Plant Direct

Cotton (Gossypium hirsutum) is an economically important crop, but it faces increasing pest outbreaks, especially in non-irrigated areas. In this study, 20 cotton farms using center-pivot irrigation were sampled in southern Georgia to assess chemical differences between non-irrigated and irrigated areas. Proton (1H) nuclear magnetic resonance (NMR) data were obtained from cotton leaves, and Principal Component Analysis (PCA) was performed to assess differences in chemical composition. Across all samples, farm site accounted for most of the variability, but within each farm site, the PCA scores plots showed clear separation between non-irrigated and irrigated conditions in 10 sites. Inspecting the PCA loadings revealed significant resonances resembling a lipid-like signal. After reverse-phase fractionation, we observed that many of these resonances appeared together in later fractions, suggesting a lipid, specifically a fatty acid such as linoleic acid. We hypothesized that differences in net lipid saturation level may drive separation between non-irrigated and irrigated samples. Six farm sites had a significantly or marginally significantly higher degree of unsaturation in irrigated samples, while one farm site had significantly higher unsaturation in non-irrigated samples. Our results indicate that drought stress likely affects lipid profile composition, which could be driving higher herbivorous pest densities in drought-stressed crops.

Cannabis is well known for its pungent, skunk-like aroma. Recent chemical studies have identified prenylated and C6 volatile sulfur compounds as contributors to its skunky and citrus-like aromas, but the pathways that produce these compounds remain unknown. This gap limits efforts to explain variation in sulfur-aroma traits and to selectively enhance or reduce those traits. To address this gap, we used the known chemistry of sulfur-containing volatiles in Cannabis and characterized sulfur and volatile biosynthetic pathways in other plant species to select candidate enzyme groups. Because the GMO cultivar is anecdotally associated with a pronounced sulfurous aroma, reference protein sequences and profile hidden Markov models were used to search its version 1 (v1) primary high-confidence protein set of 55,790 sequences. These searches recovered 975 unique proteins. Sequence screening retained 941 candidates across 20 reporting categories; 939 contained all expected domains, while the two candidates assigned to the methionine gamma-lyase (MGL)-nearest category had no category-specific expected-domain rule. The largest reporting category comprised 359 proteins containing a cytochrome P450 domain, recovered through a search motivated by cytochrome P450 family 74 (CYP74) enzymes involved in oxylipin and plant volatile formation. Thirteen of these proteins were also recovered by at least one full-length CYP74 reference search. Other large reporting categories included 218 sugar-transferase, 83 glutathione-transferase, and 61 alcohol dehydrogenase candidates. Comparison with the Cannabis Expression Atlas linked 168 candidates to 128 annotated genes through 100%-identity amino-acid matches spanning at least 80% of each GMO v1 candidate protein. Twenty-nine genes were tissue-specific, including 13 root-specific and 6 trichome-specific genes. These results define candidates for biochemical testing and direct searches for additional enzymes acting upstream and downstream in Cannabis sulfur-volatile pathways.

Research ConductedTo elucidate the functions of glycosylceramides, we generated and characterized mutants deficient in multiple steps contributing to their assembly in the model moss Physcomitrium patens. We mutagenized SPHINGOLIPID {Delta}8-DESATURASE, whose products are preferentially incorporated into glycosylceramides, and a suite of higher-order mutants combining sphingolipid {Delta}4-desaturase and glycosyl ceramide synthase. MethodsWe used targeted lipidomics to describe the chemotypes of all mutants. We used quantitative phenotype analysis, transcriptomics, and phytohormone profiling to understand the effects of these chemotypes on development and physiology. Key ResultsThese mutants present a range of phenotypes that collectively indicate that in P. patens (1) glycosylceramide deficiency impairs development, largely due to imbalance in free ceramide homeostasis (2) the synthesis of glycosylceramides is dependent upon the presence of a specific free ceramide profile (3) the {Delta}4-, but not the {Delta}8-desaturation, is strictly required for glycosylceramide synthesis, (4) cell division and differentiation, but not cell expansion, are affected by sphingolipid imbalance, and (5) sphingolipid imbalance results in oxylipin accumulation. ConclusionCollectively, our results elucidate the assembly and functions of glycosylceramides in a model bryophyte, and highlight conserved and specialized aspects of sphingolipid metabolism among plants.

