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Abstract ObjectivesThe University of Arizona Field Scanner (FS) is capable of generating massive amounts of data from a variety of instruments at high spatial and temporal resolution. The accompanying field infrastructure beneath the system offers capacity for controlled irrigation regimes in a hot, arid environment. Approximately 194 terabytes of raw and processed phenotypic image data were generated over two growing seasons (2020 and 2022) on a population of 434 sequence-indexed, EMS-mutagenized sorghum lines in the genetic background BTx623; the population was grown under well-watered and water-limited conditions. Collectively, these data enable links between genotype and dynamic, drought-responsive phenotypes, which can accelerate crop improvement efforts. However, analysis of these data can be challenging for researchers without background knowledge of the system and preliminary processing. Data descriptionThis dataset contains formatted tabular data generated from sensing system outputs suitable for a wide range of end-users and includes plant-level bounding areas, temperatures, and point cloud characteristics, as well as plot-level photosynthetic parameters and accompanying weather data. The dataset includes approximately 422 megabytes of tabular data totaling 1,903,412 unique unfiltered rows of FS data, 526,917 cleaned rows of FS data, and 285 rows of weather data from the two field seasons. 

Most ferns, unlike all seed plants, are homosporous and produce sexually undifferentiated spores. Sex ratio in many homosporous species is environmentally established by the secretion of antheridiogen from female/hermaphrodite gametophytes. Nearby undetermined gametophytes perceive antheridiogen, which induces male development. In the fern Ceratopteris richardii (Ceratopteris), hermaphroditic (her) mutants develop as hermaphrodites even in the presence of antheridiogen. Modern sequencing and genomic tools make the molecular identification of mutants in the 11-Gbp genome of this fern possible. We mapped 2 linked mutants, her7-14 and her7-19, to the same 16-Mbp interval on chromosome 29 of the Ceratopteris genome. An ortholog of the receptor kinase gene BRASSINOSTEROID INSENSITIVE 1 (BRI1) within this interval encoded a deletion mutation in her7-14 and a missense mutation in her7-19. Three other linked her mutants encoded missense mutations in the same gene, which we name HER7. Consistent with a function as a receptor kinase, HER7-GFP fusion protein localized to the plasma membrane and cytoplasm. Analysis of gene expression showed that brassinosteroid biosynthesis was upregulated in hermaphrodites compared with male gametophytes. Our work demonstrates that HER7 is required for sex determination in Ceratopteris and opens avenues for studying the evolution of antheridiogen systems. 

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

Identifying the genetic basis of local adaptation and fitness trade-offs across environments is a central goal of evolutionary biology. Cold acclimation is an adaptive plastic response for surviving seasonal freezing, and costs of acclimation may be a general mechanism for fitness trade-offs across environments in temperate zone species. Starting with locally adapted ecotypes ofArabidopsis thalianafrom Italy and Sweden, we examined the fitness consequences of a naturally occurring functional polymorphism inCBF2. This gene encodes a transcription factor that is a major regulator of cold-acclimated freezing tolerance and resides within a locus responsible for a genetic trade-off for long-term mean fitness. We estimated the consequences of alternate genotypes ofCBF2on 5-y mean fitness and fitness components at the native field sites by comparing near-isogenic lines with alternate genotypes ofCBF2to their genetic background ecotypes. The effects ofCBF2were validated at the nucleotide level using gene-edited lines in the native genetic backgrounds grown in simulated parental environments. The foreignCBF2genotype in the local genetic background reduced long-term mean fitness in Sweden by more than 10%, primarily via effects on survival. In Italy, fitness was reduced by more than 20%, primarily via effects on fecundity. At both sites, the effects were temporally variable and much stronger in some years. The gene-edited lines confirmed thatCBF2encodes the causal variant underlying this genetic trade-off. Additionally, we demonstrated a substantial fitness cost of cold acclimation, which has broad implications for potential maladaptive responses to climate change. 

SUMMARY A major challenge in global crop production is mitigating yield loss due to plant diseases. One of the best strategies to control these losses is through breeding for disease resistance. One barrier to the identification of resistance genes is the quantification of disease severity, which is typically based on the determination of a subjective score by a human observer. We hypothesized that image‐based, non‐destructive measurements of plant morphology over an extended period after pathogen infection would capture subtle quantitative differences between genotypes, and thus enable identification of new disease resistance loci. To test this, we inoculated a genetically diverse biparental mapping population of tomato (Solanum lycopersicum) withRalstonia solanacearum, a soilborne pathogen that causes bacterial wilt disease. We acquired over 40 000 time‐series images of disease progression in this population, and developed an image analysis pipeline providing a suite of 10 traits to quantify bacterial wilt disease based on plant shape and size. Quantitative trait locus (QTL) analyses using image‐based phenotyping for single and multi‐traits identified QTLs that were both unique and shared compared with those identified by human assessment of wilting, and could detect QTLs earlier than human assessment. Expanding the phenotypic space of disease with image‐based, non‐destructive phenotyping both allowed earlier detection and identified new genetic components of resistance. 

