Genome-wide characterization of the WRKY gene family in cultivated strawberry (Fragaria x ananassa Duch.) and the importance of several group III members in continuous cropping

WRKY transcription factors play important roles in many plant developmental processes and adaptation to the environment. However, little knowledge is available about the WRKY gene family in cultivated strawberry (Fragaria x ananassa Duch.), an important soft fruit worldwide. In this study, a total of 47 WRKY gene members were identified and renamed on the basis of their order on the chromosomes. According to their evolutionary events and conserved structure, the 47 FaWRKYs were divided into three major groups with several subgroups. A cis-element analysis showed that all FaWRKYs possessed at least one stress response-related cis-element. Comprehensive analysis, including phylogenetic analysis and expression profiling, based on real-time qPCR analysis in root, stem, leaf and fruit was performed on group III Fa WRKY genes. The phylogenetic tree of the WRKY III genes in cultivated strawberry, wild Strawberry, Arabidopsis, tomato, and rice was divided into five clades. Additionally, the expression profiles of the Fa WRKY genes in response to continuous cropping were further investigated based on RNA-seq data. FaWRKY25, FaWRKY32, and FaWRKY45, which are group III Fa WRKY genes, were upregulated after continuous cropping. The level of reactive oxygen species (ROS) and the expression levels of PR1 and peroxidase were higher in continuous cropping (CC) than in non-continuous cropping (NCC). The results indicated that group III FaWRKYs might play an important role in continuous cropping. These results provide a foundation for genetic improvements for continuous cropping tolerance in cultivated strawberry.