MADS78 and MADS79 are essential regulators of early seed development in rice

MADS-box transcription factors (TFs) are subdivided into type-I and II based on phylogenetic analysis. The type II’s regulate floral organ identity and flowering time, but type I’s are relatively less characterized. Here, we report functional characterization of two type-I MADS-box TFs in rice (Oryza sativa), MADS78 and MADS79. Transcript abundance of both these genes in developing seed peaked at 48 hours after fertilization (HAF) and was suppressed by 96 HAF, corresponding to syncytial and cellularized stages of endosperm development, respectively. Seeds overexpressing (OE) MADS78 and 79 exhibited delayed endosperm cellularization, while CRISPR-Cas9 mediated single knock-out mutants showed precocious endosperm cellularization. MADS78 and 79 were indispensable for seed development, as a double knock-out mutant failed to make viable seeds. Both MADS78 and 79 interacted with MADS89, another type-I MADS-box, which enhances nuclear localization. The expression analysis of Fie1, a rice FERTILIZATION-INDEPENDENT SEED–polycomb repressor complex 2 (FIS-PRC2) component, in MADS78 and 79 mutants and vice versa established an antithetical relation, suggesting Fie1 could be involved in negative regulation of MADS78 and 79. Mis-regulation of MADS78 and 79 perturbed auxin homeostasis and carbon metabolism, as evident by mis-regulation of genes involved in auxin transport and signaling as well as starch biosynthesis genes causing structural abnormalities in starch granules at maturity. Collectively, we show MADS78 and 79 are essential regulators of early seed developmental transition and impact both seed size and quality in rice. RNA deep sequencing of WT, MADS78 OE, MADS79 OE, MADS78 CRISPR and MADS79 CRISPR seeds 48 and 72 hours after fertilization (HAF).