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 input, thereby contributing to sustainable agriculture. However, the genetic interplay between soybean cultivars and the rhizobial species colonizing their roots under natural conditions is yet to be sufficiently assessed. In this study, we build on previous observations that have revealed a significant variation in the prevalence of rhizobial species associated with the soybean cultivars "Peking" and "Tamahomare." Using recombinant inbred lines derived from a cross between Peking and Tamahomare, we performed quantitative trait loci (QTL) analysis of the proportion of <i>Rhizobium</i> species present in the root nodules of these cultivars and accordingly identified a major QTL on chromosome 18, accounting for 42% of the phenotypic variation, which was subsequently localized to a 240-kb region. RNA-seq analysis indicated that a single gene harboring nucleotide binding site-leucine-rich repeat domains exhibited markedly different expression within the QTL region in the parent cultivars. As this locus is distinct from the chromosomal regions containing known nodule-related genes, such as <i>Rj</i> and <i>rj</i>, we speculate that it represents a novel gene involved in the symbiosis between rhizobia and soybeans. Further research on the function and role of this new gene could potentially contribute to enhancing soybean yield, and hence sustainable agriculture, under low-nitrogen fertilization conditions.