IPA1 regulates long anther development through miR156-mediated DNA hyper-methylation and post-transcriptional gene silencing in Oryza longistaminata

Background: Oryza longistaminata, despite exhibiting robust rhizomes, elongated stamen and resilience against stresses, is unable to achieve self-pollination due to its inability to produce compatible female and male gametes within the same individual plant. Although the observed sterility may appear daunting, the distinct features of elongated anthers, substantial pollen grains, and a big pollen grain count offer breeders a desirable paternal line for hybridization and the intricate biological processes and profound implications during this pivotal stage of anther development remain enigmatic, piquing the curiosity of researchers. Results: Through a rigorous multi-omics analysis during the anther development from the OlACD to OlAP stage, we discovered intricate correlations between alterations in methylation levels, siRNA variations, and transcriptional regulation within regulatory pathways, and the development of the anther during various fertile stages. This revelation highlights the intricate interplay between epigenetic and siRNA regulation in gene expression modulation. Our analysis pinpointed seven promising candidate genes, with a particular focus on IPA1. Phenotypic alterations in ipa1 mutants and overexpression miR156 revealed contrasting patterns in anther length and abundance and size of pollen grain, while 5’-Azacytidine treatment resulted in the opposite phenotype. Conclusion: In essence, recent advancements in rice anther development are governed by two mechanisms: miR156-mediated IPA1DNA hyper-methylation leading to transcriptional gene silencing (TGS) and miR156silencing IPA1 expression through degradation and inhibition of complementary IPA1 mRNAs, resulting in post-transcriptional gene silencing (PTGS), both working synergistically to ensure precise regulation of rice anther development.