Identification and characterization of the powdery mildew resistance gene in spelt accession Lsy-93

Background Powdery mildew, a widespread fungal disease caused by Blumeria graminis f. sp. tritici ( Bgt ), seriously threatens the yield and quality of wheat. The most effective and sustainable approach to disease control is utilizing resistance genes and unraveling their underlying molecular mechanisms. Spelt ( Triticum aestivum ssp. Spelta , 2n = 6x = 42, AABBDD), an ancient hexaploid wheat subspecies, has emerged as a valuable genetic resource for enhancing powdery mildew resistance in modern wheat breeding programs. Results Spelt accession Lsy-93 demonstrated resistance against powdery mildew at the whole-growth stage. Genetic analysis revealed that this resistance is conferred by a single dominant gene, tentatively designated as PmLsy-93 . Bulked segregant RNA sequencing (BSR-seq) and molecular markers positioned PmLsy-93 within a 1.5 cM interval flanked by markers S93-2 and S93-46 . Nine genes in this interval were associated with disease resistance and were considered as the candidate genes of PmLsy-93 . Furthermore, a total of 3,140 differentially expressed genes (DEGs) were identified between the two bulks, with 2,214 down-regulated and 916 up-regulated genes relative to the susceptible bulk. The integration of gene ontology (GO) and kyoto encyclopedia of genes and genomes (KEGG) pathway analysis underscores the multifaceted roles of these DEGs in plant defense, stress response, and metabolic regulation. Then, six genes, encoding disease resistance protein, serine threonine-protein kinase, or protein kinase domain, were induced with Bgt invasion via qRT-PCR. Three closely linked or co-segregated markers L93-293 , CIT02g-20 and L93-277 were confirmed to be available for marker-assisted selection (MAS) of PmLsy-93 in breeding programs. Conclusions This study successfully pinpointed critical genetic loci and candidate genes associated with powdery mildew resistance in the spelt wheat accession Lsy-93. The results provide valuable insights into plant-pathogen defense mechanisms and lay an important foundation for subsequent molecular breeding efforts to enhance crop disease resistance.