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Gray leaf spot, northern leaf blight and southern leaf blight are three of the most destructive foliar diseases affecting maize (Zea mays L.). Here we identified a gene, ZmCPK39, that encodes a calcium-dependent protein kinase and negatively regulates quantitative resistance to these three diseases. The ZmCPK39 allele in the resistant line displayed significantly lower pathogen-induced gene expression than that in the susceptible line. A marked decrease in ZmCPK39 abundance mitigated the phosphorylation and degradation of the transcription factor ZmDi19. This led to elevated expression of ZmPR10, a gene known to encode an antimicrobial protein, thereby enhancing maize resistance to foliar diseases. Moreover, the F 1 hybrid with reduced ZmCPK39 expression favored disease resistance, thereby increasing yield. Hence, the discovery of the ZmCPK39-ZmDi19-ZmPR10 immune module provides insight into the mechanisms underlying broad-spectrum quantitative disease resistance and also offers a new avenue for the genetic control of maize foliar diseases., Competing Interests: Competing interests: The authors declare no competing interests., (© 2024. The Author(s).)

The common rust disease of maize is caused by the obligate biotrophic fungus Puccinia sorghi. The maize Rp1-D allele imparts resistance against the P. sorghi IN2 isolate by initiating a defense response that includes a rapid localized programmed cell death process, the hypersensitive response (HR). In this study, to identify AvrRp1-D from P. sorghi IN2, we employed the isolation of haustoria, facilitated by a biotin-streptavidin interaction, as a powerful approach. This method proves particularly advantageous in cases where the genome information for the fungal pathogen is unavailable, enhancing our ability to explore and understand the molecular interactions between maize and P. sorghi. The haustorial transcriptome generated through this technique, in combination with bioinformatic analyses such as SignalP and TMHMM, enabled the identification of 251 candidate effectors. We ultimately identified two closely related genes, AvrRp1-D.1 and AvrRp1-D.2, which triggered an Rp1-D-dependent defense response in Nicotiana benthamiana. AvrRp1-D-induced Rp1-D-dependent HR was further confirmed in maize protoplasts. We demonstrated that AvrRp1-D.1 interacts directly and specifically with the leucine-rich repeat (LRR) domain of Rp1-D through yeast two-hybrid assay. We also provide evidence that, in the absence of Rp1-D, AvrRp1-D.1 plays a role in suppressing the plant immune response. Our research provides valuable insights into the molecular interactions driving resistance against common rust in maize., Competing Interests: The authors have declared that no competing interests exist., (Copyright: This is an open access article, free of all copyright, and may be freely reproduced, distributed, transmitted, modified, built upon, or otherwise used by anyone for any lawful purpose. The work is made available under the Creative Commons CC0 public domain dedication.)

During domestication, early farmers selected different vegetative and reproductive traits, but identifying the causative loci has been hampered by their epistasis and functional redundancy. Using chromatin immunoprecipitation sequencing combined with genome-wide association analysis, we uncovered a developmental regulator that controls both types of trait while acting upstream of multiple domestication loci. tasselsheath4 (tsh4) is a new maize domestication gene that establishes developmental boundaries and specifies meristem fates despite not being expressed within them. TSH4 accomplishes this by using a double-negative feedback loop that targets and represses the very same microRNAs that negatively regulate it. TSH4 functions redundantly with a pair of homologs to positively regulate a suite of domestication loci while specifying the meristem that doubled seed yield in modern maize. TSH4 has a critical role in yield gain and helped generate ideal crop plant architecture, thus explaining why it was a major domestication target., (© 2024. The Author(s), under exclusive licence to Springer Nature America, Inc.)

The majority of field corn, Zea mays L., in the southeastern United States has been genetically engineered to express insecticidal toxins produced by the soil bacterium, Bacillus thuringiensis (Bt). Field corn is the most important mid-season host for corn earworm, Helicoverpa zea (Boddie) (Lepidoptera: Noctuidae), which has developed resistance to all Cry toxins in Bt corn. From 2020 to 2023, corn earworm pupae were collected from early- and late-planted pyramided hybrids expressing Bt toxins and non-Bt near-isolines in North and South Carolina (16 trials). A total of 5,856 pupae were collected across all trials, with 55 and 88% more pupae collected in later-planted trials relative to early plantings in North and South Carolina, respectively. Only 20 pupae were collected from hybrids expressing Cry1F + Cry1Ab + Vip3A20 across all trials. Averaged across trials, Cry1A.105 + Cry2Ab2 hybrids reduced pupal weight by 6 and 9% in North and South Carolina, respectively, relative to the non-Bt near-isoline. Cry1F + Cry1Ab hybrids reduced pupal weight on average by 3 and 8% in North and South Carolina, respectively, relative to the non-Bt near-isoline. The impact of the Bt toxins on pupal weight varied among trials. When combined with data from 2014 to 2019 from previous studies, a significant decline in the percent reduction in pupal weight over time was found in both states and hybrid families. This study demonstrates a continued decline in the sublethal impacts of Bt toxins on corn earworm, emphasizing the importance of insect resistance management practices., (© The Author(s) 2024. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For commercial re-use, please contact reprints@oup.com for reprints and translation rights for reprints. All other permissions can be obtained through our RightsLink service via the Permissions link on the article page on our site—for further information please contact journals.permissions@oup.com.)

Helicoverpa zea (Boddie) (Lepidoptera: Noctuidae) has evolved resistance to insecticidal toxins from Bacillus thuringiensis (Bt) Berliner (Bacillales: Bacillaceae) expressed in genetically engineered corn, Zea mays L. This study provides an overview of field trials from Georgia, North Carolina, and South Carolina evaluating Bt and non-Bt corn hybrids from 2009 to 2022 to show changes in susceptibility in H. zea to Bt corn. The reduction in kernel injury relative to a non-Bt hybrid averaged across planting dates generally declined over time for Cry1A.105 + Cry2Ab2 corn. In addition, there was a significant interaction with planting date used as a covariate. The reduction in kernel injury remained above 80% and did not vary with planting date from 2009 to 2014, whereas a significant decline with planting date was found in this reduction from 2015 to 2022. For Cry1Ab + Cry1F corn, the reduction in kernel injury relative to a non-Bt hybrid averaged across planting dates did not vary among years. The reduction in kernel injury significantly declined with planting date from 2012 to 2022. Kernel injury as a proxy for H. zea pressure was greater in late-planted trials in non-Bt corn hybrids. Our study showed that Bt hybrids expressing Cry1A.105 + Cry2Ab2 are now less effective in later planted trials in reducing H. zea injury; however, this was not the case during the earlier years of adoption of corn expressing these 2 toxins when resistance alleles were likely less frequent in H. zea populations. The implications for management of H. zea and for insect resistance management are discussed., (© The Author(s) 2024. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For commercial re-use, please contact reprints@oup.com for reprints and translation rights for reprints. All other permissions can be obtained through our RightsLink service via the Permissions link on the article page on our site—for further information please contact journals.permissions@oup.com.)

Exploring feasible and renewable alternatives to reduce dependency on traditional fossil-based plastics is critical for sustainable development. These alternatives can be produced from biomass, which may have large uncertainties and variabilities in the feedstock composition and system parameters. This study develops a modeling framework that integrates cradle-to-grave life cycle assessment (LCA) with a rigorous process model and artificial intelligence (AI) models to conduct uncertainty and variability analyses, which are highly time-consuming to conduct using only the process model. This modeling framework examines polylactic acid (PLA) produced from corn stover in the U.S. An analysis of uncertainty and variability was conducted by performing a Monte Carlo simulation to show the detailed result distributions. Our Monte Carlo simulation results show that the mean life-cycle Global Warming Potential (GWP) of 1 kg PLA is 4.3 kgCO 2 eq (P5-P95 4.1-4.4) for composting PLA with natural gas combusted for the biorefinery, 3.7 kgCO 2 eq (P5-P95 3.4-3.9) for incinerating PLA for electricity with natural gas combusted for the biorefinery, and 1.9 kgCO 2 eq (P5-P95 1.6-2.1) for incinerating PLA for electricity with wood pellets combusted for the biorefinery. Tradeoffs for different environmental impact categories were identified. Based on feedstock composition variations, two AI models were trained: random forest and artificial neural networks. Both AI models demonstrated high prediction accuracy; however, the random forest performed slightly better., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024. Published by Elsevier B.V.)

