High-throughput sequencing-based profiling of endophytic bacterial community composition and diversity in seeds of Yunnan cytoplasmic male-sterile rice

Rice ( Oryza sativa L.) is a staple crop of pivotal strategic importance in Chinese agro-ecosystems. In this study, the endophytic bacterial diversity and community structure of seeds from 14 Yunnan cytoplasmic male-sterile (CMS) rice lines (42 samples in total) were systematically profiled via Illumina NovaSeq 6000 high-throughput sequencing. A total of 503 operational taxonomic units (OTUs) were recovered. At the phylum level, Proteobacteria dominated all samples, accounting for 91.53–99.95% of the bacterial microbiota. At the genus level, a conserved core microbiome comprising Pantoea (50.14–95.58%), Xanthomonas (6.23–37.49%), Kosakonia (2.97–35.91%), Enterobacter (2.06–22.97%), and Methylobacterium – Methylorubrum (1.42–5.11%) was identified. Both α- and β-diversity analyses revealed no significant inter-line differentiation, indicating a highly stable and conserved endophytic bacterial community across the Yunnan CMS rice germplasm. This study provides the first comprehensive characterization of the seed-associated core microbiome of Yunnan CMS rice lines, offering a critical reference for micro-ecological breeding strategies in rice.