Association studies for leaf rust resistance earmark differential genomic regions for silicon (Si) responsiveness in bread wheat (Triticum aestivum L.)

Abstract

Background: 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. Results: 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. Conclusions: 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.