The southern corn leaf blight epidemic of 1970 caused estimated losses of about 16% for the U.S. corn crop, equivalent to about $8 billion in current terms. The epidemic was caused by the prevalence of Texas male sterile cytoplasm ( cms -T), used to produce most of the hybrid corn seed planted that year, combined with the emergence of a novel race of the fungus Cochliobolus heterostrophus that was exquisitely virulent on cms -T corn. Remarkably, the epidemic lasted just a single year. This episode has often been portrayed in the literature and textbooks over the last 50 years as a catastrophic mistake perpetrated by corn breeders and seed companies of the time who did not understand or account for the dangers of crop genetic uniformity. In this perspective article, we aim to present an alternative interpretation of these events. First, we contend that, rather than being caused by a grievous error on the part of the corn breeding and seed industry, this epidemic was a particularly unfortunate, unusual, and unlucky consequence of a technological advancement intended to improve the efficiency of corn seed production for America's farmers. Second, we tell the story of the resolution of the epidemic as an example of timely, meticulously applied research in the public sector for the public good., Competing Interests: The author(s) declare no conflict of interest.

Key Message: Integrating disease screening data and genomic data for host and pathogen populations into prediction models provides breeders and pathologists with a unified framework to develop disease resistance. Developing disease resistance in crops typically consists of exposing breeding populations to a virulent strain of the pathogen that is causing disease. While including a diverse set of pathogens in the experiments would be desirable for developing broad and durable disease resistance, it is logistically complex and uncommon, and limits our capacity to implement dual (host-by-pathogen)-genome prediction models. Data from an alternative disease screening system that challenges a diverse sweet corn population with a diverse set of pathogen isolates are provided to demonstrate the changes in genetic parameter estimates that result from using genomic data to provide connectivity across sparsely tested experimental treatments. An inflation in genetic variance estimates was observed when among isolate relatedness estimates were included in prediction models, which was moderated when host-by-pathogen interaction effects were incorporated into models. The complete model that included genomic similarity matrices for host, pathogen, and interaction effects indicated that the proportion of phenotypic variation in lesion size that is attributable to host, pathogen, and interaction effects was similar. Estimates of the stability of lesion size predictions for host varieties inoculated with different isolates and the stability of isolates used to inoculate different hosts were also similar. In this pathosystem, genetic parameter estimates indicate that host, pathogen, and host-by-pathogen interaction predictions may be used to identify crop varieties that are resistant to specific virulence mechanisms and to guide the deployment of these sources of resistance into pathogen populations where they will be more effective., (© 2024. The Author(s).)

Increasing planting density is a key strategy for enhancing maize yields 1-3 . An ideotype for dense planting requires a 'smart canopy' with leaf angles at different canopy layers differentially optimized to maximize light interception and photosynthesis 4-6 , among other features. Here we identified leaf angle architecture of smart canopy 1 (lac1), a natural mutant with upright upper leaves, less erect middle leaves and relatively flat lower leaves. lac1 has improved photosynthetic capacity and attenuated responses to shade under dense planting. lac1 encodes a brassinosteroid C-22 hydroxylase that predominantly regulates upper leaf angle. Phytochrome A photoreceptors accumulate in shade and interact with the transcription factor RAVL1 to promote its degradation via the 26S proteasome, thereby inhibiting activation of lac1 by RAVL1 and decreasing brassinosteroid levels. This ultimately decreases upper leaf angle in dense fields. Large-scale field trials demonstrate that lac1 boosts maize yields under high planting densities. To quickly introduce lac1 into breeding germplasm, we transformed a haploid inducer and recovered homozygous lac1 edits from 20 diverse inbred lines. The tested doubled haploids uniformly acquired smart-canopy-like plant architecture. We provide an important target and an accelerated strategy for developing high-density-tolerant cultivars, with lac1 serving as a genetic chassis for further engineering of a smart canopy in maize., (© 2024. The Author(s), under exclusive licence to Springer Nature Limited.)

Brassinosteroids (BR) and gibberellins (GA) regulate plant height and leaf angle in maize (Zea mays). Mutants with defects in BR or GA biosynthesis or signaling identify components of these pathways and enhance our knowledge about plant growth and development. In this study, we characterized three recessive mutant alleles of GRAS transcription factor 42 (gras42) in maize, a GRAS transcription factor gene orthologous to the DWARF AND LOW TILLERING (DLT) gene of rice (Oryza sativa). These maize mutants exhibited semi-dwarf stature, shorter and wider leaves, and more upright leaf angle. Transcriptome analysis revealed a role for GRAS42 as a determinant of BR signaling. Analysis of the expression consequences from loss of GRAS42 in the gras42-mu1021149 mutant indicated a weak loss of BR signaling in the mutant, consistent with its previously demonstrated role in BR signaling in rice. Loss of BR signaling was also evident by the enhancement of weak BR biosynthetic mutant alleles in double mutants of nana plant1-1 and gras42-mu1021149. The gras42-mu1021149 mutant had little effect on GA-regulated gene expression, suggesting that GRAS42 is not a regulator of core GA signaling genes in maize. Single-cell expression data identified gras42 expressed among cells in the G2/M phase of the cell cycle consistent with its previously demonstrated role in cell cycle gene expression in Arabidopsis (Arabidopsis thaliana). Cis-acting natural variation controlling GRAS42 transcript accumulation was identified by expression genome-wide association study (eGWAS) in maize. Our results demonstrate a conserved role for GRAS42/SCARECROW-LIKE 28 (SCL28)/DLT in BR signaling, clarify the role of this gene in GA signaling, and suggest mechanisms of tillering and leaf angle control by BR., Competing Interests: Conflict of interest statement. None declared., (© The Author(s) 2024. Published by Oxford University Press on behalf of American Society of Plant Biologists.)

Seed endophytic bacteria have been shown to promote the growth and development of numerous plants. However, the underlying mechanism still needs to be better understood. The present study aims to investigate the role of a seed endophytic bacterium Lysinibacillus sp. (ZM1) in promoting plant growth and shaping the root architecture of maize seedlings. The study explores how bacteria-mediated auxin biosynthesis and nitrogen metabolism affect plant growth promotion and shape the root architecture of maize seedlings. The results demonstrate that ZM1 inoculation significantly enhances root length, root biomass, and the number of seminal roots in maize seedlings. Additionally, the treated seedlings exhibit increased shoot biomass and higher levels of photosynthetic pigments. Confocal laser scanning microscopy (CLSM) analysis revealed extensive colonization of ZM1 on root hairs, as well as in the cortical and stellar regions of the root. Furthermore, LC-MS analysis demonstrated elevated auxin content in the roots of the ZM1 treated maize seedlings compared to the uninoculated control. Inoculation with ZM1 significantly increased the levels of endogenous ammonium content, GS, and GOGAT enzyme activities in the roots of treated maize seedlings compared to the control, indicating enhanced nitrogen metabolism. Furthermore, inoculation of bacteria under nitrogen-deficient conditions enhanced plant growth, as evidenced by increased root shoot length, fresh and dry weights, average number of seminal roots, and content of photosynthetic pigments. Transcript analysis indicated upregulation of auxin biosynthetic genes, along with genes involved in nitrogen metabolism at different time points in roots of ZM1-treated maize seedlings. Collectively, our findings highlight the positive impact of Lysinibacillus sp. ZM1 inoculation on maize seeds by improving root architecture through modulation of auxin biosynthesis and affecting various nitrogen metabolism related parameters. These findings provide valuable insights into the potential utilization of seed endophytic bacteria as biofertilizers to enhance plant growth and yield in nutrient deficient soils., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2024 Elsevier Masson SAS. All rights reserved.)

