Comprehensive GWAS and transcriptome analysis discovered new candidate genes for powdery mildew response in pea (Pisum sativum L.)

Pea powdery mildew is a major disease that causes substantial yield losses and reduces crop quality. Identifying new resistance genes is essential for developing cultivars with durable resistance and high productivity. In this study, we applied two complementary approaches, genome-wide association study (GWAS) and transcriptomics, to identify genetic loci and candidate genes involved in the pea response to powdery mildew. For GWAS, infection type (IT) and disease severity (DS) were evaluated in 376 genetically diverse pea accessions grown across four environments. Ten significant single nucleotide polymorphism (SNP) loci were detected for IT in three environments, and eleven loci were detected for DS in two environments; in total, 70 genes were located near these peak SNPs. Transcriptome analysis of one susceptible accession and five resistant accessions was carried out at four infection time points. By integrating GWAS with weighted gene co-expression network analysis (WGCNA) and series test of cluster analysis, we identified eight candidate genes likely contributing to powdery mildew resistance. These results provide new SNP loci and candidate genes for studying the resistance mechanism of pea powdery mildew and for breeding resistant cultivars.