Stalk lodging causes global maize (Zea mays L.) yield losses exceeding $6 billion annually. The poorly resolved genetic architecture of stalk lodging resistance, a key determinant of the ability of a plant to remain upright, poses a major constraint for genetic improvement. Characterizing natural variation in plant traits that influence stalk strength across multiple biological scales, referred to as intermediate phenotypes, is critical for enhancing lodging resistance. Here, we present a high-density phenotypic dataset comprising 11 intermediate phenotypes measured on 31,260 stalks from a maize diversity panel of 566 inbred lines grown in four environments. The dataset captures variation in structural and geometric properties of stalks and provides a foundation for genetic mapping, predictive modeling, and machine learning analyses to dissect the genetic basis of stalk lodging resistance. Moreover, trait-level resolution across a genetically diverse panel enables evaluation of the relative contribution of individual phenotypes to stalk strength. Beyond maize improvement for grain and forage production, this dataset offers valuable opportunities for improving stalk lodging resistance in other grasses.

The world has food security needs that are currently not being met. Stalk lodging undermines crop productivity and incurs global yield losses of at least $6 billion in maize ( Zea mays L.). Genetic architecture of stalk lodging resistance, a measure of the ability of the stalk to withstand lodging, remains poorly resolved, creating a bottleneck for genetic improvement. Identification of diverse plant traits at multiple length scales of biological organizations that contribute to stalk lodging resistance and characterization of natural variation for these traits is critical for improving stalk lodging resistance. We identified and evaluated 11 intermediate phenotypes, traits associated with stalk lodging resistance, in a maize diversity panel of 566 inbred lines evaluated over four environments. The identity of each of the 31,260 stalks evaluated in the study was preserved throughout the phenotyping pipeline which enabled capturing variation at the individual plant level. This high-density phenotypic dataset provided a foundation for statistical genomics, predictive modeling, and machine learning analyses to identify genes and genetic elements underlying stalk lodging resistance. Additionally, phenotypic characterization of multiple intermediate phenotypes on a diverse set of inbred lines provided excellent opportunities to understand the relative contribution of these traits to stalk lodging resistance. Besides improvement of maize for grain and animal feedstock, the inferences from this data will be valuable for improvement of stalk lodging resistance in other grass species. ### Competing Interest Statement The authors have declared no competing interest. * ⁰C : degrees Celsius cm : Centimeter ex-PVP : Expired Plant Variety Protection Act certificate KY : Kentucky mm : Millimeter N : Newton Nm : Newton*meter PVC : Polyvinyl chloride RH : Relative humidity SC : South Carolina

White oak (Quercus alba) is an abundant forest tree species across eastern North America that is ecologically, culturally, and economically important. We report the first haplotype-resolved chromosome-scale genome assembly of Q. alba and conduct comparative analyses of genome structure and gene content against other published Fagaceae genomes. We investigate the genetic diversity of this widespread species and the phylogenetic relationships among oaks using whole genome data. Despite strongly conserved chromosome synteny and genome size across Quercus, certain gene families have undergone rapid changes in size, including defense genes. Unbiased annotation of resistance (R) genes across oaks revealed that the overall number of R genes is similar across species - as are the chromosomal locations of R gene clusters - but, gene number within clusters is more labile. We found that Q. alba has high genetic diversity, much of which predates its divergence from other oaks and likely impacts divergence time estimations. Our phylogenetic results highlight widespread phylogenetic discordance across the genus. The white oak genome represents a major new resource for studying genome diversity and evolution in Quercus. Additionally, we show that unbiased gene annotation is key to accurately assessing R gene evolution in Quercus.