Southern leaf blight (SLB) is a foliar disease caused by the fungus Cochliobolus heterostrophus infecting maize plants in humid, warm weather conditions. SLB causes production losses to corn producers in different regions of the world such as Latin America, Europe, India, and Africa. In this paper, we demonstrate a non-destructive method to quantify the signs of fungal infection in SLB-infected corn plants using a deep UV (DUV) fluorescence spectrometer, with a 248.6 nm excitation wavelength, to acquire the emission spectra of healthy and SLB-infected corn leaves. Fluorescence emission spectra of healthy and diseased leaves were used to train an Autoencoder (AE) anomaly detection algorithm-an unsupervised machine learning model-to quantify the phenotype associated with SLB-infected leaves. For all samples, the signature of corn leaves consisted of two prominent peaks around 450 nm and 325 nm. However, SLB-infected leaves showed a higher response at 325 nm compared to healthy leaves, which was correlated to the presence of C. heterostrophus based on disease severity ratings from Visual Scores (VS). Specifically, we observed a linear inverse relationship between the AE error and the VS (R2 = 0.94 and RMSE = 0.935). With improved hardware, this method may enable improved quantification of SLB infection versus visual scoring based on e.g., fungal spore concentration per unit area and spatial localization., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Banah et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

The Goss's wilt and leaf blight is a disease of maize ( Zea mays ) caused by Clavibacter nebraskensis , which was widespread in the last several years throughout the Midwest in the United States, south in Texas, and north to Canada. The bacterium is included within the high-risk list of quarantine pathogens by many plant protection organizations and countries including Mexico. Severe blight symptoms on maize plants were found in different provinces from Coahuila and Tlaxcala, Mexico, in 2012 and 2021, respectively. Twenty bacterial isolates with morphology similar to C. nebraskensis were obtained from the diseased maize leaves. The isolates were confirmed by phenotypic tests and 16S rRNA and gyrB sequencing. Two strains were tested for pathogenicity tests on seven hybrid sweet corn cultivars available in Mexico, and the most sensitive cultivar was tested for all the strains to fulfill Koch's postulates. The phylogenetic reconstruction based on two single loci reveals a remarkable clustering of Mexican strains to American strains reported approximately 50 years ago. The presence of this pathogen represents a risk and a significant challenge for plant protection strategies in Mexico and maize diversity., Competing Interests: The author(s) declare no conflict of interest.

Gray leaf spot (GLS), caused by the fungal pathogens Cercospora zeae-maydis and Cercospora zeina, is a major foliar disease of maize worldwide (Zea mays L.). Here we demonstrate that ZmWAKL encoding cell-wall-associated receptor kinase-like protein is the causative gene at the major quantitative disease resistance locus against GLS. The ZmWAKL Y protein, encoded by the resistance allele, can self-associate and interact with a leucine-rich repeat immune-related kinase ZmWIK on the plasma membrane. The ZmWAKL Y /ZmWIK receptor complex interacts with and phosphorylates the receptor-like cytoplasmic kinase (RLCK) ZmBLK1, which in turn phosphorylates its downstream NADPH oxidase ZmRBOH4. Upon pathogen infection, ZmWAKL Y phosphorylation activity is transiently increased, initiating immune signaling from ZmWAKL Y , ZmWIK, ZmBLK1 to ZmRBOH4, ultimately triggering a reactive oxygen species burst. Our study thus uncovers the role of the maize ZmWAKL-ZmWIK-ZmBLK1-ZmRBOH4 receptor/signaling/executor module in perceiving the pathogen invasion, transducing immune signals, activating defense responses and conferring increased resistance to GLS., (© 2024. The Author(s).)

Importance: Synthetic communities (SynComs) are an invaluable tool to characterize and model plant-microbe interactions. Multimember SynComs approximate intricate real-world interactions between plants and their microbiome, but the complexity and time required for their construction increase enormously for each additional member added to the SynCom. Therefore, researchers who study a diversity of microbiomes using SynComs are looking for ways to simplify the use of SynComs. In this manuscript, we evaluate the feasibility of creating ready-to-use freezer stocks of a well-studied seven-member SynCom for maize roots. The frozen ready-to-use SynCom stocks work according to the principle of "just add buffer and apply to sterilized seeds or seedlings" and thus can save time applied in multiple days of laborious growing and combining of multiple microorganisms. We show that ready-to-use SynCom stocks provide comparable results to those of freshly constructed SynComs and thus allow for significant time savings when working with SynComs., Competing Interests: The authors declare no conflict of interest.

Objective: To determine the K-constant for body surface area calculation from body weight in corn snakes (Pantherophis guttatus) through the use of computed tomography (CT) measurements., Animals: 12 adult corn snakes held by North Carolina State University for research purposes underwent CT between November 2022 and January 2023., Methods: Each snake had a CT scan, physical examination, and body weight measurement. CT images were uploaded into software able to perform 3-D reconstruction and measure body surface area. The species-specific K-constant was determined using nonlinear regression analysis between body surface area and (body weight in grams)2/3., Results: The mean body weight of the 12 adult corn snakes was 228 g, with a mean body surface area of 505.1 cm2. The calculated K-constant was 13.6 (P < .001). The resulting formula for body surface area in corn snakes is BSA in cm2 = 13.6 X (body weight in grams)2/3., Clinical Relevance: The body surface area formula developed for corn snakes will allow for improved dosing accuracy for medications with low therapeutic safety margins. Additional pharmacokinetic and pharmacodynamic studies are necessary to determine the safety and efficacy of individual medications.

Bacterial leaf streak (BLS) of maize is an emerging foliar disease of maize in the Americas. It is caused by the gram-negative nonvascular bacterium Xanthomonas vasicola pv. vasculorum . There are no chemical controls available for BLS, and thus, host resistance is crucial for managing X. vasicola pv. vasculorum . The objective of this study was to examine the genetic determinants of resistance to X. vasicola pv. vasculorum in maize, as well as the relationship between other defense-related traits and BLS resistance. Specifically, we examined the correlations among BLS severity, severity for three fungal diseases, flg-22 response, hypersensitive response, and auricle color. We conducted quantitative trait locus (QTL) mapping for X. vasicola pv. vasculorum resistance using the maize recombinant inbred line population Z003 (B73 × CML228). We detected three QTLs for BLS resistance. In addition to the disease resistance QTL, we detected a single QTL for auricle color. We observed significant, yet weak, correlations among BLS severity, levels of pattern-triggered immunity response and leaf flecking. These results will be useful for understanding resistance to X. vasicola pv. vasculorum and mitigating the impact of BLS on maize yields., Competing Interests: The author(s) declare no conflict of interest.

