Toward unveiling transcriptome dynamics and regulatory modules at the maternal/filial interface of developing maize kernel

Abstract

SUMMARYThe basal region of maize (Zea mays) kernels, which includes the pedicel, placenta‐chalazal, and basal endosperm transfer layers, serves as the maternal/filial interface for nutrient transfer from the mother plant to the developing seed. However, transcriptome dynamics of this maternal/filial interface remain largely unexplored. To address this gap, we conducted high‐temporal‐resolution RNA sequencing of the basal and upper kernel regions between 4 and 32 days after pollination and deeply analyzed transcriptome dynamics of the maternal/filial interface. Utilizing 790 specifically and highly expressed genes in the basal region, we performed the gene ontology (GO) term and weighted gene co‐expression network analyses. In the early‐stage basal region, we identified five MADS‐box transcription factors (TFs) as hubs. Their homologs have been demonstrated as pivotal regulators at the maternal/filial interface of rice or Arabidopsis, suggesting their potential roles in maize kernel development. In the filling‐stage basal region, numerous GO terms associated with transcriptional regulation and transporters are significantly enriched. Furthermore, we investigated the molecular function of three hub TFs. Through genome‐wide DNA affinity purification sequencing combined with promoter transactivation assays, we suggested that these three TFs act as regulators of 10 basal‐specific transporter genes involved in the transfer of sugars, amino acids, and ions. This study provides insights into transcriptomic dynamic and regulatory modules of the maternal/filial interface. In the future, genetic investigation of these hub regulators must advance our understanding of maternal/filial interface development and function.

Recent advances in exploring transcriptional regulatory landscape of crops

“…High-temporal-resolution RNA sequencing was conducted on the basal and upper regions of maize kernels. Weighted gene co-expression network analyses were performed, identifying numerous hub regulators that are worthy of subsequent functional characterization ( He et al., 2024 ).…”