Evolution and regulatory roles of the KNOX gene in Eucommia ulmoides in growth, development, and multiple stress responses

Abstract Background KNOX (KNOTTED1-like HOMEOBOX) belongs to an important class of homeobox genes, these genes encode homeodomain proteins that bind to specific cis -elements of target genes and participate in plant development, secondary metabolism, and stress adaptation. 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, with number within the same subgroup sharing similar intron numbers. 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. EuKNOXs contribute to bark, fruit and leaf development, Eu-rubber biosynthesis and leaf-color formation. qRT-PCR results showed that NaCl and GA 3 induced the expression of most EuKNOXs , especially, EuKNOX5 was induced by 343-fold at 24 h under NaCl stress. Whereas MeJA treatment suppressed the expression of most EuKNOXs genes. EuKNOX s showed a trend of first increasing, then decreasing and then increasing under drought and ABA treatment. Conclusion This study systematically identified and characterized the KNOX superfamily in E. ulmoides . Our results revealed differential expression of the EuKNOX genes in response to NaCl, GA 3 , MeJA and ABA stresses These findings provide a foundation for future functional investigations of EuKNOX genes and offer valuable insights into the genetic improvement of abiotic stress resistance in E. ulmoides .