Abstract The developmental genetics of reproductive structure control in maize must consider both the staminate florets of the tassel and the pistillate florets of the ear synflorescences. Pistil abortion takes place in the tassel florets, and stamen arrest is affected in ear florets to give rise to the monoecious nature of maize. Gibberellin (GA) deficiency results in increased tillering, a dwarfed plant syndrome, and the retention of anthers in the ear florets of maize. Thesilkless1mutant results in suppression of silks in the ear. We demonstrate in this study that jasmonic acid (JA) and GA act independently and show additive phenotypes resulting in androeciousdwarf1;silkless1double mutant plants. The persistence of pistils in the tassel can be induced by multiple mechanisms, including JA deficiency, GA excess, genetic control of floral determinacy, and organ identity. Thesilkless1mutant can suppress both silks in the ear and the silks in the tassel of JA‐deficient and AP2 transcription factortasselseedmutants. We previously demonstrated that GA production was required for brassinosteroid (BR) deficiency to affect persistence of pistils in the tassel. We find that BR deficiency affects pistil persistence by an independent mechanism from thesilkless1mutant and JA pathway. Thesilkless1mutant did not prevent the formation of pistils in the tassel bynana plant2in double mutants. In addition, we demonstrate that there is more to thesilkless1mutant than just a suppression of pistil growth. We document novel phenotypes ofsilkless1mutants including weakly penetrant ear fasciation and anther persistence in the ear florets. Thus, the JA/AP2 mechanism of pistil retention in the tassel and silk growth in the ear are similarly sensitive to loss of the SILKLESS1 protein, while the BR/GA mechanism is not. 

The origins of maize were the topic of vigorous debate for nearly a century, but neither the current genetic model nor earlier archaeological models account for the totality of available data, and recent work has highlighted the potential contribution of a wild relative,Zea maysssp.mexicana. Our population genetic analysis reveals that the origin of modern maize can be traced to an admixture between ancient maize andZea maysssp.mexicanain the highlands of Mexico some 4000 years after domestication began. We show that variation in admixture is a key component of maize diversity, both at individual loci and for additive genetic variation underlying agronomic traits. Our results clarify the origin of modern maize and raise new questions about the anthropogenic mechanisms underlying dispersal throughout the Americas. 

Abstract The Arabidopsis (Arabidopsis thaliana) BYPASS1 (BPS1) gene encodes a protein with no functionally characterized domains, and loss-of-function mutants (e.g. bps1-2 in Col-0) present a severe growth arrest phenotype that is evoked by a root-derived graft-transmissible small molecule that we call dalekin. The root-to-shoot nature of dalekin signaling suggests it could be an endogenous signaling molecule. Here, we report a natural variant screen that allowed us to identify enhancers and suppressors of the bps1-2 mutant phenotype (in Col-0). We identified a strong semi-dominant suppressor in the Apost-1 accession that largely restored shoot development in bps1 and yet continued to overproduce dalekin. Using bulked segregant analysis and allele-specific transgenic complementation, we showed that the suppressor is the Apost-1 allele of a BPS1 paralog, BYPASS2 (BPS2). BPS2 is one of four members of the BPS gene family in Arabidopsis, and phylogenetic analysis demonstrated that the BPS family is conserved in land plants and the four Arabidopsis paralogs are retained duplicates from whole genome duplications. The strong conservation of BPS1 and paralogous proteins throughout land plants, and the similar functions of paralogs in Arabidopsis, suggests that dalekin signaling might be retained across land plants. 

Plants typically orient their organs with respect to the Earth’s gravity field by a dynamic process called gravitropism. To discover conserved genetic elements affecting seedling root gravitropism, we measured the process in a set of Zea mays (maize) recombinant inbred lines with machine vision and compared the results with those obtained in a similar study of Arabidopsis thaliana . Each of the several quantitative trait loci that we mapped in both species spanned many hundreds of genes, too many to test individually for causality. We reasoned that orthologous genes may be responsible for natural variation in monocot and dicot root gravitropism. If so, pairs of orthologous genes affecting gravitropism may be present within the maize and Arabidopsis QTL intervals. A reciprocal comparison of sequences within the QTL intervals identified seven pairs of such one-to-one orthologs. Analysis of knockout mutants demonstrated a role in gravitropism for four of the seven: CCT2 functions in phosphatidylcholine biosynthesis, ATG5 functions in membrane remodeling during autophagy, UGP2 produces the substrate for cellulose and callose polymer extension, and FAMA is a transcription factor. Automated phenotyping enabled this discovery of four naturally varying components of a conserved process (gravitropism) by making it feasible to conduct the same large-scale experiment in two species.