Breeding for stalk lodging resistance is of paramount importance to maintain and improve maize (Zea mays L.) yield and quality and meet increasing food demand. The integration of environmental, phenotypic, and genotypic information offers the opportunity to develop genomic prediction strategies that can improve the genetic gain for complex traits such as stalk lodging. However, implementation of genomic predictions for stalk lodging resistance has been sparse primarily due to the lack of reliable and reproducible phenotyping strategies. In this study, we measured 10 traits related to stalk lodging resistance obtained from a novel phenotyping platform on approximately 31,000 individual stalks. These traits were combined with environmental information and whole-genome resequence data to investigate the predictive ability of different single and multi-environment genomic prediction models. In total, 555 maize inbred lines from the Wisconsin diversity panel were evaluated in four environments. The multi-environment models more than doubled the prediction accuracy compared to the single-environment model for most traits, particularly when predicting lines in a sparse testing design. Predictive correlations for stalk bending strength and stalk flexural stiffness, a nondestructive method for assessment of stalk lodging resistance, were moderately high and ranged between 0.32-0.89 and 0.26-0.88, respectively. In contrast, rind thickness was the most difficult trait to predict. Our results show that the use of multi-environmental data could improve genomic prediction accuracy for stalk lodging resistance and its intermediate phenotypes. This study will serve as a first step toward genetic improvement and the development of maize varieties resistant to stalk lodging.

Stalk lodging in the monocot Zea mays is an important agricultural issue that requires the development of a genome-to-phenome framework, mechanistically linking intermediate and high-level phenotypes. As part of that effort, tools are needed to enable better mechanistic understanding of the microstructure in herbaceous plants. A method was therefore developed to create finite element models using CT scan data for Zea mays. This method represents a pipeline for processing the image stacks and developing the finite element models. 2-dimensional finite element models, 3-dimensional watertight models, and 3-dimensional voxel-based finite element models were developed. The finite element models contain both the cell and cell wall structures that can be tested in silico for phenotypes such as structural stiffness and predicted tissue strength. This approach was shown to be successful, and a number of example analyses were presented to demonstrate its usefulness and versatility. This pipeline is important for two reasons: (1) it helps inform which microstructure phenotypes should be investigated to breed for more lodging-resistant stalks, and (2) represents an essential step in the development of a mechanistic hierarchical framework for the genome-to-phenome modeling of herbaceous plant stalk lodging.

### Competing Interest Statement The authors have declared no competing interest.

In this study, we investigated the interplay between the spermosphere inoculum, host plant physiology, and endophytic compartment (EC) microbial community. Using 16S ribosomal RNA gene sequencing of root, stem, and leaf endophytic compartment communities, we established a baseline microbiome for Nicotiana sp. Phenotypic differences were observed due to the addition of some bacterial inoculants, correlated with endogenous auxin loads using transgenic plants expressing the auxin reporter pB-GFP::P87. When applied as spermosphere inoculants, select bacteria were found to create reproducible variation within the root EC microbiome and, more systematically, the host plant physiology. Our findings support the assertion that the spermosphere of plants is a zone that can influence the EC microbiome when applied in a greenhouse setting.

Quercus alba L., also known as white oak, eastern white oak, or American white oak, is a quintessential North American species within the white oak section (Quercus) of the genus Quercus, subgenus Quercus. This species plays a vital role as a keystone species in eastern North American forests and plays a significant role in local and regional economies. As a long-lived woody perennial covering an extensive natural range, Q. alba’s biology is shaped by a myriad of adaptations accumulated throughout its natural history. Populations of Q. alba are crucial repositories of genetic, genomic, and evolutionary insights, capturing the essence of successful historical adaptations and ongoing responses to contemporary environmental challenges in the Anthropocene. This intersection offers an exceptional opportunity to integrate genomic knowledge with the discovery of climate-relevant traits, advancing tree improvement, forest ecology, and forest management strategies. This review provides a comprehensive examination of the current understanding of Q. alba’s biology, considering past, present, and future research perspectives. It encompasses aspects such as distribution, phylogeny, population structure, key adaptive traits to cyclical environmental conditions (including water use, reproduction, propagation, and growth), as well as the species’ resilience to biotic and abiotic stressors. Additionally, this review highlights the state-of-the-art research resources available for the Quercus genus, including Q. alba, showcasing developments in genetics, genomics, biotechnology, and phenomics tools. This overview lays the groundwork for exploring and elucidating the principles of longevity in plants, positioning Q. alba as an emerging model tree species, ideally suited for investigating the biology of climate-relevant traits.