Plants make diverse metabolites to outcompete neighboring organisms for space and resources. Some of these toxic metabolites broadly disrupt conserved molecular mechanisms, such as protein biosynthesis. Nonproteogenic amino acids (NPAAs) are a structurally diverse class of metabolites that interfere with protein biosynthesis. The proline (Pro) analog azetidine-2-carboxylic acid (Aze) inhibits plant growth through misincorporation during protein biosynthesis. However, it is unknown if a cascade of downstream stress responses is triggered following Aze misincorporation. Here, we investigate the morphological and stress responses in Arabidopsis grown on Aze. Investigation of root morphological responses show not only reduced root growth, but increased root branching following growth on Aze. Altered root morphology is coupled with a reduced gravitropic response. Aboveground organs were also affected by Aze, including reduced chlorophyll content, reduced photosynthetic efficiency, and increased anthocyanin content. We then tested whether Aze induces reactive oxygen species (ROS) accumulation using multiple approaches and observed both immediate and sustained accumulation of general ROS and H2O2 following treatment with Aze. When plants were grown on Aze supplemented with Pro, ROS levels were restored to normal levels, suggesting that reducing misincorporation events results in less downstream stress responses. In summary, we find that following Aze treatment a cascade of downstream stress responses is induced that exacerbates the effects of toxic NPAAs. This study sheds light on the mechanism of action of NPAAs and provides information on the downstream consequences of translational errors.

A strategy to improve agricultural water productivity is to increase water use efficiency (WUE) at the level of plant transpiration through genetic selection. This requires detectable genetic variability in WUE and the ability to phenotype and select plants with higher WUE within a population. A proxy for phenotyping leaf level WUE by measuring carbon isotope signature ({delta}13Cleaf) has been supported by theory and data in C4 species. However, the functional relationship of {delta}13Cleaf and WUE in C4 species can be driven by genetics and environment. Therefore, a wide survey of existing natural variation is needed to quantify the heritability and identify various genetic factors that influence {delta}13Cleaf and WUE. In this study a genome-wide association panel was used to quantify the heritability of {delta}13Cleaf. We measured {delta}13Cleaf across a population of 360 genetically diverse lines of the C4 species Sorghum bicolor with single nucleotide polymorphic (SNP) markers determined from whole-genome resequencing. This analysis was conducted on two independent field environments where heritability of {delta}13Cleaf was evident and was driven by small genetic effects from loci that were consistently identified across environments. Candidate genes are presented that offer insights on future targets to manipulate and explore the functional relationship between {delta}13Cleaf and WUEi in C4 plants.

Cassava (Manihot esculenta Crantz) is a major staple crop across tropical and subtropical regions. Despite advances in genomic selection, delayed, non-flowering, and asynchronous flowering remain key bottlenecks in breeding programs. To better understand the molecular basis of flowering-time variation, we performed RNA sequencing across three genotypes with contrasting flowering phenotypes (early, late, and non-flowering) sampled at three developmental stages under contrasting light regimes in field conditions (natural light and three-hour night-break with white light). Comparative transcriptomic analysis revealed distinct gene expression patterns associated with flowering responses. Genotype comparisons with no light supplementation revealed stage-specific enrichment of biological processes. Light supplementation was associated with changes in the expression of key components of photoperiodic and circadian regulation, as well as pathways involved in flowering-time integration and hormone and sugar-related signaling. These findings suggest that coordinated changes across multiple biological pathways regulate flowering behavior in cassava. The candidate genes and expression patterns reported provide a foundation for functional studies and advance our understanding of molecular mechanisms governing flowering-time regulation in cassava.

