Genetic Dissection of Powdery Mildew Resistance in Emmer Wheat WL509 using Bulked Segregated RNA Sequencing

Emmer wheat (<i>Triticum dicoccum</i>, 2n = 4x = 28, AABB), as the ancestral species of common wheat, is a crucial gene donor for improving common wheat against powdery mildew, a destructive wheat disease worldwide. Cultivated emmer wheat accession WL509 exhibits broad and high level of resistance to powdery mildew. Using inheritance analysis, bulked segregated RNA sequencing, and molecular marker detection, we identified a dominant gene, tentatively designated <i>PmWL509</i>, and mapped it to 757.2 to 776.4 Mb interval on chromosome arm 2AL based on the reference genome of wild emmer (v2.0). <i>PmWL509</i> was then mapped to the <i>Pm4</i> locus using linked and diagnostic markers of <i>Pm4</i>. Homologous cloning and sequence alignment revealed that <i>PmWL509</i> shares identical amino acid sequences with <i>Pm4a</i> but exhibits distinct resistance spectra and expression patterns. To explore potential regulatory mechanisms and key genes controlling resistance, 1,024 differential expression genes (DEGs) between resistant and susceptible bulks were annotated and analyzed by Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment. Six DEGs in the mapping interval and three pathogenesis-related (<i>PR</i>) genes were screened and evaluated by qRT-PCR when invaded by the <i>Blumeria graminis</i> f. sp. <i>tritici</i> isolate E09, and the result indicated that the two DEGs <i>TRIDC2AG078910</i> and <i>TRIDC2AG081650</i> and the two <i>PR</i> genes <i>PR5</i> and <i>PR9</i> could be considered to play a key role in the resistant pathway of <i>PmWL509</i>. The diagnostic marker <i>JS717/JS718</i> was confirmed to be available for efficiently transferring <i>PmWL509</i> into different wheat backgrounds.