Natural Variation of NAR5 Determines Nitrogenase Activity and the Yield in Soybean

ABSTRACT Symbiotic nitrogen fixation (SNF) serves as a vital process through which legumes acquire atmospheric nitrogen, directly influencing plant growth, yield, and soil fertility. Nitrogenase activity represents a key determinant of SNF efficiency, yet only a limited number of genes regulating this process have been identified in soybean nodules. In this study, a genome‐wide association analysis uncovered a major quantitative trait locus (QTL) on chromosome 5, named NAR5 ( Nitrogenase Activity Related Gene 5 ), which governs variation in nitrogenase activity among natural soybean populations under controlled greenhouse conditions. NAR5 encodes a subtilisin‐like serine protease. Functional characterization demonstrated that NAR5 overexpression downregulates the transcription of senescence‐associated genes in nodules, thereby sustaining nitrogenase function. Moreover, plants overexpressing NAR5 exhibited enhanced field performance, with increased yield and improved adaptation to low‐nitrogen conditions. Population analysis revealed that NAR5 is subject to selection pressure during domestication, and that the elite haplotype NAR5 HapI‐1 linked to superior nitrogenase activity and greater seed weight has been preferentially incorporated into modern breeding germplasm. In summary, these findings identify NAR5 as a candidate genetic regulator of SNF efficiency in soybean, providing a promising molecular target for breeding high‐yield, nitrogen‐efficient cultivars.