Biology subjects

Eveland, A. L.

Publications and source records attributed to Eveland, A. L..

9 recordsLinked to original sources

bioRxiv2025

A core genetic mechanism integrates growth hormone signals to control meristem fate and inflorescence architecture in setaria and maize

Inflorescence architecture in cereals is a major determinant of grain yield and harvestability. Architecture is determined by the number, arrangement and order of lateral branches, which are formed from clusters of stem cells called meristems. Variation in branching patterns arises from regulation of meristem determinacy, i.e., indeterminate meristems maintain meristematic activity allowing for higher order branching and determinate meristems form a terminal organ. The timing by which an indeterminate branch meristem acquires a determinate fate and transitions to a spikelet meristem (SM), ultimately forming the grain-bearing spikelet, defines architecture and grain yield potential. This study leverages the unique inflorescence morphology of model grass Setaria viridis (setaria) to identify factors controlling SM fate and determinacy and characterize their interactions. In setaria, axillary branches terminate either in a spikelet or sterile bristle, where the latter loses SM identity due to brassinosteroid (BR)-mediated disruption of organ boundary formation. A forward genetics screen identified two mutants with only bristles on their panicles; one defective in gibberellic acid (GA) signaling caused extreme elongation and disruption of spikelet development and the other homeotically converted spikelets to bristles. The latter named spikeletless (spkl) was mapped and validated as an ortholog of the maize determinacy factor ramosa1 (ra1). Genetic analyses showed that SvRa1 acts upstream of BR-mediated regulation of SM identity and determinacy. A model is proposed where SvRA1 maintains SM fate by modulating GA homeostasis, spatially restricting BR signaling and preserving boundary gene expression and determinacy. In bristle primordia, which are generally paired with spikelets, GA and BR act synergistically. Comparative analyses in maize highlight pathway conservation in inflorescence architecture with some specific variations.

plant biology↗

bioRxiv2024

Genomic prediction of cereal crop architecture traits using models informed by gene regulatory circuitries from maize

Plant architecture is a major determinant of planting density, which enhances productivity potential for crops per unit area. Genomic prediction is well-positioned to expedite genetic gain of plant architecture traits since they are typically highly heritable. Additionally, the adaptation of genomic prediction models to query predictive abilities of markers tagging certain genomic regions could shed light on the genetic architecture of these traits. Here, we leveraged transcriptional networks from a prior study that contextually described developmental progression during tassel and leaf organogenesis in maize (Z. mays) to inform genomic prediction models for architecture traits. Since these developmental processes underlie tassel branching and leaf angle, two important agronomic architecture traits, we tested whether genes prioritized from these networks quantitatively contribute to the genetic architecture of these traits. We used genomic prediction models to evaluate the ability of markers in the vicinity of prioritized network genes to predict breeding values of tassel branching and leaf angle traits for two diversity panels in maize, and diversity panels from sorghum (S. bicolor) and rice (O. sativa). Predictive abilities of markers near these prioritized network genes were similar to those using whole-genome marker sets. Notably, markers near highly connected transcription factors from core network motifs in maize yielded predictive abilities that were significantly greater than expected by chance in not only maize but also closely related sorghum. We expect that these highly connected regulators are key drivers of architectural variation that are conserved across closely related cereal crop species. Article summaryWe used an approach typically used for breeding to infer the contributions of biological gene networks to plant architectural traits. We found that markers near genes belonging to smaller, specialized gene networks from maize could predict breeding values of leaf angle better than expected by chance for both maize and sorghum.

genetics↗

bioRxiv2024

Quantifying Leaf Symptoms of Sorghum Charcoal Rot in Images of Field-Grown Plants 9 Using Deep Neural Networks

