Deciphering the genetic basis of nodule number through integrative analysis of host genotype and endophytes

• Peanut nodule number is determined by the host genotype and endophytes. • AhatpB positively regulates nodule number and Bradyrhizobium ASV1 abundance. • Superior haplotype of AhatpB has higher nodule number, Bradyrhizobium abundance, and pod yield. • The oxidative phosphorylation in the nodules of varieties carrying the Hap2 of AhatpB is inhibited. • Genes regulating the abundance of endophytes associated with nodule number were identified. • This study provided gene resources for breeding nitrogen-efficient peanut varieties. Peanut nodule number is determined by the host genotype and endophytes. However, the genetic mechanisms regulating nodule number and the abundance of endophytes significantly associated with nodule number remain unclear. This study aims to elucidate the genetic basis of nodule number through integrated analysis of host genotype and endophytes. Genome-wide association studies (GWAS) were conducted to identify genes regulating nodule number and the abundance of endophytes significantly correlated with nodulation. After verifying the functions of key genes regulating nodule number and the microsymbiont Bradyrhizobium abundance, the mechanism underlying differences in the abundance of Bradyrhizobium in nodules of different haplotypes carrying functional genes was investigated through multi-omics analysis. This research identified and validated a gene encoding the ATP synthase β subunit ( AhatpB ), which positively regulates both nodule number and the abundance of the microsymbiont Bradyrhizobium ASV1. Varieties carrying superior AhatpB haplotype exhibited higher pod yields. Compared with the nodules of varieties carrying the superior AhatpB haplotypes, the transcription and metabolism of oxidative phosphorylation were inhibited during nodule development in varieties carrying normal AhatpB haplotypes, leading to the accumulation of adenosine-5′-diphosphate, dihydrogen phosphate, and succinic acid, which were insufficient to maintain Bradyrhizobium growth and promote nodule development. Additionally, four endophytes (ASV7696, ASV4913, ASV1693, and ASV495) were found to be significantly positively correlated with nodule number, and most of the genes regulating their abundance encoded senescence-associated proteins ( Arahy.4RGJ1T , Arahy.AA4TUV , Arahy.74ZQZH , Arahy.8PDB05 ). Furthermore, candidate genes ( Arahy.FQH7NX , Arahy.2C7VNA , Arahy.T63ME6 , Arahy.X7L1IJ , Arahy.JBBQ4L, and Arahy.IT8ZEZ ) that regulate the abundance of endophytes significantly negatively correlated with nodule number were detected. This study identified key genes regulating peanut nodule number and the abundance of endophytes significantly associated with nodule number, providing potential targets for breeding nitrogen-efficient peanut varieties.