Genome-Wide Identification and Expression Analysis of the TIR-NBS-LRR Gene Family and Its Response to Fungal Disease in Rose (Rosa chinensis)

SIMPLE SUMMARY: TIR-NBS-LRR (TNL) is a disease resistance gene family that responds to biotic stress in many plants, but the systematic analysis of this gene family and the expression response to biotic stress have rarely been reported in roses. In the present study, 96 intact TNL gene family members were identified by bioinformatics in Rosa chinensis, and analyzed from the perspectives of evolutionary relationships, conserved structures, expression regulation, collinear relationships, and expression patterns. Some of the TNL genes responded to hormones and fungal disease: RcTNL23 demonstrated strong responses to three hormones and three pathogens. In addition, some TNL genes responded significantly to the black spot pathogen that we isolated, and different members may be involved in different stages of disease defense. In conclusion, we found that the TNL gene family is involved in the response to fungal disease and may function as a disease resistance gene in the rose. The present study lays a theoretical foundation for the functional study of TNL genes and the mining of disease resistance gene in roses, which will inform the selection and breeding of disease-resistant varieties. ABSTRACT: Roses, which are one of the world’s most important ornamental plants, are often damaged by pathogens, resulting in serious economic losses. As a subclass of the disease resistance gene family of plant nucleotide-binding oligomerization domain (NOD)-like receptors, TIR-NBS-LRR (TNL) genes play a vital role in identifying pathogen effectors and activating defense responses. However, a systematic analysis of the TNL gene family is rarely reported in roses. Herein, 96 intact TNL genes were identified in Rosa chinensis. Their phylogenies, physicochemical characteristics, gene structures, conserved domains and motifs, promoter cis-elements, microRNA binding sites, and intra- and interspecific collinearity relationships were analyzed. An expression analysis using transcriptome data revealed that RcTNL genes were dominantly expressed in leaves. Some RcTNL genes responded to gibberellin, jasmonic acid, salicylic acid, Botrytis cinerea, Podosphaera pannosa, and Marssonina rosae (M. rosae); the RcTNL23 gene responded significantly to three hormones and three pathogens, and exhibited an upregulated expression. Furthermore, the black spot pathogen was identified as M. rosae. After inoculating rose leaves, an expression pattern analysis of the RcTNL genes suggested that they act during different periods of pathogen infection. The present study lays the foundations for an in-depth investigation of the TNL gene function and the mining of disease resistance genes in roses.