Charcoal rot of sorghum (CRS) is a significant disease affecting sorghum crops, with limited genetic resistance available. The causative agent, Macrophomina phaseolina (Tassi) Goid, is a highly destructive fungal pathogen that targets over 500 plant species globally, including essential staple crops. Utilizing field image data for precise detection and quantification of CRS could greatly assist in the prompt identification and management of affected fields and thereby reduce yield losses. The objective of this work was to implement various machine learning algorithms to evaluate their ability to accurately detect and quantify CRS in red-green-blue (RGB) images of sorghum plants exhibiting symptoms of infection. EfficientNet-B3 and a fully convolutional network (FCN) emerged as the top-performing models for image classification and segmentation tasks, respectively. Among the classification models evaluated, EfficientNet-B3 demonstrated superior performance, achieving an accuracy of 86.97%, a recall rate of 0.71, and an F1 score of 0.73. Of the segmentation models tested, FCN proved to be the most effective, exhibiting a validation accuracy of 97.76%, a recall rate of 0.68, and an F1 score of 0.66. As the size of the image patches increased, both models validation scores increased linearly, and their processing time decreased exponentially. The models, in addition to being immediately useful for breeders and growers of sorghum, advance the domain of automated plant phenotyping and may serve as a base for drone-based or other automated field phenotyping efforts. Additionally, the models presented herein can be accessed through a web-based application where users can easily analyze their own images. Core ideasO_LIAutomated phenotyping tools are required for the efficient detection and quantification of charcoal rot of sorghum. C_LIO_LIClassification and segmentation models can distinguish between concurrent plant stresses with similar symptoms. C_LIO_LILarger image patch sizes generally improve model performance and reduce processing time. C_LI

plant biology↗

bioRxiv2023

Regulatory variation controlling architectural pleiotropy in maize

An early event in plant organogenesis is establishment of a boundary between the meristem and differentiating lateral organ. In maize (Zea mays), evidence suggests a common gene network functions at boundaries of distinct organs and contributes to pleiotropy between leaf angle and tassel branch number, two agronomic traits. To uncover regulatory variation at the nexus of these two traits, we used regulatory network topologies derived from specific developmental contexts to guide multivariate genome-wide association analyses. In addition to defining network plasticity around core pleiotropic loci, we identified new transcription factors that contribute to phenotypic variation in canopy architecture, and structural variation that contributes to cis-regulatory control of pleiotropy between tassel branching and leaf angle across maize diversity. Results demonstrate the power of informing statistical genetics with context-specific developmental networks to pinpoint pleiotropic loci and their cis-regulatory components, which can be used to fine-tune plant architecture for crop improvement.

plant biology↗

bioRxiv2021

Boundary domain genes were recruited to suppress bract growth and promote branching in maize

Grass inflorescence development is diverse and complex and involves sophisticated but poorly understood interactions of genes regulating branch determinacy and leaf growth. Here, we use a combination of transcript profiling, genetic and phylogenetic analyses to investigate tasselsheath1 (tsh1) and tsh4, two maize genes that simultaneously suppress inflorescence leaf growth and inhibit branching. We identify a regulatory network of inflorescence leaf suppression that involves the phase change gene tsh4 upstream of tsh1 and the ligule identity gene liguleless2 (lg2). We also find that a series of duplications in the tsh1 gene lineage facilitated its shift from boundary domain in non-grasses to suppressed inflorescence leaves of grasses. Collectively, these results suggest that the boundary domain genes tsh1 and lg2 were recruited to inflorescence leaves where they suppress growth and regulate a non-autonomous signaling center that promotes inflorescence branching, an important component of yield in cereal grasses.

plant biology↗

bioRxiv2021

High Light and High Temperature Reduce Photosynthesis via Different Mechanisms in the C4 Model Setaria viridis

C4 plants frequently experience damaging high light (HL) and high temperature (HT) conditions in native environments, which reduce growth and yield. However, the mechanisms underlying these stress responses in C4 plants have been under-explored, especially the coordination between mesophyll (M) and bundle sheath (BS) cells. We investigated how the C4 model plant Setaria viridis responded to a four-hour HL or HT treatment at the photosynthetic, transcriptomic, and ultrastructural levels. Although we observed a comparable reduction of photosynthetic efficiency in HL- or HT-treated leaves, detailed analysis of multi-level responses revealed important differences in key pathways and M/BS specificity responding to HL and HT. We provide a systematic analysis of HL and HT responses in S. viridis, reveal different acclimation strategies to these two stresses in C4 plants, discover unique light/temperature responses in C4 plants in comparison to C3 plants, and identify potential targets to improve abiotic stress tolerance in C4 crops.

