OsRPN10, a 26S Proteasome Regulatory Particle Subunit, Regulates Primary Root Elongation in Rice

Primary root elongation during seedling establishment is a key determinant of rice (Oryza sativa L.) vigor and productivity, yet its genetic basis remains incompletely understood. Here, a genome-wide association study (GWAS) of 194 diverse rice accessions identified three loci, qPRL3, qPRL6, and qPRL12, associated with primary root length. By integrating local association signals, organ-level expression profiles, and haplotype analysis, we identified OsRPN10, which encodes a regulatory particle non-ATPase subunit of the 26S proteasome, as the most likely candidate gene underlying qPRL3. Natural allelic variation at OsRPN10 was significantly associated with divergence in primary root length, and CRISPR/Cas9-mediated loss of function markedly impaired primary root elongation, confirming its positive role in root growth. Protein–protein interaction prediction and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses suggested potential associations between OsRPN10 and proteasome-related pathways. Population genetic and geographic analyses revealed strong selective signatures and clear geographic differentiation at the OsRPN10 locus during rice domestication and diversification. Collectively, these findings identify OsRPN10 as a previously unrecognized regulator of primary root elongation in rice, expand current understanding of proteasome-mediated control of root development, and provide a promising molecular target for improving rice root architecture.