Genome-Wide Landscape of Alternative Polyadenylation in Rice: Impact on Developmental Gene Expression Regulation and QTL

Alternative polyadenylation (APA), a phenomenon that a transcript uses one of multiple poly(A) sites to produce a defined 3’-end and a poly(A) tail, has been recognized as a wide-spread regulatory mechanism in eukaryotic gene expression. Using a Poly(A)-Tag sequencing (PAT-seq) protocol, we compared APA in 14 different tissues/developmental stages of rice. These include different tissues roots and leaves, and different stages in embryo, endosperm, imbibed seeds and flower parts (i.e. husk, mature pollen, anther, and pistil). A total of 68,220 poly(A) sites on 13,419 APA genes (~48% of total expressed genes) were identified. We also found that many important function genes have APA switching events between different developmental stages or different tissues, e.g., a rubisco small subunit gene associated with photosynthesis has an APA switching pattern in leaves between seedling and tillering stages. Poly(A) sites across pollen are unique when compared to all other tissues, with the most tissue-specific poly(A) sites and very different poly(A) signals of the intronic poly(A) sites. Using statistical analysis, it was found that Quantitative Trait Loci (QTL) tend to have APA genes. In addition, we found that many APA genes of high expression levels were mainly distributed in three category QTL, yield, vigor, and anatomy, further suggesting that APA gene may play an essential role in the determination of agronomic traits in rice. Besides aiding rice genome annotation, these data provide the most comprehensive and highest resolution APA information in plants for further interrogation of the role of APA in plants.