A deletion in 𝘍𝘓𝘚2 and its expansion after domestication caused global dissemination of melon cultivars defective in flagellin recognition

Abstract

𝘍𝘓𝘈𝘎𝘌𝘓𝘓𝘐𝘕 𝘚𝘌𝘕𝘚𝘐𝘕𝘎 2 (𝘍𝘓𝘚2) encodes a pattern recognition receptor that perceives bacterial flagellin. While putative 𝘍𝘓𝘚2 orthologs are broadly conserved in plants, their functional characterization remains limited. Here, we report the identification of orthologs in cucumber (𝘊𝘶𝘤𝘶𝘮𝘪𝘴 𝘴𝘢𝘵𝘪𝘷𝘶𝘴) and melon (𝘊. 𝘮𝘦𝘭𝘰), named 𝘊𝘴𝘍𝘓𝘚2 and 𝘊𝘮𝘍𝘓𝘚2, respectively. Homology searching identified 𝘊𝘴𝘍𝘓𝘚2, and virus-induced gene silencing (VIGS) demonstrated that 𝘊𝘴𝘍𝘓𝘚2 is required for flg22-triggered ROS generation. Interestingly, genome re-sequencing of melon cv. Lennon and subsequent genomic PCR revealed that Lennon has two 𝘊𝘮𝘍𝘓𝘚2 haplotypes, haplotype I encoding full-length 𝘊𝘮𝘍𝘓𝘚2 and haplotype II encoding a truncated form. We show that VIGS-mediated knockdown of 𝘊𝘮𝘍𝘓𝘚2 haplotype I resulted in a significant reduction in both flg22-triggered ROS generation and immunity to a bacterial pathogen in melon cv. Lennon. Remarkably, genomic PCR of 𝘊𝘮𝘍𝘓𝘚2 revealed that 68% of tested commercial melon cultivars possess only 𝘊𝘮𝘍𝘓𝘚2 haplotype II: these cultivars thus lack functional 𝘊𝘮𝘍𝘓𝘚2. To explore evolutionary aspects of 𝘊𝘮𝘍𝘓𝘚2 haplotype II occurrence, we genotyped the 𝘊𝘮𝘍𝘓𝘚2 locus in 142 melon accessions by genomic PCR and analyzed 437 released sequences. The results suggest that 𝘊𝘮𝘍𝘓𝘚2 haplotype II is derived from 𝘊. 𝘮𝘦𝘭𝘰 subsp. 𝘮𝘦𝘭𝘰. Furthermore, we suggest that the proportion of 𝘊𝘮𝘍𝘓𝘚2 haplotype II increased among the improved 𝘮𝘦𝘭𝘰 group compared with the primitive 𝘮𝘦𝘭𝘰 group. Collectively, these findings suggest that the deleted 𝘍𝘓𝘚2 locus generated in the primitive 𝘮𝘦𝘭𝘰 subspecies expanded after domestication, resulting in the spread of commercial melon cultivars defective in flagellin recognition, which is critical for bacterial immunity.