Salinity is a major abiotic stress that severely limits plant growth and productivity, causing substantial yield losses. Despite barleys relative tolerance to salinity, the underlying physiological and molecular mechanisms remain incompletely understood. In this study, we employed an integrative approach combining agronomic, physiological, biochemical, and transcriptomic analyses to investigate salinity responses in the spring barley cultivar Giza 134 under both field and lysimeter-based conditions. Salinity stress significantly reduced growth and yield-related traits, with more pronounced effects observed under lysimeter-imposed salinity, reflecting higher stress intensity. These reductions were associated with impaired water status, altered leaf structural traits, and declines in photosynthetic pigment content. In contrast, proline accumulation increased, indicating activation of osmotic adjustment mechanisms. Salinity also disrupted ionic homeostasis, as evidenced by elevated Na+ levels, reduced K+ content, and an increased Na+/K+ ratio. Enhanced lipid peroxidation and elevated catalase and peroxidase activities suggested increased oxidative stress and activation of antioxidant defenses. Transcriptome profiling identified 4,298 differentially expressed genes, including 1,764 upregulated and 2,534 downregulated genes. Functional enrichment analyses revealed upregulation of pathways related to stress adaptation, redox regulation, and metabolic reprogramming, while genes associated with photosynthesis, ribosome biogenesis, and protein synthesis were strongly suppressed. Several novel stress-responsive genes involved in signaling, osmoprotection, antioxidant defense, and central metabolism were highly induced, supported by coordinated enrichment of cis-regulatory motifs in their promoter regions. Together, these findings provide a comprehensive physiological and molecular framework for salinity tolerance in Giza 134 and highlight candidate genes and pathways for breeding salt-resilient cultivars suited to saline-prone environments.

Peptide hormone signaling coordinates plant growth and osmotic stress responses, yet how the transition between these responses is regulated remains poorly understood. Here, we investigated the function of the rice PLANT PEPTIDES CONTAINING SULFATED TYROSINE 8 (OsPSY8) peptide in osmotic stress responses. OsPSY8 was predominantly expressed in root tissues under non-stress conditions, with preferential expression in lateral roots where it promoted root growth. Osmotic stress rapidly reduced OsPSY8 expression in roots through the OsWRKY24 transcription factor. Loss-of-function ospsy8 mutants exhibited enhanced osmotic stress tolerance, whereas OsPSY8 overexpression increased osmotic stress susceptibility. Transcriptomic analyses revealed that disruption of OsPSY8 activated stress-responsive pathways, including those associated with lignin biosynthesis, compatible solute production, cell wall remodeling, and reactive oxygen species (ROS) scavenging, and was accompanied by increased lignin accumulation in roots. In contrast, overexpression of OsPSY8 resulted in maintenance of growth-associated transcriptional programs while suppressing stress-responsive pathways under osmotic stress. Together, these findings identify OsPSY8 as an important regulator of the transition from growth to stress adaptation in rice and suggest that stress-induced repression of PSY signaling is required to disengage growth programs and activate adaptive responses during osmotic stress. Significance StatementCrop survival during drought depends on the ability to transition from growth to stress adaptation. Plant peptide hormones have emerged as important regulators of this critical transition, highlighting the importance of investigating their roles and potential for improving crop resilience. We show that a rice peptide hormone regulates this transition. Under non-stress conditions, this peptide hormone, predominantly expressed in rice roots, promotes root growth while suppressing stress responses. During osmotic stress, expression of the peptide hormone decreases, resulting in activation of stress-responsive pathways, such as lignin biosynthesis and reactive oxygen species scavenging. These findings demonstrate that a peptide hormone coordinates the balance between growth and stress adaptation in rice, with broader implications for understanding and improving crop resilience.

Water-use efficiency (WUE), the ratio of accumulated plant biomass to water lost through transpiration has conventionally been determined using a destructive single-point measurement. Recent advances in high-throughput phenotyping now enable repeated, non-destructive estimation of biomass and WUE. However, these digital measurements must be statistically validated against conventional destructive methods to validate their use as reliable proxies. Therefore, we compared digital biomass determined point clouds produced from multispectral camera scanners with destructive harvests across eight harvests using Samsun tobacco grown under both drought and high-water conditions. WUE efficiency, calculated using the digital biomass estimated from a point cloud and gravimetric water use determinations, were compared to destructive harvest determinations. The coefficient of variation (CV) showed there were no significant differences in digital and destructive measurements for either biomass or WUE. Indicating that digital measurements can be used in place of destructive measurements. Drought plants used significantly less water and were significantly smaller than high-water plants from Harvests 4 through 8. However, there were no significant differences in the ratio of evapotranspiration to leaf area or WUE, indicating that drought plants were simply smaller and used less water than the high-water plants. This work validates that estimating plant biomass from a digital point coupled with continuous gravimetric determination of water use provides a reliable nondestructive measure of WUE in high-throughput measurements across the full plant life cycle.

