Elucidation of resistance signaling and identification of powdery mildew resistant mapping loci (ClaPMR2) during watermelon-Podosphaera xanthii interaction using RNA-Seq and whole-genome resequencing approach

Watermelon is an important vegetable crop and is widely cultivated in USA with an approximate global production of > 100 million tons. Powdery mildew (PM) caused by Podosphaera xanthii is a major production-limiting factor on watermelon and other cucurbits. Numerous PM and multiple disease resistant (MDR) watermelon germplasm lines have been developed by the USDA in Charleston, SC. To gain a better understanding of the innate and activated molecular defense mechanisms involved during compatible and incompatible PM-watermelon interactions, we inoculated PM susceptible (USVL677-PMS) and resistant (USVL531-MDR) watermelon plants with 10(5) conidia ml(−1) of P. xanthii. RNA-seq profiling was done on leaf samples collected at 0, 1, 3, and 8 days post inoculation (DPI). A total of 2,566 unique differentially expressed genes (DEGs) were identified between compatible and incompatible interactions with P. xanthii. The compatible interactions resulted in distinct plant gene activation (> twofold unique transcripts, 335:191:1762 :: 1:3:8 DPI) as compared to incompatible interaction (> twofold unique transcripts, 314:681:487 :: 1:3:8 DPI). Further, comparative whole-genome resequencing analysis of USVL531-PMR, USVL677-PMS and four introgressed PM resistant recombinant inbred lines (RIL, USVL531-PMR × USVL677-PMS) were performed to identify the region of PM resistance introgressed break points along with other traits inherent by USVL531-PMR by comparing the SNPs and InDels. Based on SNPs identification and CAPS markers, the resistance gene was identified as ClaPMR2, Citrullus lanatus PM Resistance gene 2 {Chr2 : 26750001 .. 26753327 (−)}, a NBS-LRR resistance protein (R) with homology to the Arabidopsis thaliana PM resistance protein, RPW8. The transcriptome data also revealed a complex regulatory network associated with the introgressed junctions mediated by PM resistance R proteins (R genes) that may involve multiple signal regulators and transducers, carbohydrate metabolism, cell wall modifications and the hormone-signaling pathway.