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Background: With soil salinity levels rising at an alarming rate, accelerated by climate change and human interventions, there is a growing need for crop varieties that can grow on saline soils. Alfalfa (Medicago sativa) is a cool-season perennial leguminous crop, commonly grown as forage, biofuel feedstock and soil conditioner. It demonstrates significant potential for agricultural circularity and sustainability, for example by fixing nitrogen, sequestering carbon and improving soil structures. Although alfalfa is traditionally regarded as a moderately salt-tolerant species, modern alfalfa varieties display specific salt-tolerance mechanisms, which could be used to pave its role as a leading crop able to grow on saline soils., Scope: Alfalfa's salt tolerance underlies a large variety of cascading biochemical and physiological mechanisms. These are partly enabled by its complex genome structure and out-crossing nature, but which entail impediments for molecular and genetic studies. This review first summarizes the general effects of salinity on plants and the broad-ranging mechanisms for dealing with salt-induced osmotic stress, ion toxicity and secondary stress. Second, we address the defensive and adaptive strategies that have been described for alfalfa, such as the plasticity of alfalfa's root system, hormonal crosstalk for maintaining ion homeostasis, spatiotemporal specialized metabolite profiles and the protection of alfalfa-rhizobia associations. Finally, bottlenecks for research of the physiological and molecular salt-stress responses as well as biotechnology-driven improvements of salt tolerance are identified and discussed., Conclusion: Understanding morpho-anatomical, physiological and molecular responses to salinity is essential for the improvement of alfalfa and other crops in saline land reclamation. This review identifies potential breeding targets for enhancing the stability of alfalfa performance and general crop robustness for rising salt levels as well as to promote alfalfa applications in saline land management., (© The Author(s) 2024. Published by Oxford University Press on behalf of the Annals of Botany Company.)

The virtual crop stands as a vital content in crop model research field, and has become an indispensable tool for exploring crop phenotypes. The focal objective of this undertaking is to realize three-dimensional (3D) dynamic visualization simulations of rice individual and rice populations, as well as to predict rice phenotype using virtual rice. Leveraging our laboratory's existing research findings, we have realized 3D dynamic visualizations of rice individual and populations across various growth degree days (GDD) by integrating the synchronization relationship between the above-ground parts and the root system in rice plant. The resulting visualization effects are realistic with better predictive capability for rice morphological changes. We conducted a field experiment in Anhui Province in 2019, and obtained leaf area index data for two distinct rice cultivars at the tiller stage, jointing stage, and flowering stage. A method of segmenting leaf based on the virtual rice model is employed to predict the leaf area index. A comparative analysis between the measured and simulated leaf area index yielded relative errors spanning from 7.58% to 12.69%. Additionally, the root mean square error, the mean absolute error, and the coefficient of determination were calculated as 0.56, 0.55, and 0.86, respectively. All the evaluation criteria indicate a commendable level of accuracy. These advancements provide both technical and modeling support for the development of virtual crops and the prediction of crop phenotypes., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Zhang 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.)

Understanding trait-trait coordination is essential for successful plant breeding and crop modeling. Notably, plant size drives variation in morphological, physiological, and performance-related traits, as described by allometric laws in ecology. Yet, as allometric relationships have been limitedly studied in crops, how they influence and possibly limit crop performance remains unknown. Here, we review how an allometry perspective on crops gains insights into the phenotypic evolution during crop domestication, the breeding of varieties adapted to novel conditions, and the prediction of crop yields. As allometry is an active field of research, modeling and manipulating crop allometric relationships can help to develop more resilient and productive agricultural systems to face future challenges., (© 2024 The Author(s). New Phytologist © 2024 New Phytologist Foundation.)