plant biology↗

bioRxiv2020

Regulatory signatures of drought response in stress resilient Sorghum bicolor

The effects of drought stress can be devastating to crop production worldwide. A grand challenge facing agriculture is development of crop varieties with improved drought resilience through breeding or biotechnology. To accelerate this, a mechanistic understanding is needed of the regulatory networks underlying drought response in crop genomes and the genetic elements that modulate them. Here, we explore the regulatory landscape of sorghum [Sorghum bicolor (L.) Moench] in response to controlled-environment drought stress. Sorghum is a C4 cereal crop with innate drought resilience. To define molecular signatures of drought response, we mapped genome-wide chromatin accessibility using an Assay for Transposase Accessible Chromatin by sequencing and analyzed parallel transcriptional profiles in drought-stressed sorghum shoot and root tissues. Drought-responsive changes in accessibility were largely in proximal promoters of differentially expressed genes and also in distal regions. Data were integrated to infer gene network connections and cis-regulatory modules underlying drought response and the transcription factors that control them. Inspection of pan-genomic data and phenotyping across sorghum diversity revealed variation in genomic signatures that associated with water use efficiency. Our analyses provide drought-inducible regulatory modules in sorghum that can be leveraged for fine-tuning responses to stress, mining for advantageous alleles, and translating across species.

plant biology↗

bioRxiv2020

SvFUL2, an A-class MADS-box transcription factor, is necessary for inflorescence determinacy in model panicoid cereal, Setaria viridis

Inflorescence architecture in cereal crops directly impacts yield potential through regulation of seed number and harvesting ability. Extensive architectural diversity found in inflorescences of grass species is due to spatial and temporal activity and determinacy of meristems, which control the number and arrangement of branches and flowers, and underlie plasticity. Timing of the floral transition is also intimately associated with inflorescence development and architecture, yet little is known about the intersecting pathways and how they are rewired during development. Here, we show that a single mutation in a gene encoding an AP1 A-class MADS-box transcription factor significantly delays flowering time and disrupts multiple levels of meristem determinacy in panicles of the C4 model panicoid grass, Setaria viridis. Previous reports of A-class genes in cereals have revealed extensive functional redundancy, and in panicoid grasses, no associated inflorescence phenotypes have been described. In S. viridis, perturbation of SvFul2, both through chemical mutagenesis and CRISPR/Cas9-based gene editing, converted a normally determinate inflorescence habit to an indeterminate one, and also repressed determinacy in axillary branch and floral meristems. Our analysis of gene networks connected to disruption of SvFul2 identified regulatory hubs at the intersect of floral transition and inflorescence determinacy, providing insights into the optimization of cereal crop architecture.

plant biology↗

bioRxiv2019

The regulatory landscape of early maize inflorescence development

BackgroundThe functional genome of agronomically important plant species remains largely unexplored, yet presents a virtually untapped resource for targeted crop improvement. Functional elements of regulatory DNA revealed through profiles of chromatin accessibility can be harnessed for fine-tuning gene expression to optimal phenotypes in specific environments. ResultHere, we investigate the non-coding regulatory space in the maize (Zea mays) genome during early reproductive development of pollen- and grain-bearing inflorescences. Using an assay for differential sensitivity of chromatin to micrococcal nuclease (MNase) digestion, we profile accessible chromatin and nucleosome occupancy in these largely undifferentiated tissues and classify at least 1.6 percent of the genome as accessible, with the majority of MNase hypersensitive sites marking proximal promoters, but also 3 ends of maize genes. This approach maps regulatory elements to footprint-level resolution. Integration of complementary transcriptome profiles and transcription factor occupancy data are used to annotate regulatory factors, such as combinatorial transcription factor binding motifs and long non-coding RNAs, that potentially contribute to organogenesis, including tissue-specific regulation between male and female inflorescence structures. Finally, genome-wide association studies for inflorescence architecture traits based solely on functional regions delineated by MNase hypersensitivity reveals new SNP-trait associations in known regulators of inflorescence development as well as new candidates. ConclusionsThese analyses provide a comprehensive look into the cis-regulatory landscape during inflorescence differentiation in a major cereal crop, which ultimately shapes architecture and influences yield potential.

plant biology↗