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Genome-wide transcriptome analysis using RNA-Seq of  Lilium longiflorum  revealed valuable genes responding to biotic stresses. WRKY transcription factors are regulatory proteins playing essential roles in defense processes under environmental stresses, causing considerable losses in flower quality and production. Thirty-eight  WRKY  genes were identified from the transcriptomic profile from lily genotypes, exhibiting leaf blight caused by  Botrytis elliptica . Lily WRKYs have a highly conserved motif, WRKYGQK, with a common variant, WRKYGKK. Phylogeny of  LlWRKY s with homologous genes from other representative plant species classified them into three groups- I, II, and III consisting of seven, 22, and nine genes, respectively. Base on functional annotation, 22  LlWRKY  genes were associated with biotic stress, nine with abiotic stress, and seven with others. Sixteen unique  LlWRKY  were studied to investigate responses to stress conditions using gene expression under biotic and abiotic stress treatments. Five genes— LlWRKY3 ,  LlWRKY4 ,  LlWRKY5 ,  LlWRKY10 , and  LlWRKY12 —were substantially upregulated, proving to be biotic stress-responsive genes in vivo and in vitro conditions. Moreover, the expression patterns of  LlWRKY  genes varied in response to drought, heat, cold, and different developmental stages or tissues. Overall, our study provides structural and molecular insights into  LlWRKY  genes for use in the genetic engineering in  Lilium  against  Botrytis  disease.

Genome-Wide Transcriptomic Identification and Functional Insight of Lily WRKY Genes Responding to Botrytis Fungal Disease