Cloning and functional analysis of qCmr2.1, a novel gene for Cucumber mosaic virus resistance in Capsicum frutescens.

A novel TIR -NB -LRR class CMV resistance gene qCmr2.1 was cloned from C. frutescens cv. PBC688, and its essential role in conferring CMV resistance was validated via VIGS silencing, heterologous overexpression, and near-isogenic line assays. The core mechanism of qCmr2.1-mediated CMV-Fny resistance in pepper relies on the SA signaling pathway. Cucumber mosaic virus (CMV) poses a significant threat to pepper production worldwide, underscoring the need for resistant cultivars. Although disease resistance genes can expedite breeding, no CMV resistance gene had been cloned from pepper, leaving its molecular mechanism unknown. Here, we cloned a novel resistance gene, designated qCmr2.1, from the resistant accession C. frutescens cv. PBC688. It encodes a 1244‑amino‑acid TIR‑NB‑LRR protein and shares high sequence homology with the N gene from Nicotiana tabacum and its orthologs. Comparison between PBC688 and the susceptible accession Capsicum annuum G29 identified three key nonsynonymous mutations. Combined analysis of ELISA, disease indices (DI), and the three mutations in 26 pepper accessions suggests that residues 128 and 154 within the TIR domain are particularly important for qCmr2.1‑mediated resistance. Functional validation showed that virus-induced gene silencing (VIGS)‑mediated silencing of qCmr2.1 in PBC688 abolished resistance, leading to high viral accumulation. Conversely, heterologous overexpression in Nicotiana benthamiana and introgression into the susceptible background (near-isogenic lines NILs G29‑qCmr2.1) both conferred strong CMV‑Fny resistance. Non‑targeted hormone profiling revealed that salicylic acid (SA) pathway upregulation is a conserved core response in resistant transgenic N. benthamiana and G29-qCmr2.1 NILs. However, the regulation and amplitude of other hormonal pathways, including jasmonic acid (JA), cytokinin, auxin, abscisic acid (ABA), and ethylene (ETH), varied. These results establish qCmr2.1 as a key TIR‑NB‑LRR gene conferring CMV‑Fny resistance in pepper, primarily via SA signaling, with other hormones subject to contextual modulation.

© 2026. The Author(s), under exclusive licence to Springer-Verlag GmbH Germany, part of Springer Nature.