Genome-wide association study identifies key chromosomal regions in rice promoting the enrichment of diazotrophic iron-reducing bacteria in paddy soil

Abstract Background and aim The overuse of nitrogen fertilizers has led to significant environmental issues. Diazotrophic iron-reducing bacteria (IRB), particularly Anaeromyxobacter and Geobacter , are abundant in paddy soil and may increase nitrogen fixation when ferric compounds are present. This study investigated the effects of rice cultivation on the abundance of IRB and identified genetic regions in rice that regulate this process. Methods We established a microcosm system using cups filled with paddy soil, separated by a nylon mesh to differentiate rhizosphere and bulk soils. The abundance of IRB in the rhizosphere of 143 japonica rice varieties was evaluated. A genome-wide association study (GWAS) with a unified mixed-model was conducted to identify genomic regions associated with IRB abundance. Results Our experiments revealed a weak but significant correlation ( r = 0.19, p = 0.022) between rice variety and IRB abundance. GWAS identified peaks on chromosomes (Chr) 2, 3, 4, 9, 10, and 11. Linkage disequilibrium analysis highlighted regions on Chr3, Chr4, Chr9, Chr10, and Chr11 linked to higher IRB abundance. Notably, the chromosome segment substitution line SL609, which incorporates fragments from Nipponbare into Koshihikari, presented increased IRB abundance, confirming the genetic influence of Chr3. Conclusion This study demonstrated genetic variation in IRB abundance among japonica rice cultivars and identified the associated genomic regions. These findings enhance our understanding of the genetic factors influencing IRB and offer insights for improving nitrogen acquisition in rice production.