Herbicide-resistant weeds are increasingly a problem in crop fields when exposed to similar chemistry over time. To avoid future yield losses, identifying herbicidal chemistry needs to be accelerated. We screened 50,000 small molecules using a liquid-handling robot and light microscopy focusing on pre-emergent herbicides in the family of cellulose biosynthesis inhibitors. Through phenotypic, chemical, genetic, and in silico methods we uncovered 6-{[4-(2-fluorophenyl)-1-piperazinyl]methyl}-N-(2-methoxy-5-methylphenyl)-1,3,5-triazine-2,4-diamine (fluopipamine). Symptomologies support fluopipamine as a putative antagonist of cellulose synthase enzyme 1 (CESA1) from Arabidopsis (Arabidopsis thaliana). Ectopic lignification, inhibition of etiolation, phenotypes including loss of anisotropic cellular expansion, swollen roots, and live cell imaging link fluopipamine to cellulose biosynthesis inhibition. Radiolabeled glucose incorporation of cellulose decreased in short-duration experiments when seedlings were incubated in fluopipamine. To elucidate the mechanism, ethylmethanesulfonate mutagenized M2 seedlings were screened for fluopipamine resistance. Two loci of genetic resistance were linked to CESA1. In silico docking of fluopipamine, quinoxyphen, and flupoxam against various CESA1 mutations suggests that an alternative binding site at the interface between CESA proteins is necessary to preserve cellulose polymerization in compound presence. These data uncovered potential fundamental mechanisms of cellulose biosynthesis in plants along with feasible leads for herbicidal uses.

Stalk lodging contributes to significant crop yield losses. Therefore, understanding the biomechanical strength and structural rigidity of grain stalks can contribute to improving stalk lodging resistance in crops. From the structural constituents of the stalk, the rind provides the principal structure, supporting cells against tension and bending loads. In this work, the biomechanical and viscoelastic behavior of the rind from the internodes of two sweet sorghum varieties (Della and REDforGREEN (RG)), grown in two different growing seasons, were evaluated by three-point micro-bending tests using a dynamic mechanical analyzer (DMA). In addition, the chemical composition of rinds and the microfibril angle (MFA) of the cell wall were determined using XRD. The results revealed that the biomechanical behavior of Della varieties was stiffer and more resistant to loads than that of RG varieties. Two features of the rind biomechanical properties, flexural modulus (FM) and flexural strength (FS), showed a significant reduction for RG. Particularly, a reduction in FS of 16–37% and in FM of 22–41% were detected for RG1. Changes in the stalks’ rind biomechanical properties were attributed to cell wall components. Total lignin and glucan/cellulose contents were positively correlated with the FM and FS of the rind. Subsequently, an increase in the two cell wall components drove an increase in stiffness. Furthermore, the MFA of the rind was also found to influence the rind strength.

This study sought to better understand how time of day (ToD) or turgor pressure might affect the flexural stiffness of sweet sorghum stalks and potentially regulate stalk lodging resistance. Stalk flexural stiffness measured across a 48 h period in 2019 showed a significant diurnal association with leaf water potential and stalk flexural stiffness. While the correlation between stalk flexural stiffness and this proxy for internal turgor status was statistically significant, it only accounted for roughly 2% of the overall variance in stiffness. Given that turgor status is a dynamic rather than fixed physiological variable like the cellular structure, these data suggest that internal turgor plays a small yet significant role in influencing the flexural stiffness of fully mature stalks prior to a stalk lodging event. The association was assessed at earlier developmental stages across three distinct cultivars and found not to be significant. Panicle weight and stalk basal weight, but not stalk Brix or water content, were found to be better predictors of stalk flexural stiffness than either ToD or turgor status. Observation across three cultivars and four distinct developmental stages ranging from the vegetative to the hard-dough stages suggests that stalk flexural stiffness changes significantly as a function of time. However, neither ToD nor turgor status appear to meaningfully contribute to observed variations in stalk flexural stiffness in either individual stalks or across larger populations. As turgor status was not found to meaningfully influence stalk strength or flexural stiffness at any developmental time point examined in any of the three sweet sorghum cultivars under study, turgor pressure likely offers only inconsequential contributions to the biomechanics underlying sweet sorghum stalk lodging resistance.