Sustainably enhancing crop production is a global necessity to meet the escalating demand for staple crops while sustainably managing their associated carbon/nitrogen inputs. Leveraging plant-associated microbiomes is a promising avenue for addressing this demand. However, studying these communities and engineering them for sustainable enhancement of crop production have remained a challenge due to limited genetic tools and methods. In this work, we detail the development of the Maize Root Microbiome ToolKit (MRMTK), a rapid Modular Cloning (MoClo) toolkit that only takes 2.5 h to generate desired constructs (5400 potential plasmids) that replicate and express heterologous genes in Enterobacter ludwigii strain AA4 ( Elu ), Pseudomonas putida strain AA7 ( Ppu ), Herbaspirillum robiniae strain AA6 ( Hro ), Stenotrophomonas maltophilia strain AA1 ( Sma ), and Brucella pituitosa strain AA2 ( Bpi ), which comprise a model maize root synthetic community (SynCom). In addition to these genetic tools, we describe a highly efficient transformation protocol (10 7 -10 9 transformants/μg of DNA) 1 for each of these strains. Utilizing this highly efficient transformation protocol, we identified endogenous Expression Sequences (ES; promoter and ribosomal binding sites) for each strain via genomic promoter trapping. Overall, MRMTK is a scalable and adaptable platform that expands the genetic engineering toolbox while providing a standardized, high-efficiency transformation method across a diverse group of root commensals. These results unlock the ability to elucidate and engineer plant-microbe interactions promoting plant growth for each of the 5 bacterial strains in this study.

In maize, the community-standard transformant line B104 is a useful model for dissecting features of transfer DNA (T-DNA) integration due to its compatibility with Agrobacterium-mediated transformation and the availability of its genome sequence. Knowledge of transgene integration sites permits the analysis of the genomic environment that governs the strength of gene expression and phenotypic effects due to the disruption of an endogenous gene or regulatory element. In this study, we optimized a fusion primer and nested integrated PCR (FPNI-PCR) technique for T-DNA detection in maize to characterize the integration sites of 89 T-DNA insertions in 81 transformant lines. T-DNA insertions preferentially occurred in gene-rich regions and regions distant from centromeres. Integration junctions with and without microhomologous sequences as well as junctions with de novo sequences were detected. Sequence analysis of integration junctions indicated that T-DNA was incorporated via the error-prone repair pathways of nonhomologous (predominantly) and microhomology-mediated (minor) end-joining. This report provides a quantitative assessment of Agrobacterium-mediated T-DNA integration in maize with respect to insertion site features, the genomic distribution of T-DNA incorporation, and the mechanisms of integration. It also demonstrates the utility of the FPNI-PCR technique, which can be adapted to any species of interest., Competing Interests: Conflicts of interest The authors declare no conflict of interest., (Published by Oxford University Press on behalf of The Genetics Society of America 2023.)

Objectives: This release note describes the Maize GxE project datasets within the Genomes to Fields (G2F) Initiative. The Maize GxE project aims to understand genotype by environment (GxE) interactions and use the information collected to improve resource allocation efficiency and increase genotype predictability and stability, particularly in scenarios of variable environmental patterns. Hybrids and inbreds are evaluated across multiple environments and phenotypic, genotypic, environmental, and metadata information are made publicly available., Data Description: The datasets include phenotypic data of the hybrids and inbreds evaluated in 30 locations across the US and one location in Germany in 2020 and 2021, soil and climatic measurements and metadata information for all environments (combination of year and location), ReadMe, and description files for each data type. A set of common hybrids is present in each environment to connect with previous evaluations. Each environment had a collaborator responsible for collecting and submitting the data, the GxE coordination team combined all the collected information and removed obvious erroneous data. Collaborators received the combined data to use, verify and declare that the data generated in their own environments was accurate. Combined data is released to the public with minimal filtering to maintain fidelity to the original data., (© 2023. BioMed Central Ltd., part of Springer Nature.)

Tropical maize can be used to diversify the genetic base of temperate germplasm and help create climate-adapted cultivars. However, tropical maize is unadapted to temperate environments, in which sensitivities to long photoperiods and cooler temperatures result in severely delayed flowering times, developmental defects, and little to no yield. Overcoming this maladaptive syndrome can require a decade of phenotypic selection in a targeted, temperate environment. To accelerate the incorporation of tropical diversity in temperate breeding pools, we tested if an additional generation of genomic selection can be used in an off-season nursery where phenotypic selection is not very effective. Prediction models were trained using flowering time recorded on random individuals in separate lineages of a heterogenous population grown at two northern U.S. latitudes. Direct phenotypic selection and genomic prediction model training was performed within each target environment and lineage, followed by genomic prediction of random intermated progenies in the off-season nursery. Performance of genomic prediction models was evaluated on self-fertilized progenies of prediction candidates grown in both target locations in the following summer season. Prediction abilities ranged from 0.30 to 0.40 among populations and evaluation environments. Prediction models with varying marker effect distributions or spatial field effects had similar accuracies. Our results suggest that genomic selection in a single off-season generation could increase genetic gains for flowering time by more than 50% compared to direct selection in summer seasons only, reducing the time required to change the population mean to an acceptably adapted flowering time by about one-third to one-half., (Published by Oxford University Press on behalf of The Genetics Society of America 2023.)

The corn planthopper, Peregrinus maidis, is a vector of several maize viruses and is consequently a significant agricultural pest in many tropical and subtropical regions. As P. maidis has developed resistance to insecticides, the aim of this study was to develop transgenic P. maidis strains that could be used for future genetic biocontrol programs. To facilitate the identification of transgenic P. maidis, we isolated and characterized the promoters for the P. maidis ubiquitin-like and profilin genes. Transient expression assays with P. maidis embryos showed that both promoters were active. Transgenic lines were established using piggyBac vectors and fluorescent protein marker genes. The lines carried an auto-regulated tetracycline transactivator (tTA) gene, which has been widely used to establish conditional lethal strains in other insect species. The transgenic lines showed low levels of tTA expression but were viable on diet with or without doxycycline, which inhibits the binding of tTA to DNA. We discuss possible modifications to the tTA overexpression system that could lead to the successful development of conditional lethal strains. To our knowledge, this is the first report of a transgenic Hemiptera. The approach we have taken could potentially be applied to other Hemiptera and, for P. maidis, the technology will facilitate future functional genomics studies., (© 2023 The Authors. Insect Molecular Biology published by John Wiley & Sons Ltd on behalf of Royal Entomological Society.)

Objectives: The Genomes to Fields (G2F) 2022 Maize Genotype by Environment (GxE) Prediction Competition aimed to develop models for predicting grain yield for the 2022 Maize GxE project field trials, leveraging the datasets previously generated by this project and other publicly available data., Data Description: This resource used data from the Maize GxE project within the G2F Initiative [1]. The dataset included phenotypic and genotypic data of the hybrids evaluated in 45 locations from 2014 to 2022. Also, soil, weather, environmental covariates data and metadata information for all environments (combination of year and location). Competitors also had access to ReadMe files which described all the files provided. The Maize GxE is a collaborative project and all the data generated becomes publicly available [2]. The dataset used in the 2022 Prediction Competition was curated and lightly filtered for quality and to ensure naming uniformity across years., (© 2023. The Author(s).)

Recent reverse genetics technologies have enabled genetic manipulation of plant negative-strand RNA virus (NSR) genomes. Here, we report construction of an infectious clone for the maize-infecting Alphanucleorhabdovirus maydis, the first efficient NSR vector for maize. The full-length infectious clone was established using agrobacterium-mediated delivery of full-length maize mosaic virus (MMV) antigenomic RNA and the viral core proteins (nucleoprotein N, phosphoprotein P, and RNA-directed RNA polymerase L) required for viral transcription and replication into Nicotiana benthamiana. Insertion of intron 2 ST-LS1 into the viral L gene increased stability of the infectious clone in Escherichia coli and Agrobacterium tumefaciens. To monitor virus infection in vivo, a green fluorescent protein (GFP) gene was inserted in between the N and P gene junctions to generate recombinant MMV-GFP. Complementary DNA (cDNA) clones of MMV-wild type (WT) and MMV-GFP replicated in single cells of agroinfiltrated N. benthamiana. Uniform systemic infection and high GFP expression were observed in maize inoculated with extracts of the infiltrated N. benthamiana leaves. Insect vectors supported virus infection when inoculated via feeding on infected maize or microinjection. Both MMV-WT and MMV-GFP were efficiently transmitted to maize by planthopper vectors. The GFP reporter gene was stable in the virus genome and expression remained high over three cycles of transmission in plants and insects. The MMV infectious clone will be a versatile tool for expression of proteins of interest in maize and cross-kingdom studies of virus replication in plant and insect hosts., (© 2022 The Authors. Molecular Plant Pathology published by British Society for Plant Pathology and John Wiley & Sons Ltd.)

