Association studies for leaf rust resistance earmark differential genomic regions for silicon (Si) responsiveness in...

Silicon (Si), an important quasi-element, influences various genetic and physiological responses in enhancing plant resilience to biotic and abiotic stresses in many crops. Its uptake and deposition are markedly influenced by genetic makeup. It plays a significant role in enhancing photosynthetic efficiency, modulating hormonal balance, and activating defence mechanisms through regulating antioxidant systems and expressing defence-related genes, leading to increased stress tolerance and improved yield.

This study investigates the genetic basis of silicon (Si) response in wheat, focusing on its role in enhancing resistance to leaf rust. A diverse wheat genotype panel, coupled with multi-year data, was utilized to perform genome-wide association studies (GWAS) to identify quantitative trait loci (QTLs) associated with Si response. The results revealed significant genotype-specific responses under Si-treated (Si⁺) and untreated (Si^-) conditions, for leaf rust resistance, highlighting Si's involvement in both physical and molecular resistance mechanisms. Si application led to a substantial reduction in the coefficient of infection (COI) for leaf rust. Linkage disequilibrium (LD)-block-based analysis using haploview identified 11 significant QTLs for leaf rust resistance, with key loci mapped on chromosomes 4B, 7 A, 7B, and 4D. Notably, eight novel Si-responsive QTLs were detected under Si⁺-three associated with leaf rust resistance (qLr7AS.1_Si+, qLr6DS.1_Si+, and qLr7BL.1_Si+). Functional annotation of candidate genes revealed the involvement of key pathways, including cation transport, isomerase and, ethylene-responsive transcription factors reflecting Si's multifaceted role in enhancing mineral uptake, stress tolerance, and overall plant growth. The identified Si-responsive QTLs, once validated across diverse wheat populations, hold significant promise for developing Si-responsive genotypes with improved resistance.

Our results provide important insights into the genetic basis of Si response and can assist in developing molecular markers for selecting and integrating Si-responsive genomic regions into wheat breeding lines.