Rice (Oryza sativa L.) producers in the Mid-south are experiencing difficulties with herbicide-resistant weeds such as barnyardgrass [Echinochloa crus-galli (L.) P. Beauv.]. As a result, methods that can alter E. crus-galli ecology are needed. This research evaluated the ecological implications of rice cultivar and row widths on crop and E. crus-galli growth. Overall, for E. crus-galli, as the row width increased, greater density, panicle counts, and seed production occurred. Echinochloa crus-galli density was 120% greater in a 38-cm row width than the 13-cm row width at the preflood rice stage. Reduced early-season rice canopy coverage in the wider row widths allowed for increased E. crus-galli densities. At the preharvest stage, E. crus-galli panicle counts were similar for the 13- and 19-cm rows. Row width did not affect rice yield, indicating wider row widths could be feasible agronomically, but additional weed management efforts would be needed because greater ecological advantages were obtained in narrower rows. Less E. crus-galli seed production occurred in competition with hybrid cultivars compared to inbred cultivars. Overall, the standard row width (19-cm) and hybrid cultivars would provide the greatest ecological advantage over E. crus-galli., (© 2024. The Author(s).)

Seed microbial communities have been known to have a crucial role in the life cycle of a plant. In this study, we examined the distribution of the fungal communities in three compartments (husk, brown rice, and milled rice) of the fourteen rice seed samples. Ten fungal genera distributed throughout the three compartments of the rice seeds were identified as the core mycobiome of the rice seeds, regardless of collecting regions or cultivars. Based on the diversity analysis, the distribution of the fungal community in milled rice was found to be more diversified, evenly distributed, and differently clustered from the other two compartments. Among the core mycobiome, Moesziomyces dominated almost 80% of the fungal communities in the outer compartments of rice seeds, whereas the abundances of other endophytic pathogenic fungi declined. Our results provide that antagonistic yeast Moesziomyces may be able to control the endogenous pathogenic fungal communities in rice seeds, hence maintaining the quality of rice seeds. In addition, the distribution of fungal communities differs depending on the rice seed's compartment, indicating that the compartment can affect the distribution of the seed microbial community., (© 2024. The Author(s).)

Crops generally have seeds larger than their wild progenitors´ and with reduced dormancy. In wild plants, seed mass and allocation to the seed coat (a proxy for physical dormancy) scale allometrically so that larger seeds tend to allocate less to the coats. Larger seeds and lightweight coats might thus have evolved as correlated traits in crops. We tested whether 34 crops and 22 of their wild progenitors fit the allometry described in the literature, which would indicate co-selection of both traits during crop evolution. Deviations from the allometry would suggest that other evolutionary processes contribute to explain the emergence of larger, lightweight-coated seeds in crops. Crops fitted the scaling slope but deviated from its intercept in a consistent way: Seed coats of crops were lighter than expected by their seed size. The wild progenitors of crops displayed the same trend, indicating that deviations cannot be solely attributed to artificial selection during or after domestication. The evolution of seeds with small coats in crops likely resulted from a combination of various pressures, including the selection of wild progenitors with coats smaller than other wild plants, further decreases during early evolution under cultivation, and indirect selection due to the seed coat-seed size allometry., (© 2024 The Authors. New Phytologist © 2024 New Phytologist Foundation.)

Background: The plant architecture traits of maize determine the yield. Plant height, ear position, leaf angle above the primary ear and internode length above the primary ear together determine the canopy structure and photosynthetic efficiency of maize and at the same time affect lodging and disease resistance. A flat and tall plant architecture confers an obvious advantage in the yield of a single plant but is not conducive to dense planting and results in high rates of lodging; thus, it has been gradually eliminated in production. Although using plants that are too compact, short and density tolerant can increase the yield per unit area to a certain extent, the photosynthetic efficiency of such plants is low, ultimately limiting yield increases. Genetic mapping is an effective method for the improvement of plant architecture to identify candidate genes for regulating plant architecture traits., Results: To find the best balance between the yield per plant and the yield per unit area of maize, in this study, the F2:3 pedigree population and a RIL population with the same male parent were used to identify QTL for plant height (PH), ear height (EH), leaf angle and internode length above the primary ear (LAE and ILE) in Changchun and Gongzhuling for 5 consecutive years (2016-2020). A total of 11, 13, 23 and 13 QTL were identified for PH, EH, LAE, and ILE, respectively. A pleiotropic consistent QTL for PH overlapped with that for EH on chromosome 3, with a phenotypic variation explanation rate from 6.809% to 21.96%. In addition, there were major consistent QTL for LAE and ILE, and the maximum phenotypic contribution rates were 24.226% and 30.748%, respectively. Three candidate genes were mined from the three consistent QTL regions and were involved in the gibberellin-activated signal pathway, brassinolide signal transduction pathway and auxin-activated signal pathway, respectively. Analysis of the expression levels of the three genes showed that they were actively expressed during the jointing stage of vigorous maize growth., Conclusions: In this study, three consistent major QTL related to plant type traits were identified and three candidate genes were screened. These results lay a foundation for the cloning of related functional genes and marker-assisted breeding of related functional genes., (© 2022. The Author(s).)

