Large-scale translatome profiling annotates the functional genome and reveals the key role of genic 3′ untranslated regions in translatomic variation in plants

The translatome, a profile of the translational status of genetic information within cells, provides a new perspective on gene expression. Although many plant genomes have been sequenced, comprehensive translatomic annotations are not available for plants due to a lack of efficient translatome profiling techniques. Here, we developed a new technique termed 3′ ribosome-profiling sequencing (3′Ribo-seq) for reliable, robust translatomic profiling. 3′Ribo-seq combines polysome profiling and 3′ selection with a barcoding and pooling strategy. Systematic translatome profiling of different tissues of Arabidopsis, rice, and maize using conventional ribosome profiling (Ribo-seq) and 3′Ribo-seq revealed many novel translational genomic loci, thereby complementing functional genome annotation in plants. Using the low-cost, efficient 3′Ribo-seq technique and genome-wide association mapping of translatome expression (eGWAS), we performed a population-level dissection of the translatomes of 159 diverse maize inbred lines and identified 1,777 translational expression quantitative trait loci (eQTLs). Notably, local eQTLs are significantly enriched in the 3′ untranslated regions of genes. Detailed eQTL analysis suggested that sequence variation around the polyadenylation (polyA) signal motif plays a key role in translatomic variation. Our study provides a comprehensive translatome annotation of plant functional genomes and introduces 3′Ribo-seq, which paves the way for deep translatomic analysis at the population level. This study reports a new method, 3′Ribo-Seq, for translatome profiling and systematically annotates the genomes of Arabidopsis, rice, and maize using both conventional Ribo-seq and 3′Ribo-Seq, thereby uncovering many new functional loci in plants. A genome-wide association study of translatomic expression at the population level reveals a key role for genic 3′ untranslated regions in translatomic variation.