QTL Mapping and Functional Identification of Candidate Genes Regulated by Sinorhizobium fredii HH103 and Associated with Nodulation Traits in Soybean

Large amounts of nitrogen fertilizer are annually applied to improve soybean yield. However, the overuse of nitrogen fertilizers has resulted in significant environmental pollution. Biological nitrogen fixation is an ecological and environmentally friendly method to increase soybean yield. However, the signaling pathway and function of genes in the plant host regulated by rhizobia under the symbiotic relationship remain unknown. In this study, the chromosome region in soybean responsive to Sinorhizobium fredii HH103 was identified using chromosome-segment-substituted lines produced from a cross between cultivated soybean SN14 and wild soybean Zyd00006. In addition, candidate genes associated with nodulation traits and regulated by S. fredii HH103 were identified. In total, three quantitative trait loci (QTLs) containing 68 genes were identified on chromosomes 02, 05, and 20. The differentially expressed genes among the QTL regions were determined using RNA-seq and qRT-PCR. Glyma. 05G240500, a potential gene responding to S. fredii HH103 and positively regulating soybean nodulation, was identified. To explore the relationships between haplotypes and soybean nodulation phenotypes, SNPs found in the regulatory areas of Glyma.05G240500 haplotype were investigated. Our study revealed the role of Glyma.05G240500 in symbiosis and provided a reference for facilitating symbiotic nitrogen fixation in the field and for marker-assisted selection.