Flowers are produced by floral meristems, groups of stem cells that give rise to floral organs. In grasses, including the major cereal crops, flowers (florets) are contained in spikelets, which contain one to many florets, depending on the species. Importantly, not all grass florets are developmentally equivalent, and one or more florets are often sterile or abort in each spikelet. Members of the Andropogoneae tribe, including maize (Zea mays), produce spikelets with two florets; the upper and lower florets are usually dimorphic, and the lower floret is greatly reduced compared to the upper floret. In maize ears, early development appears identical in both florets but the lower floret ultimately aborts. To gain insight into the functional differences between florets with different fates, we used laser capture microdissection coupled with RNA-sequencing to globally examine gene expression in upper and lower floral meristems in maize. Differentially expressed genes were involved in hormone regulation, cell wall, sugar, and energy homeostasis. Furthermore, cell wall modifications and sugar accumulation differed between the upper and lower florets. Finally, we identified a boundary domain between upper and lower florets, which we hypothesize is important for floral meristem activity. We propose a model in which growth is suppressed in the lower floret by limiting sugar availability and upregulating genes involved in growth repression. This growth repression module may also regulate floret fertility in other grasses and potentially be modulated to engineer more productive cereal crops., (© American Society of Plant Biologists 2021. All rights reserved. For permissions, please email: journals.permissions@oup.com.)

Phosphorus (P) deficiency affects soybean growth and development, resulting in significant reduction of yields. However, the regulatory mechanism of P deficiency tolerance in soybean is still largely unclear. WRKY transcription factors are a family of regulators involved in a variety of abiotic stresses in plants while rarely reported in P deficiency. Here, we demonstrated that a soybean GmWRKY46 gene, belonging to group III of WRKY TF family, was involved in the regulation of P deficiency tolerance in soybean. The expression of GmWRKY46 in low P sensitive soybean varieties was significantly higher than that in tolerant soybean varieties. It was primarily expressed in roots and strongly induced by P deprivation. GmWRKY46 was localized in the nucleus. Compared with the control expressing the empty vector, overexpression of GmWRKY46 in soybean hairy roots exhibited more sensitive phenotypes to low P stress, while the RNA interfered GmWRKY46 significantly enhanced P deficiency tolerance by increasing the proliferation, elongation and P absorption efficiency of hairy roots. Expression patterns of a number of P-responsive genes (GmPht1;1, GmPht1;4, GmPTF1, GmACP1, GmPAP21 and GmExpansin-A7) were altered in both overexpression and gene silenced plants. The results provided a novel insight into how soybean responds to low P stress and new gene that may be used to improve soybean low P tolerance through gene editing approach., (Copyright © 2021 Elsevier B.V. All rights reserved.)

Crop plant architecture is an important agronomic trait that contributes greatly to crop yield. Tiller angle is one of the most critical components that determine crop plant architecture, which in turn substantially affects grain yield mainly owing to its large influence on plant density. Gravity is a fundamental physical force that acts on all organisms on earth. Plant organs sense gravity to control their growth orientation, including tiller angle in rice (Oryza sativa). This review summarizes recent research advances made using rice tiller angle as a research model, providing insights into domestication of rice tiller angle, genetic regulation of rice tiller angle, and shoot gravitropism. Finally, we propose that current discoveries in rice can shed light on shoot gravitropism and improvement of plant tiller/branch angle in other species, thereby contributing to agricultural production in the future., (Copyright © 2021 The Author. Published by Elsevier Inc. All rights reserved.)