Arabidopsis Leucine-Rich Repeat-Malectin Receptor Kinase (LRR-MAL RK) genes have been previously implicated in the early stages of pollen-pistil interactions to support compatible pollen. One member, Receptor Kinase in Flowers 1 (RKF1), has been associated with roles in the stigma to support pollen hydration as well as pollen tube growth. To better understand the function of RKF1 in these processes, a yeast two-hybrid screen was conducted with the RKF1 cytosolic kinase domain. Two positive interactors identified from this screen were the Group VII Ethylene Response Factors (ERFVIIs), RELATED TO APETALA 2.12 (RAP2.12) and RAP2.3. Their putative roles in pollen-pistil interactions were investigated using the quintuple erfvii mutant, and novel pistil-mediated pollen tube callose deposition phenotypes were uncovered during the pollen tube growth stage. Loss of seven LRR-MAL RKs including RKF1 in the pistil was previously found to cause an unusual phenotype where shorter callose plugs were deposited in wildtype pollen tubes compared to that seen in wildtype Col-0 pistils. Contrary to this, wildtype pollen tubes growing through the quintuple erfvii mutant pistil deposited callose plugs that were more elongated than that seen in wildtype Col-0 pistils. Further analyses with the proteolysis 6 (prt6) mutant and RAP2.12 rescue constructs were consistent with these phenotypes providing support that RKF1 is a negative regulator of RAP2.12 and RAP2.3 in the pistil during pollen tube growth.

High-phenolic plant genera present a major technical limitation in genomic research. Standard extraction approaches that perform reliably across diverse flora often perform poorly when applied to recalcitrant taxa, producing low DNA yield and integrity incompatible with sequencing requirements. The genus Anigozanthos (Kangaroo paws) from the family Haemodoraceae exemplifies this problem. We identified key physicochemical factors governing extraction failure in this genus and resolved them through targeted modifications to lysis chemistry and contaminant management. The resulting protocol achieved a near threefold improvement in DNA purity, substantially reducing contaminant carry over and consistently yielded high-integrity, long DNA fragments (DIN > 7) across a diverse sample set spanning cultivated and wild material across four diverse genera of Haemodoraceae. We also tested a straightforward purity assessment framework that can be implemented in any standard molecular laboratory, enabling rapid pre-submission quality assessment without the need for specialised equipment. Together these advances open a practical path to genomic characterisation of Anigozanthos that establishes a transferable model for genomic research across Australia ' s chemically complex native flora.

Thermal adaptation is critical for organismal viability, with acquired thermotolerance (AT) in Arabidopsis thaliana typically conferred by acclimation temperatures between 34{degrees}C and 37{degrees}C, while acclimation at 40{degrees}C fails to protect against lethal heat stress. To elucidate the transcriptional mechanisms underlying the loss of AT at higher temperatures we performed RNA-seq profiling of Arabidopsis seedlings across a single-degree thermal gradient from 37{degrees}C to 40{degrees}C. Our analysis reveals that all of these temperatures result in a robust heat shock response, characterized by the upregulation of genes involved in protein folding and stress responses. However, each temperature elicits a distinct transcriptional signature. These findings demonstrate that temperature-specific fine-tuning of the heat shock response occurs within this narrow range and that these differences may dictate the successful acquisition of thermotolerance. This dataset provides a valuable resource for understanding the molecular architecture of heat-stress adaptation and the distinct transcriptional states associated with different thermal regimes.

