Evolution and Regulatory Roles of the KNOX Gene Family in Eucommia ulmoides in Response to Phytohormones and Abiotic Stresses

Abstract Background KNOX (KNOTTED1-like HOMEOBOX) belongs to a class of important homeobox genes, which encode the homeodomain proteins binding to the specific element of target genes, and widely participate in plant growth and development, secondary metabolite synthesis, biotic and abiotic stresses responses. However, genome-wide identification of the KNOX gene family has not been reported in E. ulmoides . Result In this study, 8 KNOX proteins were identified based on genomic database of E. ulmoides . Phylogenetic analysis showed that the EuKNOX proteins were distributed in five subgroups based on homology with KNOX proteins in Arabidopsis , these genes were unevenly distributed across six chromosomes. Gene structure analysis revealed that EuKNOX genes contained between three and four introns. The number of introns within members of the same evolutionary branch was generally consistent. Prediction of cis-regulatory elements indicated that the EuKNOX genes were involved in hormone response, light response and stress response. RNA-seq data revealed tissue-specific expression patterns, among which five EuKNOXs were highly expressed in the xylem. The expression levels of most EuKNOXs were higher in female flowers than in male flowers. Functional analysis suggested that EuKNOXs contribute to bark, fruit and leaf development, Eu-rubber biosynthesis and leaf-color formation. qRT-PCR analysis demonstrated that EuKNOXs may act as positive regulators of NaCl and GA 3 treatments, however, EuKNOXs may act as negative regulators of MeJA treatments, EuKNOX s showed a trend of first increasing, then decreasing and then increasing under drought and ABA treatment, especially, EuKNOX5 was induced 343-fold at 24 h under NaCl stress, suggesting that KNOX genes in E. ulmoides regulate plant growth and respond to different stresses by following different hormone signaling pathways, which laid a valuable foundation for further understanding the function of KNOX genes in multiple stress responses and phytohormone crosstalk in E. ulmoides. Conclusion This study systematically identified and characterized the KNOX superfamily genes in E. ulmoides . Abiotic stress-responsive candidate genes were identified via qRT-PCR analysis under multiple stress conditions. The findings furnish essential insights into subsequent functional investigations of E. ulmoides KNOX genes and the genetic improvement of E. ulmoides abiotic stress resistance.