Identification and Expression Analysis of Kinase Proteins in Land Plants and Their Expression in Gossypium hirsutum Under Salt Stress.

Abstract

The kinase proteins are a superfamily in plants and are involved in diverse biological and molecular functions for better adaptation of land plants. Protein kinase diversification is hypothesized to enhance plant adaptation to abiotic stress, particularly salinity. This study tests whether evolutionary expansions of stress-responsive kinase subfamilies correlate with functional variation in salt tolerance. The study identified a total of 49,611 genes in 32 land plants across mosses, bryophytes, lycophytes, gymnosperms, and angiosperms. All identified genes were classified into 26 major classes (I-XXVI) based on domain architectures, e.g., protein kinase tyrosine (PkT), leucine-rich repeat (LRR), LRR-protein kinases (LRR-Pk), LRR-Pk tyrosine kinases (LRR-PkT), and protein kinase (Pk) and the X domain representing other than the listed domains. RNA-seq-based expression profiling under biotic and abiotic stresses and in various plant tissue of Arabidopsis thaliana (Ath), Glycine max (Gma), Gossypium hirsutum (Ghi), Zea mays (Zma), and Oryza sativa (Osa) highlighted potential OGs including OG₁₂, OG₃₅, and OG₄₄ showing response in all plants. Furthermore, upregulation of OG₁₂_LR_GhPk08 in Ghi under both biotic, (e.g., Xanthomonas citri) and abiotic (e.g., salt, heat, and cold) stress, as well as in specific tissues like roots and seedlings, suggest a potential role in stress responses. Molecular docking analysis demonstrated the preferential binding of ATP to Ghi kinase proteins, indicating their conserved phosphorylation mechanisms. Furthermore, SNP and InDel analyses in salt-resistant (Mac7) and salt-susceptible (Coker 312) cotton genotypes revealed genetic variations potentially linked to differential stress responses. Moreover, the qRT-PCR-based expression analysis of two genes (Gohir.D08G10000; OG₁₂_LR_GhPk08, Gohir.D05G155340; OG₃₅_Pk_GhPk02) out of three, showed salt-responsive transcription under the tested condition in Mac7 and Coker 312 cotton genotypes, supporting their prioritization as candidate genes for further functional validation and characterization. Thus, the study provides a deep insight into diversity and functional responses of kinase genes in land plants, particularly, in cotton leading to future research on kinase studies.