Objectives: This report provides information about the public release of the 2018-2019 Maize G X E project of the Genomes to Fields (G2F) Initiative datasets. G2F is an umbrella initiative that evaluates maize hybrids and inbred lines across multiple environments and makes available phenotypic, genotypic, environmental, and metadata information. The initiative understands the necessity to characterize and deploy public sources of genetic diversity to face the challenges for more sustainable agriculture in the context of variable environmental conditions., Data Description: Datasets include phenotypic, climatic, and soil measurements, metadata information, and inbred genotypic information for each combination of location and year. Collaborators in the G2F initiative collected data for each location and year; members of the group responsible for coordination and data processing combined all the collected information and removed obvious erroneous data. The collaborators received the data before the DOI release to verify and declare that the data generated in their own locations was accurate. ReadMe and description files are available for each dataset. Previous years of evaluation are already publicly available, with common hybrids present to connect across all locations and years evaluated since this project's inception., (© 2023. The Author(s).)

Southern leaf blight (SLB), caused by the necrotrophic fungal pathogen Cochliobolus heterostrophus (anamorph Bipolaris maydis), is a major foliar disease which causes significant yield losses in maize worldwide. A major quantitative trait locus, qSLB 3.04 , conferring recessive resistance to SLB was previously mapped on maize chromosome 3. Using a combination of map-based cloning, association analysis, ethyl methanesulfonate and transposon mutagenesis, and CRISPR-Cas9 editing, we demonstrate that a leucine-rich repeat receptor-like kinase gene which we have called ChSK1 (Cochliobolus heterostrophus Susceptibility Kinase 1) at qSLB 3.04 causes increased susceptibility to SLB. Genes of this type have generally been associated with the defense response. We present evidence that ChSK1 may be associated with suppression of the basal immune response. These findings contribute to our understanding of plant disease susceptibility genes and the potential to use them for engineering durable disease resistance., (© 2023 The Authors New Phytologist published by John Wiley & Sons Ltd on behalf of New Phytologist Foundation This article has been contributed to by U.S. Government employees and their work is in the public domain in the USA.)

Crop genetic diversity for climate adaptations is globally partitioned. We performed experimental evolution in maize to understand the response to selection and how plant germplasm can be moved across geographical zones. Initialized with a common population of tropical origin, artificial selection on flowering time was performed for two generations at eight field sites spanning 25° latitude, a 2800 km transect. We then jointly tested all selection lineages across the original sites of selection, for the target trait and 23 other traits. Modeling intergenerational shifts in a physiological reaction norm revealed separate components for flowering-time plasticity. Generalized and local modes of selection altered the plasticity of each lineage, leading to a latitudinal pattern in the responses to selection that were strongly driven by photoperiod. This transformation led to widespread changes in developmental, architectural, and yield traits, expressed collectively in an environment-dependent manner. Furthermore, selection for flowering time alone alleviated a maladaptive syndrome and improved yields for tropical maize in the temperate zone. Our findings show how phenotypic selection can rapidly shift the flowering phenology and plasticity of maize. They also demonstrate that selecting crops to local conditions can accelerate adaptation to climate change., (© 2023 The Authors. New Phytologist © 2023 New Phytologist Foundation.)

Free coelomic fluid can be a physiologic or pathologic finding in snakes. In this study, ultrasonography was used to assess the presence, volume, and type of coelomic fluid in 18 (16 females, 2 males) clinically healthy corn snakes ( Pantherophis guttatus ) using a semiquantitative scoring system. Each snake was divided into five equal regions (R1-R5) by length (from rostrum to vent) and fluid volume was scored on a scale of 0 to 4. Coelomic fluid was sampled when possible and cytologic analysis was performed. The majority of snakes (16/18) were found to have some degree of free coelomic fluid. The coelomic fluid samples that were collected ( n = 6) were classified as transudates, acellular or primarily lymphocytic. Fluid was most likely to be found in R3 compared with all other regions and least likely to be found in R1 compared with R2, R3, and R4. A higher score of volume was found in R3 compared with R1 and R5. This study describes the distribution and abundance of coelomic fluid in snakes, as well as a method for point of care ultrasound (POCUS) in this species.

Grass inflorescences support floral structures that each bear a single grain, where variation in branch architecture directly impacts yield. The maize (Zea mays) RAMOSA1 (ZmRA1) transcription factor acts as a key regulator of inflorescence development by imposing branch meristem determinacy. Here, we show RA1 transcripts accumulate in boundary domains adjacent to spikelet meristems in sorghum (Sorghum bicolor, Sb) and green millet (Setaria viridis, Sv) inflorescences similar as in the developing maize tassel and ear. To evaluate the functional conservation of syntenic RA1 orthologs and promoter cis sequences in maize, sorghum, and setaria, we utilized interspecies gene transfer and assayed genetic complementation in a common inbred background by quantifying recovery of normal branching in highly ramified ra1-R mutants. A ZmRA1 transgene that includes endogenous upstream and downstream flanking sequences recovered normal tassel and ear branching in ra1-R. Interspecies expression of two transgene variants of the SbRA1 locus, modeled as the entire endogenous tandem duplication or just the nonframeshifted downstream copy, complemented ra1-R branching defects and induced unusual fasciation and branch patterns. The SvRA1 locus lacks conserved, upstream noncoding cis sequences found in maize and sorghum; interspecies expression of a SvRA1 transgene did not or only partially recovered normal inflorescence forms. Driving expression of the SvRA1 coding region by the ZmRA1 upstream region, however, recovered normal inflorescence morphology in ra1-R. These data leveraging interspecies gene transfer suggest that cis-encoded temporal regulation of RA1 expression is a key factor in modulating branch meristem determinacy that ultimately impacts grass inflorescence architecture., Competing Interests: Conflict of interest statement. None declared., (© American Society of Plant Biologists 2022. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

Two experiments were conducted to test the hypothesis that corn kernel hardness and drying temperature influence the ileal digestibility of starch and amino acids (AA), as well as apparent total tract digestibility (ATTD) of gross energy (GE) and total dietary fiber (TDF) in diets for growing pigs. Two corn varieties with average or hard endosperm were grown and harvested under similar conditions, and after harvest, each variety was divided into 2 batches that were dried at 35 and 120 °C, respectively. Therefore, four batches of corn were used. In experiment 1, 10 pigs (67.00 ± 2.98 kg) with a T-cannula installed in the distal ileum were allotted to a replicated 5 × 5 Latin square design with 5 diets and 5 periods giving 10 replicates per diet. A nitrogen-free diet and four diets containing each source of corn as the only AA source were formulated. Results indicated that neither variety of corn nor drying temperature influenced apparent ileal digestibility of starch in the grain. The standardized ileal digestibility of most AA was less (P < 0.05) in corn dried at 120 °C compared with corn dried at 35 °C resulting in concentrations of most standardized ileal digestible AA being less (P < 0.05) in corn dried at 120 °C than in corn dried at 35 °C. In experiment 2, 40 pigs (20.82 ± 1.74 kg) were housed in metabolism crates and allotted to 4 diets with 10 replicate pigs per diet. The four corn-based diets used in experiment 1 were also used in experiment 2. Feces and urine were collected using the marker-to-marker approach with 5-d adaptation and 4-d collection periods. Results indicated that diets containing hard endosperm corn had greater (P < 0.05) ATTD of TDF than diets containing average endosperm corn. The ATTD of GE in hard endosperm corn was also greater (P < 0.05), and concentrations of digestible energy and metabolizable energy in hard endosperm corn were greater (P < 0.01) than in average endosperm corn. Diets containing corn dried at 120 °C had greater (P < 0.05) ATTD of TDF compared with diets containing corn dried at 35 °C; however, drying temperature did not influence the ATTD of GE. In conclusion, endosperm hardness did not influence the digestibility of AA and starch; however, drying corn at 120 °C reduced digestible AA concentrations. Hard endosperm corn had greater ATTD of GE and TDF, but drying temperature did not influence energy digestibility., (© The Author(s) 2023. Published by Oxford University Press on behalf of the American Society of Animal Science. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.)

