Temporal and spatial auxin responsive networks in maize primary roots

Abstract

Auxin is a key regulator of root morphogenesis across angiosperms. To better understand auxin regulated networks underlying maize root development we have characterized auxin responsive transcription across two time points (30 and 120 minutes) and four regions of the primary root: the meristematic zone, elongation zone, cortex, and stele. Hundreds of auxin-regulated genes involved in diverse biological processes were quantified in these different root regions. In general, most auxin regulated genes are region unique and are predominantly observed in differentiated tissues compared to the root meristem. Auxin gene regulatory networks (GRNs) were reconstructed with these data to identify key transcription factors that may underlie auxin responses in maize roots. Additionally, Auxin Response Factor (ARF) subnetworks were generated to identify target genes which exhibit tissue or temporal specificity in response to auxin. These networks describe novel molecular connections underlying maize root development and provide a foundation for functional genomic studies in a key crop.

The Auxin Response Factor ARF27 is required for maize root morphogenesis

“…In addition, Class A and Class B ARFs exhibited fairly distinct DNA binding landscapes 16 . A recent reconstruction of maize ARF gene regulatory networks in primary roots was in line with these findings 18 .…”

“…3C). B73 seedlings exhibited the classical response of primary root growth inhibition following exogenous auxin treatment 18 (Table S3). Similar to B73, most maize inbred genotypes also exhibited ~74% inhibition following auxin treatment (Fig.…”

“…The differentially upregulated or downregulated genes were determined from QuantSeq data using PoissonSeq as previously described 18 . Differential expression was determined using a False Discovery Rate (FDR) <0.05.…”

“…Differential expression was determined using a False Discovery Rate (FDR) <0.05. Upset plots were generated in R as previously described 18 .…”

“…ARF transcription factors are conserved among land plants and have been well studied in Arabidopsis, Marchantia polymorpha and Physcomitrium patens 15 . The maize ARF family consists of 33 members, which display a high degree of overlap in transcriptional expression patterns [16][17][18] . Notably, protein abundance data for maize ARFs indicates that these transcription factors may exhibit some tissue specificity throughout development 19 .…”