Genome-Wide Association Analyses Reveal the Genetic Basis of Symbiotic Nitrogen Fixation in African Soybean

Symbiotic nitrogen fixation (SNF) increases sustainability by supplying biological nitrogen for crops to enhance yields without damaging the ecosystem. A better understanding of this complex biological process is critical for addressing the triple challenges of food security, environmental degradation and climate change. Soybean plants, the most important legume worldwide, can form a mutualistic interaction with specialized soil bacteria, bradyrhizobia, to fix atmospheric nitrogen. Here we report the most comprehensive genome-wide association study (GWAS) of SNF in African soybean, using 11 SNF-related traits and 79K GBS-derived SNPs. We identified 24 QTL regions encompassing 40 putative SNF-related genes including 20 candidate genes with no prior known role in SNF. A line with a large deletion (164 kb), encompassing a QTL region containing a strong candidate gene (CASTOR), exhibited a marked decrease of SNF. Haplotype-phenotype association analysis of candidate genes revealed the favorable haplotypes for SNF efficiency. This study performed on elite African soybean lines provides fundamental insights into SNF and yielded a rich catalogue of candidate SNF-related genes that will accelerate future efforts aimed at sustainable agriculture.