Oryza sativa lncRNA Raw sequence reads

Interpreting functional consequences of millions of discovered of non-coding regionvariations is one of the biggest challenges in genomic researches. Here we assess therole of long noncoding RNAs in domestication-associated expression changes based on a selection of cultivated japonica and wild rice accessions. Among 3,363 lncRNAtranscripts identified in early-developing rice panicles, 95% of those with differentialexpression between japonica and wild rice were significantly downregulated in thedomesticate. In-depth analyses multi-omics datasets showed directional selectionglobally altered expression of energy metabolism genes during domestication. Transgenic experiments and population analyses with three focal lncRNAs illustrate that selection on these loci led to increased starch content and grain weight during japonica domestication. Together our findings indicate that genome-wide selection for lncRNAs reshapes the rice transcriptome in the evolution of domestication traits that haveengendered a more comprehensive understanding of rice domestication and breeding.