Plant metabolites are the basis of human nutrition and have biological relevance in ecology. Farmers selected plants with favorable characteristics since prehistoric times and improved the cultivars, but without knowledge of underlying mechanisms. Understanding the genetic basis of metabolite production can facilitate the successful breeding of plants with augmented nutritional value. To identify genetic factors related to the metabolic composition in maize, we generated mass profiles of 198 recombinant inbred lines (RILs) and their parents (B73 and Mo17) using direct-injection electrospray ionization mass spectrometry (DLI-ESI MS). Mass profiling allowed the correct clustering of samples according to genotype. We quantified 71 mass features from grains and 236 mass features from leaf extracts. For the corresponding ions, we identified tissue-specific metabolic 'Quantitative Trait Loci' (mQTLs) distributed across the maize genome. These genetic regions could regulate multiple metabolite biosynthesis pathways. Our findings demonstrate that DLI-ESI MS has sufficient analytical resolution to map mQTLs. These identified genetic loci will be helpful in metabolite-focused maize breeding. Mass profiling is a powerful tool for detecting mQTLs in maize and enables the high-throughput screening of loci responsible for metabolite biosynthesis., Competing Interests: Declaration of Competing Interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2022 Elsevier B.V. All rights reserved.)

Maize is a staple food of smallholder farmers living in highland regions up to 4,000 m above sea level worldwide. Mexican and South American highlands are two major highland maize growing regions, and population genetic data suggest the maize's adaptation to these regions occurred largely independently, providing a case study for convergent evolution. To better understand the mechanistic basis of highland adaptation, we crossed maize landraces from 108 highland and lowland sites of Mexico and South America with the inbred line B73 to produce F1 hybrids and grew them in both highland and lowland sites in Mexico. We identified thousands of genes with divergent expression between highland and lowland populations. Hundreds of these genes show patterns of convergent evolution between Mexico and South America. To dissect the genetic architecture of the divergent gene expression, we developed a novel allele-specific expression analysis pipeline to detect genes with divergent functional cis-regulatory variation between highland and lowland populations. We identified hundreds of genes with divergent cis-regulation between highland and lowland landrace alleles, with 20 in common between regions, further suggesting convergence in the genes underlying highland adaptation. Further analyses suggest multiple mechanisms contribute to this convergence in gene regulation. Although the vast majority of evolutionary changes associated with highland adaptation were region specific, our findings highlight an important role for convergence at the gene expression and gene regulation levels as well., (© The Author(s) 2022. Published by Oxford University Press on behalf of Society for Molecular Biology and Evolution.)

Maize is a globally valuable commodity and one of the most extensively studied genetic model organisms. However, we know surprisingly little about the extent and potential utility of the genetic variation found in wild relatives of maize. Here, we characterize a high-density genomic variation map from 744 genomes encompassing maize and all wild taxa of the genus Zea, identifying over 70 million single-nucleotide polymorphisms. The variation map reveals evidence of selection within taxa displaying novel adaptations. We focus on adaptive alleles in highland teosinte and temperate maize, highlighting the key role of flowering-time-related pathways in their adaptation. To show the utility of variants in these data, we generate mutant alleles for two flowering-time candidate genes. This work provides an extensive sampling of the genetic diversity of Zea, resolving questions on evolution and identifying adaptive variants for direct use in modern breeding., (© 2022. The Author(s), under exclusive licence to Springer Nature America, Inc.)

Eukaryotic Macrotransposons (MTns) can be formed by 2 nearby elements flanking a segment of host DNA. The maize Ac transposon can form Ac::MTns, but little is known about Ac::MTn transposition activities. Here, we studied 3 Ac::MTns at the maize p1 locus, each of which is composed of a segment of maize p1 genomic DNA (up to 15 kb) bounded by a fractured Ac element (fAc, 2039 bp), and a full-length Ac element in direct orientation. The resulting Ac::MTns are of 16, 16.5, and 22 kb total length. From these 3 Ac::MTns, we identified 10 independent cases of macrotransposition, and observed similar features of transposition between Ac::MTn and standard Ac/Ds, including characteristic excision footprints and insertion target site duplications. Nine out of the 10 Ac::MTn reinsertion targets were genetically linked to the donor sites, another similarity with Ac/Ds standard transposition. We also identified a MTn-like structure in the maize B73 reference genome and 5 NAM founder lines. The MTn in diverse lines is flanked by target site duplications, confirming the historic occurrence of MTn transposition during genome evolution. Our results show that Ac::MTns are capable of mobilizing segments of DNA long enough to include a typical full-length plant gene and in theory could erode gene colinearity in syntenic regions during plant genome evolution., (© The Author(s) 2022. Published by Oxford University Press on behalf of Genetics Society of America. All rights reserved. For permissions, please email: journals.permissions@oup.com.)

Native Americans domesticated maize ( Zea mays ssp. mays ) from lowland teosinte parviglumis ( Zea mays ssp. parviglumis) in the warm Mexican southwest and brought it to the highlands of Mexico and South America where it was exposed to lower temperatures that imposed strong selection on flowering time. Phospholipids are important metabolites in plant responses to low-temperature and phosphorus availability and have been suggested to influence flowering time. Here, we combined linkage mapping with genome scans to identify High PhosphatidylCholine 1 ( HPC1 ), a gene that encodes a phospholipase A1 enzyme, as a major driver of phospholipid variation in highland maize. Common garden experiments demonstrated strong genotype-by-environment interactions associated with variation at HPC1, with the highland HPC1 allele leading to higher fitness in highlands, possibly by hastening flowering. The highland maize HPC1 variant resulted in impaired function of the encoded protein due to a polymorphism in a highly conserved sequence. A meta-analysis across HPC1 orthologs indicated a strong association between the identity of the amino acid at this position and optimal growth in prokaryotes. Mutagenesis of HPC1 via genome editing validated its role in regulating phospholipid metabolism. Finally, we showed that the highland HPC1 allele entered cultivated maize by introgression from the wild highland teosinte Zea mays ssp. mexicana and has been maintained in maize breeding lines from the Northern United States, Canada, and Europe. Thus, HPC1 introgressed from teosinte mexicana underlies a large metabolic QTL that modulates phosphatidylcholine levels and has an adaptive effect at least in part via induction of early flowering time.

