Genome-Wide Mining and Identification of Protein Kinase Gene Family Impacts Salinity Stress Tolerance in Highly Dense Genetic Map Developed from Interspecific Cross between G. hirsutum L. and G. darwinii G. Watt

Abiotic stress is an important limiting factor in crop growth and yield around the world. Owing to the continued genetic erosion of the upland cotton germplasm due to intense selection and inbreeding, attention has shifted towards wild cotton progenitors which offer unique traits that can be introgressed into the cultivated cotton to improve their genetic performance. The purpose of this study was to characterize the Pkinase gene family in a previously developed genetic map of the F-2 population derived from a cross between two cotton species: Gossypium hirsutum (CCRI 12-4) and Gossypium darwinii (5-7). Based on phylogenetic analysis, Pkinase (PF00069) was found to be the dominant domain with 151 genes in three cotton species, categorized into 13 subfamilies. Structure analysis of G. hirsutum genes showed that a greater percentage of genes and their exons were highly conserved within the group. Syntenic analysis of gene blocks revealed 99 duplicated genes among G. hirsutum, Gossypium arboreum and Gossypium raimondii. Most of the genes were duplicated in segmental pattern. Expression pattern analysis showed that the Pkinase gene family possessed species-level variation in induction to salinity and G. darwinii had higher expression levels as compared to G. hirsutum. Based on RNA sequence analysis and preliminary RT-qPCR verification, we hypothesized that the Pkinase gene family, regulated by transcription factors (TFs) and miRNAs, might play key roles in salt stress tolerance. These findings inferred comprehensive information on possible structure and function of Pkinase gene family in cotton under salt stress.