Unveiling the role of the <i>TIR1/AFB</i> gene family in <i>Capsicum annuum</i>: genome-wide identification, characterization, and transcriptomic analysis under <i>Ralstonia solanacearum</i> infection

TIR1/AFB proteins play key roles in plants responding to <italic>Solanum</italic> crop disease. In this study, five putative TIR1/AFB proteins were identified in pepper (<italic>Capsicum annuum</italic>). Chromosomal mapping revealed that <italic>CaTIR1/AFB</italic> genes are located on chromosomes DH02, DH03, DH04, and DH06. Phylogenetic tree analysis based on TIR1/AFB protein sequences from <italic>Arabidopsis,</italic> tomato, and eggplant revealed that the CaTIR1/AFB genes in pepper belong to three of the four identified subgroups. One collinear gene pair (<italic>CaTIR1C</italic> and <italic>CaTIR1B</italic>) was identified in pepper, suggesting the TIR1/AFB gene family in pepper experienced segmental duplications in evolution. Seventy-eight cis-elements related to the hormone, defense, drought, and light response were identified. RNA-sequencing data and expression profiling showed that <italic>TIR1/AFB</italic> genes were expressed differently under <italic>R. solanacearum</italic> treatment; downregulated expression of all <italic>CaTIR1/AFBs</italic> was observed in the resistant variety, while <italic>CaTIR1C</italic> was upregulated in the susceptible variety. Subcellular localization analysis showed that CaTIR1C is a nuclear-localized protein. Further virus-induced gene silencing (VIGS) assays revealed that knocking down <italic>CaTIR1C</italic> enhanced pepper resistance to <italic>R. solanacearum</italic>, indicating that <italic>CaTIR1C</italic> is a negative regulator in response to <italic>R. solanacearum</italic>. These findings contribute to the molecular breeding of bacterial wilt-resistant pepper and hold the potential to improve disease control efficiency by further exploring the function of <italic>CaTIR1C</italic>.