Biology subjects

Draves, M. A.

Publications and source records attributed to Draves, M. A..

5 recordsLinked to original sources

bioRxiv2026

Cis-regulatory variation and transcription factor binding contribute to allelic genotype-by-environment interactions for gene expression in maize

Genotype-by-environment interactions (GxE), or differences in how genotypes perform across varying environments, are a pervasive source of phenotypic variation and underlie differences in local adaptation. Though GxE is well characterized across kingdoms of life, less is known about what causes GxE interactions, particularly at the molecular level. In this study, we use allele-specific gene expression estimates in a maize (Zea mays L.) B73 x Mo17 hybrid to isolate cis-regulatory effects on gene expression for each of the two parental alleles. The hybrid was grown in two environments, and expression differences between the parental alleles were used to characterize allele-by-environment (AxE) interactions and study the influence of gene-proximal sequence variation on transcript abundance AxE. We tested the hypothesis that gene-proximal sequence variation can cause GxE in gene expression by modifying transcription factor binding. Our results show that sequence variation in gene promoter regions has a small but consistent enrichment in genes that show transcriptional AxE. Further, we demonstrate that differential transcription factor binding potential caused by sequence variation is also enriched in AxE genes. Predictive models trained on sequence and transcription factor binding variation show that while these features contain some information about whether a gene will show transcriptional AxE, they alone are not sufficient to reliably distinguish AxE genes. These findings support the hypothesis that gene expression GxE can be caused by sequence variation that modifies transcription factor binding, while also reinforcing the complex and context-specific nature of GxE interactions.

genomics↗

bioRxiv2024

Identification of phenotypic and transcriptomic signatures underpinning maize crown root systems

Maize is pivotal in supporting global agriculture and addressing food security challenges. Crop root systems are critical for water uptake and nutrient acquisition, which impacts yield. Quantitative trait phenotyping is essential to understand better the genetic factors underpinning maize root growth and development. Root systems are challenging to phenotype given their below-ground, soil-bound nature. In addition, manual trait annotations of root images are tedious and can lead to inaccuracies and inconsistencies between individuals, resulting in data discrepancies. To address these issues, we have developed an automated phenotyping pipeline for field-grown maize crown roots by leveraging open-source software. Phenotypic variation of 20 maize genotypes from the Wisconsin Diversity panel was significant for numerous root traits, suggesting a genetic basis for the observed developmental deviations. In addition, juvenile root traits from controlled environment conditions exhibited inconsistent correlation with field-grown adult root traits, underscoring the developmental plasticity prevalent during maize root morphogenesis. Transcripts involved in hormone signaling and stress responses were among differentially expressed genes in roots from 20 maize genotypes, suggesting many molecular processes may underlie the observed phenotypic variance. This study furthers our understanding of genotype-phenotype relationships, which is relevant for informing agricultural strategies to improve maize root physiology.

plant biology↗

bioRxiv2023

The Auxin Response Factor ARF27 is required for maize root morphogenesis

Crop root systems are central to nutrition acquisition and water usage. Root hairs and lateral roots contribute to fine-scale patterning of root systems and can offer many advantages for improving root function without drastically impacting overall system architecture. Key genetic regulators underpinning root hair morphogenesis have been well characterized in the model plant Arabidopsis but are less understood in maize. Here, we identify a novel determinant of root hair morphogenesis and auxin responses in maize, AUXIN RESPONSE FACTOR27 (ARF27), using both reverse and quantitative genetic approaches. ARF27 is enriched in maize primary root tissues at both the transcript and protein level. Loss of ARF27 leads to short primary roots and reduced root hair formation, while lateral root density is unaltered. In arf27 roots, auxin-responsive gene expression is dysregulated, which is consistent with the predicted function of this transcription factor. Moreover, a genome wide association study (GWAS) to uncover genetic determinants of auxin-dependent root traits identified ARF27 as a candidate gene. Furthermore, auxin hypersensitive maize genotypes exhibit altered crown root length and surface area in field-grown plants. A gene regulatory network (GRN) was reconstructed and an ARF27 subnetwork was integrated with DAP-seq and GWAS data to identify ARF27 target genes. The ARF27 GRN includes known maize root development genes, such as ROOTLESS CONCERNING CROWN ROOTS (RTCS), ROOTHAIRLESS 3 (RTH3) and RTH6. Altogether this work identifies a novel genetic driver of auxin-mediated root morphogenesis in maize that can inform agricultural strategies for improved crop performance.

plant biology↗

bioRxiv2023

ZmPILS6 is an auxin efflux carrier required for maize root morphogenesis

Plant root systems play a pivotal role in plant physiology and exhibit diverse phenotypic traits. Understanding the genetic mechanisms governing root growth and development in model plants like maize is crucial for enhancing crop resilience to drought and nutrient limitations. This study focused on identifying and characterizing ZmPILS6, an annotated auxin efflux carrier, as a key regulator of various crown root traits in maize. ZmPILS6-modified roots displayed reduced network area and suppressed lateral root formation, desirable traits during drought and low phosphate conditions. The research revealed that ZmPILS6 localizes to the endoplasmic reticulum and plays a vital role in controlling the spatial distribution of indole-3-acetic acid (IAA or "auxin") in primary roots. The study also demonstrated that ZmPILS6 can actively efflux IAA when expressed in yeast. Furthermore, the loss of ZmPILS6 resulted in significant proteome remodeling in maize roots, particularly affecting hormone signaling pathways. To identify potential interacting partners of ZmPILS6, a weighted gene co-expression analysis (WGNA) was performed. Altogether, this research contributes to the growing knowledge of essential genetic determinants governing maize root morphogenesis, which is crucial for guiding agricultural improvement strategies. Significance StatementCrop yield and stress resilience are significantly influenced by crown root architecture. A reverse genetic screen aimed at identifying novel regulators of maize root morphogenesis led to the discovery of ZmPILS6, an auxin efflux carrier. The loss of ZmPILS6 negatively impacts numerous root traits that are linked to plant physiology and function. Proteomic characterization of pils6-1 roots revealed that this evolutionarily conserved transporter is required for the proper expression of numerous phytohormone pathways, including abscisic acid, gibberellins, and jasmonic acid. Notably, ZmPILS6 appears to have a contrasting role in regulating root morphogenesis compared to its Arabidopsis ortholog, PILS6. This finding emphasizes the need for functional characterization of candidate genes directly within key crops of interest, which cannot always be correctly inferred from other model plants.

plant biology↗

bioRxiv2022

Temporal and spatial auxin responsive networks in maize primary roots

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.

plant biology↗