Noncanonical open reading frames from lncRNAs encode functional micropeptides that help shape agronomic traits in...

Functional open reading frames (ORFs) originating from long noncoding RNAs (lncRNAs) have historically been overlooked, in part due to the technical challenges associated with their identification and detection in plants. Here, we presented a comprehensive analysis by integrating 119 Ribo-seq (ribosome profiling sequencing) datasets from multiple rice tissues and developmental stages, and examined the biological potential of micropeptides encoded by ORFs translated from lncRNAs (lncORFs). 8,253 lncORFs were identified in the rice (Oryza sativa) genome. We confirmed the existence of 776 lncORF micropeptides by analyzing 1,188 mass spectrometry datasets and experimentally validated a set of lncORF-encoded micropeptides. Evolutionary and variant-association analysis pointed to the contributions of lncORF micropeptides to agronomic traits. Specifically, gain/loss-of-function experiments showed that the micropeptides regulate grain yield by affecting the number of small vascular bundles. Our findings expand the known functional scope of lncRNAs and provide valuable resources for rice improvement.