Transcriptome changes in seeds during coleorhiza hair formation in rice

Abstract Coleorhiza hairs are hairlike structures in seeds of the grass family (Poaceae). The molecular mechanisms underlying its formation are largely unknown, study on this topic will expand our understanding of the effects of water status on germination during rice (Oryza sativa L.) direct seeding. Seeds of Nipponbare were treated under two water conditions: in one, half of the seed surface was immersed in water and the other half was embryo side in air (EIA), and in the other, the whole seed was covered by water (CBW). Coleorhiza hairs formed only in EIA samples. Transcriptomics was used to identify the gene regulation during coleorhiza hair formation in EIA (vs. CBW) embryos and endosperm. Embryos displayed more transcriptome modulation even though smaller in size than the endosperm. Differentially expressed genes (DEGs) were enriched in both primary and secondary metabolism and showed changes in abscisic acid, auxin, jasmonic acid, and salicylic acid signatures. Metabolites enrichment data were positively correlated with gene expression changes in the affected metabolic functional pathways. The presence of shorter coleorhiza hairs in an OsRHL1 (Os06g0184000, a coleorhiza hair formation regulation candidate gene) knockout mutant suggested that root hair-associated DEGs share molecular regulators that control the formation of coleorhiza hairs.