Background: Characterizing Helicoverpa zea (Boddie) damage to maize (Zea mays L.) in relation to the spatiotemporal composition of Bt crops is essential to understand how landscape composition affects H. zea abundance. To examine this relationship, paired Bt (expressing Cry1A.105 + Cry2Ab2) and non-Bt maize plots were sampled across North and South Carolina during 2017-2019. Kernel damage and larval exit holes were measured following larval development. To understand how maize abundance surrounding sample sites related to feeding damage and larval development, we quantified maize abundance in a 1 km buffer surrounding the sample site and examined the relationship between local maize abundance and kernel damage and larval exit holes., Results: Across the years and locations, damage in Bt maize was widespread but significantly lower than in non-Bt maize, indicating that despite the widespread occurrence of resistance to Cry toxins in maize, Bt maize still provides a measurable reduction in damage. There were negative relationships between kernel injury and ears with larval exit holes in both Bt and non-Bt maize and the proportion of maize in the landscape during the current year., Conclusion: Despite the widespread occurrence of resistance to Cry toxins in maize, this resistance is incomplete, and on average Bt maize continues to provide a measurable reduction in damage. We interpret the negative relationship between abundance of maize within 1 km of the sample location and maize infestation levels, as measured by kernel damage and larval exit holes, to reflect dispersion of the ovipositing moth population over available maize within the local landscape. © 2022 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry., (© 2022 The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.)

SignificanceProteins are the machinery which execute essential cellular functions. However, measuring their abundance within an organism can be difficult and resource-intensive. Cells use a variety of mechanisms to control protein synthesis from mRNA, including short open reading frames (uORFs) that lie upstream of the main coding sequence. Ribosomes can preferentially translate uORFs instead of the main coding sequence, leading to reduced translation of the main protein. In this study, we show that uORF sequence variation between individuals can lead to different rates of protein translation and thus variable protein abundances. We also demonstrate that natural variation in uORFs occurs frequently and can be linked to whole-plant phenotypes, indicating that uORF sequence variation likely contributes to plant adaptation.

Generations of farmer selection in the central Mexican highlands have produced unique maize varieties adapted to the challenges of the local environment. In addition to possessing great agronomic and cultural value, Mexican highland maize represents a good system for the study of local adaptation and acquisition of adaptive phenotypes under cultivation. In this study, we characterize a recombinant inbred line population derived from the B73 reference line and the Mexican highland maize variety Palomero Toluqueño. B73 and Palomero Toluqueño showed classic rank-changing differences in performance between lowland and highland field sites, indicative of local adaptation. Quantitative trait mapping identified genomic regions linked to effects on yield components that were conditionally expressed depending on the environment. For the principal genomic regions associated with ear weight and total kernel number, the Palomero Toluqueño allele conferred an advantage specifically in the highland site, consistent with local adaptation. We identified Palomero Toluqueño alleles associated with expression of characteristic highland traits, including reduced tassel branching, increased sheath pigmentation and the presence of sheath macrohairs. The oligogenic architecture of these three morphological traits supports their role in adaptation, suggesting they have arisen from consistent directional selection acting at distinct points across the genome. We discuss these results in the context of the origin of phenotypic novelty during selection, commenting on the role of de novo mutation and the acquisition of adaptive variation by gene flow from endemic wild relatives., (© The Author(s) 2022. Published by Oxford University Press on behalf of Genetics Society of America.)

Technology advances have made possible the collection of a wealth of genomic, environmental, and phenotypic data for use in plant breeding. Incorporation of environmental data into environment-specific genomic prediction is hindered in part because of inherently high data dimensionality. Computationally efficient approaches to combining genomic and environmental information may facilitate extension of genomic prediction models to new environments and germplasm, and better understanding of genotype-by-environment (G × E) interactions. Using genomic, yield trial, and environmental data on 1,918 unique hybrids evaluated in 59 environments from the maize Genomes to Fields project, we determined that a set of 10,153 SNP dominance coefficients and a 5-day temporal window size for summarizing environmental variables were optimal for genomic prediction using only genetic and environmental main effects. Adding marker-by-environment variable interactions required dimension reduction, and we found that reducing dimensionality of the genetic data while keeping the full set of environmental covariates was best for environment-specific genomic prediction of grain yield, leading to an increase in prediction ability of 2.7% to achieve a prediction ability of 80% across environments when data were masked at random. We then measured how prediction ability within environments was affected under stratified training-testing sets to approximate scenarios commonly encountered by plant breeders, finding that incorporation of marker-by-environment effects improved prediction ability in cases where training and test sets shared environments, but did not improve prediction in new untested environments. The environmental similarity between training and testing sets had a greater impact on the efficacy of prediction than genetic similarity between training and test sets., (Published by Oxford University Press on behalf of Genetics Society of America 2021. This work is written by US Government employees and is in the public domain in the US.)

The plant shoot apex houses the shoot apical meristem, a highly organized and active stem-cell tissue where molecular signaling in discrete cells determines when and where leaves are initiated. We optimized a spatial transcriptomics approach, in situ sequencing (ISS), to colocalize the transcripts of 90 genes simultaneously on the same section of tissue from the maize (Zea mays) shoot apex. The RNA ISS technology reported expression profiles that were highly comparable with those obtained by in situ hybridizations (ISHs) and allowed the discrimination between tissue domains. Furthermore, the application of spatial transcriptomics to the shoot apex, which inherently comprised phytomers that are in gradual developmental stages, provided a spatiotemporal sequence of transcriptional events. We illustrate the power of the technology through PLASTOCHRON1 (PLA1), which was specifically expressed at the boundary between indeterminate and determinate cells and partially overlapped with ROUGH SHEATH1 and OUTER CELL LAYER4 transcripts. Also, in the inflorescence, PLA1 transcripts localized in cells subtending the lateral primordia or bordering the newly established meristematic region, suggesting a more general role of PLA1 in signaling between indeterminate and determinate cells during the formation of lateral organs. Spatial transcriptomics builds on RNA ISH, which assays relatively few transcripts at a time and provides a powerful complement to single-cell transcriptomics that inherently removes cells from their native spatial context. Further improvements in resolution and sensitivity will greatly advance research in plant developmental biology., (© American Society of Plant Biologists 2021. All rights reserved. For permissions, please email: journals.permissions@oup.com.)

Inbreeding depression is the reduction in fitness and vigor resulting from mating of close relatives observed in many plant and animal species. The extent to which the genetic load of mutations contributing to inbreeding depression is due to large-effect mutations versus variants with very small individual effects is unknown and may be affected by population history. We compared the effects of outcrossing and self-fertilization on 18 traits in a landrace population of maize, which underwent a population bottleneck during domestication, and a neighboring population of its wild relative teosinte. Inbreeding depression was greater in maize than teosinte for 15 of 18 traits, congruent with the greater segregating genetic load in the maize population that we predicted from sequence data. Parental breeding values were highly consistent between outcross and selfed offspring, indicating that additive effects determine most of the genetic value even in the presence of strong inbreeding depression. We developed a novel linkage scan to identify quantitative trait loci (QTL) representing large-effect rare variants carried by only a single parent, which were more important in teosinte than maize. Teosinte also carried more putative juvenile-acting lethal variants identified by segregation distortion. These results suggest a mixture of mostly polygenic, small-effect partially recessive effects in linkage disequilibrium underlying inbreeding depression, with an additional contribution from rare larger-effect variants that was more important in teosinte but depleted in maize following the domestication bottleneck. Purging associated with the maize domestication bottleneck may have selected against some large effect variants, but polygenic load is harder to purge and overall segregating mutational burden increased in maize compared to teosinte., Competing Interests: The authors have declared that no competing interests exist.

People living in the Balsas River basin in southwest México domesticated maize from the bushy grass teosinte. Nine thousand years later, in 2021, Ms. Deb Haaland - a member of the Pueblo of Laguna tribe of New Mexico - wore a dress adorned with a cornstalk when she was sworn in as the Secretary of Interior of the United States of America. This choice of garment highlights the importance of the coevolution of maize and the farmers who, through careful selection over thousands of years, domesticated maize and adapted the physiology and shoot architecture of maize to fit local environments and growth habits. Some traits such as tillering were directly selected on (arches), and others such as tassel size are the by-products (spandrels) of maize evolution. Here, we review current knowledge of the underlying cellular, developmental, physiological, and metabolic processes that were selected by farmers and breeders, which have positioned maize as a top global staple crop., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2021 Elsevier Ltd. All rights reserved.)

