Identification of novel germplasm and genetic loci for enhancing mineral element uptake in soybean

Bioavailability, uptake, and spatial distribution of essential and toxic mineral elements are pivotal factors that govern crop growth, development, and productivity. Soybean is a major leguminous crop globally, and yield losses are commonly attributed to various abiotic factors, including nutrient deficiencies or the influence of toxic minerals in the soil. Therefore, understanding the molecular basis of differential mineral element uptake, translocation, and accumulation in soybean is vital for developing improved cultivars. Here, we used portable X-ray fluorescence (p-XRF) for rapid and high -throughput mineral element profiling of a diverse set of soybean germplasm using leaves, stem, root, and seed tissues. Genome-wide association (GWAS) was performed on the element profiles of 219 soybean accessions, revealing lines with notable two to tenfold difference in various mineral nutrient uptake. These identified lines represent valuable genetic resources for germplasm development and gene discovery. The GWAS analysis pinpointed significant genomic loci and haplotypes associated with accumulation of aluminum (Al), silicon (Si), iron (Fe), and manganese (Mn). Remarkably, genes associated with the transport of solutes, metals, and ions have been pinpointed, indicating their potential involvement in the nutrient uptake and soybean improvement. To gain functional insights, Si deposition, allelic variants and expression of three Si transporter genes was studied in greater details. The high Si accumulating line PI548452 showed 12 -fold increase in leaf Si content compared to low Si lines. Expression of HiSil2b and HiSil2c effluxer genes showed root and leaf specific expression, respectively, providing evidence for tissue specific Si transport and the basis for precise management of Si uptake to improve abiotic and biotic stresses. In summary, this study uncovered the novel accessions, haplotypes, allelic diversity, and the potential candidate genes underpinning the mineral nutrient accumulation in soybean.