Summary White oak ( Quercus alba ) is an abundant forest tree species across eastern North America that is ecologically, culturally, and economically important. We report the first haplotype-resolved chromosome-scale genome assembly of Q. alba and conduct comparative analyses of genome structure and gene content against other published Fagaceae genomes. In addition, we probe the genetic diversity of this widespread species and investigate its phylogenetic relationships with other oaks using whole-genome data. Our genome assembly comprises two haplotypes each consisting of 12 chromosomes. We found that the species has high genetic diversity, much of which predates the divergence of Q. alba from other oak species and likely impacts divergence time estimation in Quercus . Our phylogenetic results highlight phylogenetic discordance across the genus and suggest different relationships among North American oaks than have been reported previously. Despite a high preservation of chromosome synteny and genome size across the Quercus phylogeny, certain gene families have undergone rapid changes in size including resistance genes (R genes). The white oak genome represents a major new resource for studying genome diversity and evolution in Quercus and forest trees more generally. Future research will continue to reveal the full scope of genomic diversity across the white oak clade.

American white (Quercus alba L.) oak casks have been used for liquid storage for centuries. Their use in aged spirits is critical to imparting flavor and mouthfeel to the final product. The reason that barrels retain liquid has been hypothesized to be the result of abundant physiological structures called tyloses in parenchyma tissues and medullary rays in white oak. Using non-destructive X-ray computed tomography (XRCT) imaging, we reveal an unprecedented view of tylose structure and quantify the pore-filling capacity of tyloses in white oak that underscores the liquid retention we observe in casks. We show that pores of white oaks are filled with sevenfold higher tylose volume compared to northern red oak (Q. rubra), consistent with prior literature that casks made from white oak retain liquid while red oak fails to do so. We propose that XRCT represents a methodological standard for observing these complex structures and should be employed to understand the many questions related to liquid losses from casks, cultural treatment of casks, and the influence of climate change on oak tyloses in the future.

This study presents a methodology for a high-throughput digitization and quantification process of plant cell walls characterization, including the automated development of two-dimensional finite element models. Custom algorithms based on machine learning can also analyze the cellular microstructure for phenotypes such as cell size, cell wall curvature, and cell wall orientation. To demonstrate the utility of these models, a series of compound microscope images of both herbaceous and woody representatives were observed and processed. In addition, parametric analyses were performed on the resulting finite element models. Sensitivity analyses of the structural stiffness of the resulting tissue based on the cell wall elastic modulus and the cell wall thickness; demonstrated that the cell wall thickness has a three-fold larger impact of tissue stiffness than cell wall elastic modulus.

