High-throughput sequencing-based analysis of the composition and diversity of endophytic bacterial community in seeds of elite rice resources from Heilongjiang area

Background and aims Rice is a major staple crop in China, and Heilongjiang Province is a core japonica rice production region. This study aimed to explore core microbiota composition and the influence of host genetic background on microbiota assembly. Methods Using Illumina NovaSeq 6000 sequencing, we analyzed endophytic bacteria diversity in 57 samples from 19 elite rice cultivars, identifying 792 OTUs. Results At the phylum level, Proteobacteria dominated (80.3%-99.73%). Core microbiota at the genus level included Pantoea , Xanthomonas , Methylobacterium - Methylorubrum , Pseudomonas , and Microbacterium . Parental genetic background significantly influenced bacterial community structure similarity, with closer genetic relationships showing more complex bacterial interaction networks. Conclusion This study showed the compositional characteristics of the core microbiota in elite rice seeds from Heilongjiang and its relationship with parental genetic background, providing a theoretical basis for microbiome-assisted breeding in rice.