Identification of QTLs Controlling Symbiotic Nitrogen Fixation in Soybean

Symbiotic nitrogen fixation (SNF) allows legumes to benefit from the conversion of atmospheric nitrogen (N₂) into useable forms of nitrogen for the plant following the establishment of a complex symbiotic relationship with rhizobacteria. Despite the importance of SNF, very few studies have been conducted to dissect the genetic architecture of SNF in soybean. We genotyped 292 lines representative of the International Institute for Tropical Agriculture (IITA) soybean germplasm with 50K high-quality SNPs obtained via genotyping-by-sequencing (GBS). Greenhouse-grown plants were either inoculated with a single strain of Bradyrhizobium japonicum or fed with nitrogen fertilizer. A total of nine traits related to nitrogen fixation were measured: Shoot Dry Weight (SDW), Root Dry Weight (RDW), Number of Nodules (NN), Nodule Dry Weight (NDW), NDW/SDW ratio, normalized NDW (nNDW), NDW/RDW ratio, SDW_inoculated/SDW_fertilized, and RDW_inoculated/RDW_fertilized. In total, GWAS analysis identified more than 14 highly significant QTL regions (q < 0.01). Among these, a highly significant association between markers on Gm19 and SDW (p=6.45E-06) was noted, but this association was found in both inoculated and N-fertilized plants. We observed that the RDW ratio between inoculated and N-fertilized plants (RDW_inoculated/RDW_fertilized) proved the most informative in terms of detecting QTLs unique to the inoculated treatment. In the interval extending 100 kb to either side of the peak marker of our QTLs, we identified 15 genes previously reported to be involved in SNF. Compared to the genome-wide occurrence of such genes, this represents an 80-fold enrichment (p=2.93E-16). We believe our results will shed further light on SNF in soybean.