Context: Stalk lodging causes up to 43 % of yield losses in maize (Zea mays L.) worldwide, significantly worsening food and feed shortages. Stalk lodging resistance is a complex trait specified by several structural, material, and geometric phenotypes. However, the identity, relative contribution, and genetic tractability of these intermediate phenotypes remain unknown.Objective: The study is designed to identify and evaluate plant-, organ-, and tissue-level intermediate phenotypes associated with stalk lodging resistance following standardized phenotyping protocols and to understand the variation and genetic tractability of these intermediate phenotypes.Methods: We examined 16 diverse maize hybrids in two environments to identify and evaluate intermediate phenotypes associated with stalk flexural stiffness, a reliable indicator of stalk lodging resistance, at physiological maturity. Engineering-informed and machine learning models were employed to understand relationships among intermediate phenotypes and stalk flexural stiffness.Results: Stalk flexural stiffness showed significant genetic variation and high heritability (0.64) in the evaluated hybrids. Significant genetic variation and comparable heritability for the cross-sectional moment of inertia and Young's modulus indicated that geometric and material properties are under tight genetic control and play a combinatorial role in determining stalk lodging resistance. Among the twelve internode-level traits measured on the bottom and the ear internode, most traits exhibited significant genetic variation among hybrids, moderate to high heritability, and considerable effect of genotype x environment interaction. The marginal statistical model based on structural engineering beam theory revealed that 74-80 % of the phenotypic variation for flexural stiffness was explained by accounting for the major diameter, minor diameter, and rind thickness of the stalks. The machine learning model explained a relatively modest proportion (58-62 %) of the variation for flexural stiffness.Conclusions: Characterization of stalk and internode properties using standard phenotyping methods revealed tremendous variation for intermediate phenotypes underlying stalk lodging resistance. The intermediate phenotypes showed moderate to high heritability, indicating their genetic tractability for improving stalk lodging resistance. Stalk geometric and material properties showed complementarity in determining stalk flexural stiffness. Engineering-informed models outperformed machine learning approaches in explaining variation for flexural stiffness.Implications: Identification of genetically tractable intermediate phenotypes will boost efforts toward genetic improvement of stalk lodging resistance in maize. Discovering the genetic architecture of the intermediate traits will enhance our understanding of the biological underpinning of stalk lodging resistance.

Increasing interest in products made from rye grain underscores the need for developing improved rye (Secale cereale L.) cultivars. In the context of consumer appeal, there are specific questions about the sensory attributes of different rye cultivars. Unfortunately, there are very few studies that focus on the flavor and other sensory attributes of rye products. In order to estimate rye-derived aroma and flavor variability, we evaluated sensory attributes in rye flatbread of forty-seven rye entries, selected from commercial rye cultivars and international accessions that are adapted to our latitude. Additionally, we evaluated distillates from eleven rye cultivars and breeding lines. We found significant differences in flatbread aroma and flavor (P < 0.001) and significant overall distillate aroma differences (P < 0.05) among tested rye entries. In our flatbread screening, heritability of nutty (h2 = 0.37), salty (h2 = 0.57), grassy (h2 = 0.37), toasted (h2 = 0.55), and raw dough-like (h2 = 0.34) flavor notes, and sweet (h2 = 0.29), fermented (h2 = 0.34), musty (h2 = 0.33), grassy (h2 = 0.37) and toasted (h2 = 0.5) aroma notes were found significant; the number of distillates evaluated was too small to estimate this parameter. We developed rye distillate aroma and flavor prediction models based on sensory evaluation of easy and quick-to-prepare flatbread. This manuscript proposes the usage of flatbread to evaluate rye grain aroma and flavor for sensory research purposes and for flavor prediction of other rye products.

Background: Stalk lodging is the structural failure of crops due to external loading such as wind. Short-stature (i. e., dwarf) varieties of wheat and rice have shown promise in reducing lodging rates. However, similar dwarfing in large gains like maize and sorghum has typically been accompanied by undesirable commercial characteris-tics, including significantly decreased grain yields. The purpose of this paper is to quantify the relationship between lodging resistance and plant height in maize to better understand the potential impact of short-stature varieties of maize on lodging resistance.Results: Results from both the engineering analysis and the experimental field study indicate a nearly 1:1 rela-tionship between plant height and plant lodging resistance. These data support the validity of the engineering analysis and suggest that there exists a nearly linear relationship between crop lodging incidence and plant height.Conclusions: Plant height has a direct and quantifiable impact on crop lodging resistance as it influences the bending stresses experienced in the plant stem. This study presents the engineering analysis, supported by field experiments, that explains the cause of this nearly linear 1:1 relationship.