Tillering plasticity is a key adaptive trait in sorghum influencing resource use efficiency via a plants ability to adjust branching to neighbour density. Neighbour detection through red:far-red (R:FR) light sensing regulates this plasticity. While molecular pathways regulating tiller outgrowth are partly known, the genetic architecture underlying density-responsive tillering has not been resolved in any grass species. A sorghum diversity panel (n = 895) was evaluated over two growing seasons (2023 and 2024) with plant spacing ranging from 5 to 60 cm. A linear mixed model incorporating neighbour distance and tiller counts estimated genotype-specific response. GWAS was conducted on isolated plants (no neighbours within 60 cm) and on estimated responsiveness to neighbours. GWAS identified 52 baseline tillering QTLs and 50 for spacing responsiveness, with 10 overlapping, suggesting shared genetic control. Comparison with 41 R:FR pathway candidate genes revealed enrichment in responsiveness QTLs (5/50, 10%) versus baseline (0/52, 0%) (Fishers exact test, P = 0.025). Our model identified 40 unique density-responsive tillering QTL regions. Reducing genotype response to neighbour absence could be a selection target to develop water-efficient sorghum varieties where controlled architecture may be more valuable than natural plasticity.

Rice (Oryza sativa) is highly sensitive to salinity, yet the metabolic mechanisms underlying salt tolerance remains incompletely understood. In this study, we performed leaf tissue-specific untargeted metabolomic profiling of the salt-tolerant introgression line JN100 (JN), its donor parent Nona Bokra (NB), and its recurrent parent Jupiter (JU) to characterize metabolic responses to salt stress. Comparative analysis identified differentially accumulated metabolites (DAMs) spanning diverse chemical classes, including amino acids, sugars and carbohydrates, lipids, organic acids, cofactors, electron carriers, and nucleotides. Under salt stress (SS), 201 DAMs (89 upregulated and 112 downregulated) were detected in JN relative to JU. Notably, metabolites such as allantoin, glycitin, nicotinamide ribotide, D-arabinono-1,4-lactone, violanthin, L-methionine S-oxide, ribitol, lysine, rutin, glutamine, pantothenic acid, and quinic acid, showed significant differential accumulation. Pathway enrichment analysis revealed significant enrichment of arginine biosynthesis, purine metabolism, and alanine, aspartate, and glutamate metabolism, indicating extensive reprogramming of nitrogen and energy-associated metabolic pathways under salinity stress. Integration of transcriptomic and metabolomic datasets from the SS experiments further identified ten differentially expressed genes (DEGs) associated with the metabolite network in the JN vs. JU comparison. Among these, OsDHQDT/SDH, OsFd-GOGAT, phenylalanyl-tRNA synthetase, OsP5CS1, OsP5CS2, and a pyridoxal phosphate-dependent transferase were linked to metabolites involved in shikimate, amino acid, and proline metabolism. Collectively, these results demonstrate that salinity tolerance in rice is associated with coordinated transcriptional and metabolic reprogramming that supports oxidative stress mitigation and adaptive stress responses.

Although the biosynthetic pathways of benzylisoquinoline alkaloids (BIAs) have been extensively investigated in several plant species, their transcriptional regulatory mechanisms remain only partially understood. Jasmonate (JA)-responsive group IX APETALA2/Ethylene Responsive Factor (AP2/ERF) transcription factors (TFs) are well-known regulators of specialized plant metabolism, including the biosynthesis of various alkaloids. However, their specific roles in BIA biosynthesis remain largely elusive. Here, we isolated five novel group IX AP2/ERF TFs, designated Benzylisoquinoline alkaloid Jasmonate-responsive AP2/ERF (BJE1-5), from Coptis japonica. Phylogenetic analysis revealed that Benzylisoquinoline alkaloid Jasmonate-responsive AP2/ERF (BJE) proteins belong to subclades distinct from group IXa, which contains well-known AP2/ERF TFs involved in alkaloid biosynthesis. Transient expression analyses in C. japonica protoplasts demonstrated that certain BJEs, particularly CjBJE3 and CjBJE5, positively regulated BIA biosynthetic genes through a mutual regulatory network among BJE members. Moreover, CjBJE3 expression was regulated by CjbHLH1, a unique-type basic helix-loop-helix (bHLH) TF specific to BIA-producing plants. Furthermore, heterologous expression of CjBJE3 and CjBJE5 in cultured Eschscholzia californica cells significantly enhanced the overall BIA production, particularly by increasing end-product benzophenanthridine BIAs, highlighting several uncharacterized biosynthetic genes clustered in the genome. Our findings suggest that BIA-producing species have developed a specific regulatory network comprised of CjbHLH1 and BJE TFs, providing valuable clues for identifying novel biosynthetic enzymes.

