Identification of novel candidate genes associated with the symbiotic compatibility of soybean with rhizobia under natural conditions

A robust symbiotic relationship between soybean and rhizobia can enhance the yield and quality of soybeans by reducing nitrogen fertilizer inputs, thereby contributing to sustainable agriculture. The genetic interplay between soybean cultivars and the rhizobial species colonizing their roots under natural conditions remains underexplored. This study builds on the observation that the prevalence of rhizobial species associated with the soybean cultivars ‘Peking’ and ‘Tamahomare’ varies significantly. Herein, we performed a quantitative trait loci (QTL) analysis of the proportion of Rhizobium species present in the root nodules of these cultivars using recombinant inbred lines derived from a cross between ‘Peking’ and ‘Tamahomare.’ A major QTL was identified on chromosome 18, accounting for 42% of the phenotypic variation, and was subsequently localized to a 240 kb region. The RNA-seq analysis indicated that a single gene featuring nucleotide binding site–leucine-rich repeat domains exhibited markedly different expression levels in parent cultivars within the QTL region. As this locus is distinct from the chromosomal regions containing known nodule-related genes, such as Rj or rj , it likely represents a novel gene involved in symbiosis between rhizobia and soybeans. Further research of the function and role of this new gene has potential to improve soybean yield and contribute to sustainable agriculture under low nitrogen fertilizer conditions.