Ge Gao, Danjing Lou, Yunpeng Li, Chao Zhang, Baolin Kan, Hao Wen, Siyu Wen, Jun Shu, Wenlong Guo, Weihua Qiao, Qingwen Yang, Youlin Peng, Kenneth M. Olsen, Qian Qian, Xiaoming Zheng
Cell Research; 2026; IF: 31.1
DOI:10.1038/s41422-026-01247-3
Abstract
Long noncoding RNAs (lncRNAs) are important regulators of plant development and stress responses, yet their population-scale functions in rice remain poorly understood. Here, strand-specific RNA sequencing of 695 samples from 188 cultivated and wild rice accessions identified 57,162 lncRNAs across four tissues and developmental stages. Integration with population genomics revealed domestication-associated lncRNAs, 127 high-confidence de novo protein-coding genes derived from ancestral lncRNAs, and diverse cis-, trans-, miRNA-mediated, and micropeptide-based regulatory mechanisms. Genome-wide association analysis of 946 rice accessions linked 4,427 trait-associated SNPs to 1,530 lncRNAs across 32 agronomic traits, with lncRNA variants contributing heritability comparable to that of mRNA variants. Combined GWAS and QTL analyses further identified lncRNAs associated with yield, morphology, physiology, and stress resistance. Functional validation focused on LBR5, a lncRNA located in the 3′ untranslated region of Xa5. CRISPR/Cas9 knockout of LBR5 reduced bacterial-blight lesion length and decreased Xa5 expression after infection, supporting a cis-regulatory role in disease resistance. Together, this study establishes a population-scale multi-omics framework linking rice lncRNAs to gene regulation, phenotypic diversity, domestication, and crop improvement.
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