Salinity stress affects rice productivity due to reduced growth and sodium ion toxicity. Previously, we identified a splice variant of RADIATION SENSITIVE23a (RAD23a) as the potential basis for variation in salt-tolerance in rice germplasm. RAD23 is a known moonlighting protein associated with protein degradation. To validate the role of RAD23a in salt stress response, we characterized gene edited mutant lines that targeted the UBL and UBA2 domains of this protein. Mutation in either domain promoted shoot growth under saline and control conditions. The mutants also differed from wildtype plants in Na and K accumulation in roots and shoots under salt stress. Transcriptome analysis of mutants versus wildtype showed differential transcript abundance of multiple inorganic phosphate (Pi) starvation related genes, including OsSPX2 and OsPHO2. As a result, mutants accumulate higher Pi compared to wildtype plants. The two allelic groups for RAD23a locus also differ in root and shoot phosphorus (P) content. Further, we show that RAD23a interacts with OsSPX2, a negative post-translational regulator of OsPHR2, the master regulator of Pi starvation response. Mutants have higher shoot growth and Pi levels under low Pi conditions, linking enhanced growth of mutants to increased Pi uptake. The UBA2 domain specific mutants have higher single grain weight and per plant grain weight than wildtype. In summary, we show that the RAD23a regulates differential growth, salt response and Pi uptake in rice in a domain-specific manner supporting the moonlighting roles of RAD23a in salt tolerance and phosphorus-dependent shoot growth.

Chickpea (Cicer arietinum) is a globally important legume crop whose productivity is frequently constrained by terminal drought, particularly in rainfed systems. We used high-throughput phenotyping of 35 diverse chickpea haplotypes at contrasting watering regimes (80% and 40% field capacity) to identify superior haplotypes. Significant haplotype:watering interactions were observed for water-use dynamics, growth rates, biomass accumulation and nodulation, indicating strong genetic control over drought responses. Certain haplotypes (e.g., ICC2210 and ICC18839) maintained relatively high water-use efficiency and growth under stress, while others exhibited pronounced reductions in biomass and nodulation. Principal Component Analyses (PCA) were used to identify haplotypes associated with tolerant and sensitive stress phenotypes. Metabolomic profiling revealed widespread reprogramming of metabolism under water limitation, with 57 of 82 metabolites significantly affected by treatment. A consistent decrease in tricarboxylic acid intermediates, including succinic acid, indicated altered energy metabolism, while accumulation of osmoprotectants such as proline and sucrose reflected adaptive responses to osmotic stress. Multivariate and ANOVA Simultaneous Component Analyses (ASCA) identified key metabolites as major contributors to haplotype-specific drought responses. These metabolites are linked to nitrogen metabolism, stress signalling and cellular protection mechanisms. These results demonstrate substantial variation in drought adaptation among chickpea haplotypes and confirm that the integration of phenotypic and metabolomic traits is a powerful approach to identify drought-resilient genotypes.

