Uncovering genomic regions associated with Rhopalosiphum maidis (Fitch) resistance in wild and synthetic wheat using genome-wide association mapping

The corn leaf aphid, Rhopalosiphum maidis (Fitch) is a major insect pest of wheat, causing significant yield and quality losses. Development of resistant cultivars through molecular approaches provides an economical and environmentally sustainable strategy for aphid management. Wild and synthetic wheats represent important reservoirs of novel genetic diversity; however, the genomic regions governing R. maidis resistance remain poorly characterized. This study employed genome-wide association mapping (GWAS) to identify genomic regions and candidate genes associated with aphid resistance in a diverse panel of wild and synthetic wheat genotypes. A panel of 287 wild and synthetic wheat genotypes was phenotyped under field and screenhouse conditions over two seasons and genotyped using the Axiom® 35K Wheat Breeder’s Array. A total of 10,971 high-quality SNP markers were retained after quality filtering. Population structure, PCoA, and kinship analyses classified the panel into three genetically distinct subpopulations, while AMOVA revealed substantial genetic differentiation among groups. GWAS identified 15 and 19 significant marker–trait associations (MTAs) under field and screenhouse conditions, respectively, distributed across chromosomes 1A, 1D, 2A, 2B, 2D, 3A, 3B, 3D, 5D, 6A, 6B, 6D, 7A, 7B, and 7D. Several genomic regions on chromosomes 2B, 2D, and 6A were detected in close physical proximity across environments, suggesting the presence of stable loci associated with aphid resistance. In silico analysis identified 11 putative candidate genes, including Ankyrin-3-like (TraesCS1D02G079400), myrosinase-binding protein 2-like (TraesCS2B02G050200), alpha-glucosidase-like (TraesCS7A02G464200), (E)-beta-caryophyllene synthase-like (TraesCS2B02G061000), and calcium-dependent protein kinase 26-like (TraesCS6A02G421000), which are implicated in insect defense, stress signaling, and anti-herbivore responses. This study provides one of the first comprehensive GWAS-based dissections of R. maidis resistance in wild and synthetic wheat germplasm. The identified resistant genotypes, significant MTAs, and putative candidate genes represent valuable genomic resources for wheat improvement. These findings can be effectively utilized in marker-assisted selection to develop aphid-resistant cultivars and support sustainable pest management strategies. Further validation of candidate genes may strengthen their application in breeding programs aimed at developing durable aphid resistance.