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Summary    Despite a much higher proportion of intragenic heterochromatin‐containing genes in crop genomes, the importance of intragenic heterochromatin in crop development remains unclear. Intragenic heterochromatin can be recognised by a protein complex, ASI1–AIPP1–EDM2 (AAE) complex, to regulate alternative polyadenylation.  Here, we investigated the impact of rice ASI1 on global poly(A) site usage through poly(A) sequencing and ASI1‐dependent regulation on rice development.  We found that OsASI1 is essential for rice pollen development and flowering. OsASI1 dysfunction has an important impact on global poly(A) site usage, which is closely related to heterochromatin marks. Intriguingly, OsASI1 interacts with the intronic heterochromatin of  OsXRNL , a nuclear XRN family exonuclease gene involved in the processing of an miRNA precursor, to promote the processing of full‐length  OsXRNL  and regulate miRNA abundance. We found that OsASI1‐mediated regulation of pollen development partially depends on OsXRNL. Finally, we characterised the rice AAE complex and its involvement in alternative polyadenylation and pollen development.  Our findings help to elucidate an epigenetic mechanism governing miRNA abundance and rice development, and provide a valuable resource for studying the epigenetic mechanisms of many important processes in crops.

Intragenic heterochromatin‐mediated alternative polyadenylation modulates miRNA and pollen development in rice