Whiskey production originated in Scotland in the 15th century and was based on malted barley. As Scotch-Irish settlers came into the Ohio river valley, they began fermenting and distilling the primary grain of North America, maize. These earlier settlers started a heritage; they created American Whiskey. The bourbon industry in Kentucky had tremendous growth in the last 20 years, and currently, distilleries have a broad increase in product innovation, new raw materials, improved sustainability, efficient processes, and product diversification. Our study presents a new lab-scale method for new-make bourbon whiskey production. It was developed to mimic distilleries’ processes; therefore, results can be extrapolated and adopted by commercial distilleries. The method focused on reproducibility with consistency from batch to batch when handled by an operator or small crew in a university lab. The method consisted of a first cooking step to make a “mash”, a fermentation phase of 96 h, a first distillation accomplished with a copper pot still to obtain the “low wines” and a second distillation carried out with an air still to collect the “hearts”. The method produced a final distillate of 500–700 mL for further sensory analysis and tasting. This lab-scale method showed consistency between samples in the different parameters quantified and will be also used to train students in fermentation and distillation studies.

Highlights Deep eutectic solvent (DES) pretreatment of endocarp biomass led to higher overall glucose yield and lignin extraction. High performance anode materials were synthesized using Si nanoparticles and DES or alkaline extracted lignin. The core-shell structure formed during pyrolysis contributes to the enhanced electrochemical performance. Abstract. A holistic use of lignocellulosic biomass by converting lignin to high-value products and cellulose and hemicelluloses to biofuel will greatly enhance the economic viability of a biorefinery. In this study, a three-dimensional, interconnected carbon/silicon composite was synthesized from silicon nanoparticles (Si NPs) with either deep eutectic solvent (DES) or alkaline pretreatment-extracted lignin from endocarp biomass. The endocarp lignin derived composite electrodes exhibited superior electrochemical performance in a half-coin cell lithium-ion battery setup. DES lignin derived C/Si NPs composite reached a discharging capacity of 1563 mAh g -1 ; while alkaline lignin derived C/Si NPs composite reaching a discharging capacity of 1605 mAh g -1 at a current density of 0.72 A g -1 . Despite the comparable electrochemical performance, DES pretreatment led to a higher overall sugar yield from the liquid streams after pretreatment and enzymatic hydrolysis. This study demonstrates the utilization of endocarp lignin in electrochemical energy storage applications. Keywords: Anode, Lignin, Lithium-ion battery, Silicon nanoparticles.

HighlightsEndocarps have higher lignin content, cellular and bulk density, and hardness than typical biomass feedstocks.The impacts of lignin content, bulk density, and mechanical properties on energy consumption are discussed.Endocarps can be a potential feedstock for a biorefinery coproducing biofuel and bioproducts.Abstract. Lignin is an abundant biopolymer and a promising source of feedstock for high-value chemicals and materials. This study aims to characterize the lignin-rich endocarp biomass and identify features of this unique feedstock that are relevant to feedstock preprocessing and logistics. The chemical composition and cellular structure of walnut and peach endocarps were characterized using HPLC and scanning electron microscopy (SEM) imaging. Mechanical properties of the endocarps were investigated using nanoindentation. Mechanical tests revealed hardness values of up to 0.48 and 0.40 GPa for walnut and peach endocarps, respectively. With screen sizes of 1 and 2 mm, the specific energy consumption was 9.21 and 1.86 MJ kg-1 for walnut and 12.6 and 2.72 MJ kg-1 for peach, respectively, as determined using a knife mill. Milling energy consumption was correlated to screen size, lignin content, bulk density, and mechanical properties. This study provides critical information on feedstock supply logistics necessary to implement a novel feedstock in biorefineries and evaluate the economic feasibility for coproduction of biofuels and lignin-derived products. Keywords: Biomass feedstock, Lignin, Mechanical properties, Nanoindentation, Size reduction.