Flower opening is a complex developmental process involving coordinated changes in cell proliferation and cell expansion. Although several regulators of flower opening have been identified, how transcriptional programs are coordinated with the cellular and metabolic changes underlying petal expansion immediately before flower opening remains incompletely understood. Japanese morning glory (Ipomoea nil) is a suitable model for investigating these processes because its flowers open synchronously at a predictable time. This study aimed to identify transcriptional regulators involved in petal development and flower opening in Japanese morning glory. Temporal analyses of petal growth, sugar metabolism, and gene expression revealed that petal development was driven by both cell proliferation and cell expansion until approximately 48 h before flower opening, whereas cell expansion predominated thereafter. Weighted gene co-expression network analysis identified two genes encoding R2R3-MYB subgroup 19 transcription factors, InMYB21A and InMYB21B, as candidate regulators associated with petal development. CRISPR/Cas9-mediated knockout analysis revealed a prominent role for InMYB21B, whose loss markedly impaired petal cell expansion and prevented flower opening. InMYB21B knockout also impaired stamen and pistil development, resulting in male and female sterility. Starch degradation and glucose accumulation were impaired in InMYB21B knockout petals. Transcriptome analysis revealed delayed transcriptomic progression during petal development and reduced expression of genes associated with starch degradation, sucrose metabolism, cell wall remodeling, and water transport. These findings identify InMYB21B as a key regulator of petal cell expansion and flower opening in Japanese morning glory and show that loss of InMYB21B disrupts both metabolic and transcriptomic progression during late petal development.

Synthetic nitrogen fertilizers have greatly increased crop yields, yet much of the applied nitrogen is lost from agroecosystems and contributes to environmental pollution and higher economic costs. Improving nitrogen uptake efficiency (NUpE) benefits from understanding how root system architecture (RSA) governs soil nitrogen capture. Although root traits have seldom been explicit breeding targets, selection for variation in above-ground nitrogen accumulation has also likely shaped differences in RSA. The Illinois Protein Strain Recombinant Inbred population, derived from more than a century of divergent selection for seed protein concentration, offers a powerful resource for dissecting RSA variation. Using multi-year field phenotyping of excavated root crowns and genome-wide association analysis, we identified a quantitative trait locus on chromosome 10 containing E1OGDH1, which encodes the E1 subunit of the 2-oxoglutarate dehydrogenase (OGDH) complex. OGDH performs a key step in the tricarboxylic acid cycle that also modulates 2-oxoglutarate, an important entry point into nitrogen metabolism and a co-factor for enzymes involved in hormone and secondary product synthesis. Long-read sequencing of inbreds derived from the divergent IHP and ILP parental populations revealed promoter polymorphisms defining E1OGDH1 alleles and differed in E1OGDH1 expression in root tissue. Field experiments in IPSRI lines carrying IHP- or ILP-associated E1OGDH1 alleles showed differences in root architectural traits over two years. CRISPR-Cas9 knockout mutants confirmed a functional role for E1OGDH1 in whole-plant performance and nitrogen-responsive root development. Mutants were shorter, had reduced biomass, and exhibited altered architectural responses to soil nitrogen levels. Transcriptome analysis further showed that loss of E1OGDH1 altered basal and nitrogen-responsive expression of genes associated with root development and nitrogen uptake and metabolism. Together, these findings identify E1OGDH1 as a strong candidate quantitative regulator of maize RSA and nitrogen plasticity, suggesting that central carbon-nitrogen metabolic genes can contribute to root developmental responses relevant to NUpE.

The glandular trichomes in Cannabis sativa, found predominantly on female flowers, produce and store a variety of unique phytocannabinoids, increasingly studied for their use in medicinal applications. Maximizing yield and cannabinoid profiles requires the optimization of the environmental factors that regulate plant growth. Light plays a prominent role, both as an energy source but also as an important developmental signal. Thus, optimization of lighting strategies, particularly through customizable light-emitting diode (LED) fixtures, has become a major focus of controlled-environment cannabis research. Here, we focus on the effect of blue-enriched and far red-enriched light spectra on the morphological traits and biochemical profiles of two THCA-dominant varieties: Pineapple Cough and Rocky Fire #7. Spectral composition exerts modest and genotype-specific effects on the plant development, inflorescence biomass, and cannabinoid concentration but we demonstrate a positive correlation between total yield and plant height in both varieties, regardless of spectra. We also show that growth under far-red enriched light affects the visible pigmentation in both varieties with significantly lower chlorophyll levels and paler fan and sugar leaves. Finally, we demonstrate that far-red light consistently increased the trichome stalk length in both varieties, suggesting that spectral composition can alter trichome development and morphology. Our data offers insights into cannabis development and secondary chemical profiles in response to different light spectra, allowing growers to adjust light spectra to obtain desirable cannabis traits for industrial production.