Regulatory signatures of drought response in stress resilientSorghum bicolor

Abstract

The effects of drought stress can be devastating to crop production worldwide. A grand challenge facing agriculture is the 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 pathways in crop genomes and the genetic elements that modulate them. In this study, 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 and is an untapped resource of allelic diversity. To define molecular signatures of drought response, we mapped genome-wide chromatin accessibility using an Assay for Transposase Accessible Chromatin by sequencing (ATAC-seq) and analyzed parallel transcriptional profiles in drought-stressed sorghum shoot and root tissues compared to well-watered controls. Drought-responsive changes in chromatin accessibility were largely found in proximal promoters of differentially expressed genes and also in distal regions of the genome. These data were integrated to infer gene network connections and cis-regulatory modules that underlie drought response in sorghum, including cross-talk among hormone and nutrient pathways and the transcription factors that control them. Our analyses provide drought-inducible regulatory modules in the sorghum genome that can be leveraged for fine-tuning responses to stress, mining diversity for advantageous alleles, and translating across species to ultimately improve productivity and sustainability in sorghum and closely related cereal crops.

cis-Regulatory Elements in Plant Development, Adaptation, and Evolution

“…In maize, however, the use of chromatin accessibility data derived from plants grown in control conditions does not improve predictions of heat or cold stress responses (158). In sorghum, drought-responsive accessible chromatin signatures were enriched for ABSCISIC ACID RESPONSE ELEMENT (ABRE)-binding sites and used to constrain gene regulatory network predictions for abscisic acid-dependent transcriptional cascades (106). Further analyses using dynamic chromatin accessibility in both control and stress samples may provide insights into whether chromatin data can improve stress-response predictions.…”

Applying cis-regulatory codes to predict conserved and variable heat and cold stress response in maize

“…Recent work has suggested that unmethylated regions may provide a catalogue of potential regulatory elements in plants (Crisp et al, 2020). Many regions that contain stress-specific regulatory elements are likely unmethylated even in control conditions while many of the regions of accessible chromatin may be more dynamic and only become accessible in specific conditions (Zeng et al, 2019; Wang et al, 2020a; Parvathaneni et al, 2020).…”

Large and stable genome edits at the sorghum alpha kafirin locus result in changes in chromatin accessibility and globally increased expression of genes encoding lysine enrichment

“…Nuclei isolation was carried out using a modified version of Parvathaneni et al., 2021’s protocol ( Parvathaneni et al., 2021 ). Fifteen developing kernels were finely chopped with razor blades in a nuclei isolation buffer (16 mM HEPES; pH8, 200 mM sucrose, 0.8 mM MgCl2, 4 mM KCl, 32% Glycerol, 0.25% Triton X-100, 1x complete protease inhibitor, 0.1% 2-ME, 0.1 mM PMSF).…”