Background: Different thermoplastic starch (TPS) films were prepared with or without the addition of microcrystalline cellulose (MCC) obtained via the melt-extrusion method, and then the hot-press method was used to produce environmentally friendly TPS-based film/paper composites to replace petroleum-based materials., Results: The paper-plastic composites exhibited good interfacial adhesion from the scannign elctron microscopy images. It was seen that 5 wt.% MCC was added to reinforce the mechanical properties of TPS films, such that it also improved the barrier properties of MCC@TPS/paper composites and extended the path of water vapor through TPS films, which decreased the water vapor transmission rate of MCC@TPS/paper composites. TPS/paper composites and MCC@TPS/paper composites have better physical properties (i.e. smoothness, flexibility and folding resistance) than only paper. In particular, it was found that the water contact angle of MCC@TPS/paper composites and TPS/paper composites were higher than single-layer paper. Furthermore, MCC reinforced paper-plastic composites demonstrated good barrier properties which can meet the requirement of the need for lower water sensitive materials in the food packaging industry., Conclusion: Thermoplastic corn starch-based film/paper composites have good application properties as a potential source of bioplastic materials. © 2021 Society of Chemical Industry., (© 2021 Society of Chemical Industry.)

Most turkey research has been conducted with a regular corn particle size set through phase-feeding programs. This study's first objective was to determine the effect of increasing corn particle size through the feed phases on performance, processing yield, and feed milling energy usage in Large White commercial male turkey production. Zinc (Zn) and manganese (Mn) are essential microminerals for animals' healthy growth. The source in which these elements are supplied to the bird will determine their bioavailability, effect on bird growth, and subsequent environmental impact. This study's second objective was to measure both inorganic and chelated Zn and Mn sources on turkey performance, turkey carcass processing yields, and subsequent litter residues. Twelve hundred Nicolas Select male poults were randomly assigned to 48 concrete; litter-covered floor pens. The experimental design was a completely randomized block design with a 2 × 2 factorial arrangement of 2 sources of minerals (organic blend vs. inorganic) formulated to match breeder recommendations and 2 types of corn mean particle size (coarse corn [1,000-3,500 µm] vs. fine corn [276 µm]). The ASABE S319.4 standard was used to measure corn mean particle size. Bird performance, carcass processing yield, litter content of Zn and Mn, and pellet mill energy consumption were analyzed in SAS 9.4 in a mixed model. There was a reduction of pellet mill energy usage of 36% when coarse corn was added post-pelleting. Birds fed increasing coarse corn mean particle size were 250 g lighter on average in body weight (BW) than birds fed a constant control mean particle size. No difference was found in feed intake (FI) or feed conversion ratio (FCR). Birds fed methionine chelated Zn and Mn blended with inorganic mineral sources were 250 g heavier on average than birds fed only an inorganic source of minerals. In addition, feeding an organic blend of Zn and Mn resulted in greater breast meat yield. Litter from birds fed the control corn mean particle size, and inorganic minerals had a higher concentration of Zn in the litter but were not different when the chelated Zn/Mn were fed. In conclusion, increasing the corn mean particle size and adding it post pellet could save money during feed milling; however, birds might have a slightly lower BW. A combination of inorganic and chelated Zn and Mn may improve performance and increase total breast meat yields., (Copyright © 2021 The Authors. Published by Elsevier Inc. All rights reserved.)

Very little is known about how domestication was constrained by the quantitative genetic architecture of crop progenitors and how quantitative genetic architecture was altered by domestication. Yang et al. [C. J. Yang et al. , Proc. Natl. Acad. Sci. U.S.A. 116, 5643-5652 (2019)] drew multiple conclusions about how genetic architecture influenced and was altered by maize domestication based on one sympatric pair of teosinte and maize populations. To test the generality of their conclusions, we assayed the structure of genetic variances, genetic correlations among traits, strength of selection during domestication, and diversity in genetic architecture within teosinte and maize. Our results confirm that additive genetic variance is decreased, while dominance genetic variance is increased, during maize domestication. The genetic correlations are moderately conserved among traits between teosinte and maize, while the genetic variance-covariance matrices ( G -matrices) of teosinte and maize are quite different, primarily due to changes in the submatrix for reproductive traits. The inferred long-term selection intensities during domestication were weak, and the neutral hypothesis was rejected for reproductive and environmental response traits, suggesting that they were targets of selection during domestication. The G -matrix of teosinte imposed considerable constraint on selection during the early domestication process, and constraint increased further along the domestication trajectory. Finally, we assayed variation among populations and observed that genetic architecture is generally conserved among populations within teosinte and maize but is radically different between teosinte and maize. While selection drove changes in essentially all traits between teosinte and maize, selection explains little of the difference in domestication traits among populations within teosinte or maize., Competing Interests: The authors declare no competing interest., (Copyright © 2021 the Author(s). Published by PNAS.)

Drying temperature (DT) of corn can influence its nutritional quality, but whether this is influenced by endosperm hardness is not clear. Two parallel experiments were conducted to investigate the effects of 2 yellow dent corn hybrids with average and hard kernel hardness, dried at 3 temperatures (35, 80, and 120°C), and 2 supplementation levels of an exogenous amylase (0, 133 g/ton of feed) on live performance, starch and protein digestibility, and energy utilization of Ross 708 male broilers. Twelve dietary treatments consisting of a 2 × 3 × 2 factorial arrangement were evaluated using 3-way ANOVA in a randomized complete block design. In Experiment 1, a total of 1,920 male-chicks were randomly allocated to 96 floor pens, whereas 480 day-old chicks were distributed among 96 cages for Experiment 2. At 40 d, interaction effects (P < 0.05) were detected on BWG, FCR, and flock uniformity. Supplementation with exogenous amylase resulted in heavier broilers, better FCR and flock uniformity, only in the diets based on corn dried at 35°C. Additionally, interaction effects were observed on FCR due to kernel hardness and DT (P < 0.01), kernel hardness and amylase supplementation (P < 0.001), and DT and amylase supplementation (P < 0.05). Exogenous amylase addition to the diets based on corn with an average hardness improved FCR up to 2 points (1.49 vs. 1.51 g:g) whereas there was no effect of amylase on FCR of broilers fed diets based on corn with hard endosperm. Total tract retention of starch was increased (P < 0.05) in broilers fed diets based on corn with average kernel hardness compared to hard kernel. Corn dried at 80 and 120°C had up to 1.21% points less starch total tract retention than the one dried at 35°C. Supplementing alpha-amylase resulted in beneficial effects for broiler live performance, energy utilization, and starch total tract digestibility results. Treatment effects on starch characteristics were explored. Corn endosperm hardness, DT and exogenous amylase can influence the live performance of broilers. However, these factors are not independent and so must be manipulated strategically to improve broiler performance., (Copyright © 2021 The Authors. Published by Elsevier Inc. All rights reserved.)

Leaves are a significant component of the shoot system in grasses, functioning in light capture and photosynthesis. Leaf width, length, and angle are expressions of development that collectively define canopy architecture. Thus, the distinctive morphology of grass leaves is an interdependent readout of developmental patterning and growth along the proximal-distal, medial-lateral, and adaxial-abaxial axes. Here, we review the chronology of patterning and growth, namely along the proximal-distal axis, during maize leaf development. We underscore that patterning and growth occur simultaneously, making use of shared developmental gradients and molecular pathways., Competing Interests: Declaration of competing interest The authors declare that they have no known competing financial interests or personal relationships that could have appeared to influence the work reported in this paper., (Copyright © 2021 Elsevier Ltd. All rights reserved.)