Root architecture can be targeted in breeding programs to develop crops with better capture of water and nutrients. In rich nations, such crops would reduce production costs and environmental pollution and, in developing nations, they would improve food security and economic development. Crops with deeper roots would have better climate resilience while also sequestering atmospheric CO 2 . Deeper rooting, which improves water and N capture, is facilitated by steeper root growth angles, fewer axial roots, reduced lateral branching, and anatomical phenotypes that reduce the metabolic cost of root tissue. Mechanical impedance, hypoxia, and Al toxicity are constraints to subsoil exploration. To improve topsoil foraging for P, K, and other shallow resources, shallower root growth angles, more axial roots, and greater lateral branching are beneficial, as are metabolically cheap roots. In high-input systems, parsimonious root phenotypes that focus on water capture may be advantageous. The growing prevalence of Conservation Agriculture is shifting the mechanical impedance characteristics of cultivated soils in ways that may favor plastic root phenotypes capable of exploiting low resistance pathways to the subsoil. Root ideotypes for many low-input systems would not be optimized for any one function, but would be resilient against an array of biotic and abiotic challenges. Root hairs, reduced metabolic cost, and developmental regulation of plasticity may be useful in all environments. The fitness landscape of integrated root phenotypes is large and complex, and hence will benefit from in silico tools. Understanding and harnessing root architecture for crop improvement is a transdisciplinary opportunity to address global challenges., (© 2021 The Authors. The Plant Journal published by Society for Experimental Biology and John Wiley & Sons Ltd.)

Measuring leaf area index (LAI) is essential for evaluating crop growth and estimating yield, thereby facilitating high-throughput phenotyping of maize (Zea mays). LAI estimation models use multi-source data from unmanned aerial vehicles (UAVs), but using multimodal data to estimate maize LAI, and the effect of tassels and soil background, remain understudied. Our research aims to (1) determine how multimodal data contribute to LAI and propose a framework for estimating LAI based on remote-sensing data, (2) evaluate the robustness and adaptability of an LAI estimation model that uses multimodal data fusion and deep neural networks (DNNs) in single- and whole growth stages, and (3) explore how soil background and maize tasseling affect LAI estimation. To construct multimodal datasets, our UAV collected red-green-blue, multispectral, and thermal infrared images. We then developed partial least square regression (PLSR), support vector regression, and random forest regression models to estimate LAI. We also developed a deep learning model with three hidden layers. This multimodal data structure accurately estimated maize LAI. The DNN model provided the best estimate (coefficient of determination [R2] = 0.89, relative root mean square error [rRMSE] = 12.92%) for a single growth period, and the PLSR model provided the best estimate (R2 = 0.70, rRMSE = 12.78%) for a whole growth period. Tassels reduced the accuracy of LAI estimation, but the soil background provided additional image feature information, improving accuracy. These results indicate that multimodal data fusion using low-cost UAVs and DNNs can accurately and reliably estimate LAI for crops, which is valuable for high-throughput phenotyping and high-spatial precision farmland management., (© American Society of Plant Biologists 2021. All rights reserved. For permissions, please email: journals.permissions@oup.com.)

Abiotic stresses increasingly threaten existing ecological and agricultural systems across the globe. Plant roots perceive these stresses in the soil and adapt their architecture accordingly. This review provides insights into recent discoveries showing the importance of root system architecture (RSA) and plasticity for the survival and development of plants under heat, cold, drought, salt, and flooding stress. In addition, we review the molecular regulation and hormonal pathways involved in controlling RSA plasticity, main root growth, branching and lateral root growth, root hair development, and formation of adventitious roots. Several stresses affect root anatomy by causing aerenchyma formation, lignin and suberin deposition, and Casparian strip modulation. Roots can also actively grow toward favorable soil conditions and avoid environments detrimental to their development. Recent advances in understanding the cellular mechanisms behind these different root tropisms are discussed. Understanding root plasticity will be instrumental for the development of crops that are resilient in the face of abiotic stress., (© The Author(s) 2021. Published by Oxford University Press on behalf of American Society of Plant Biologists.)

The geometric and color features of agricultural material along with related physical properties are critical to characterize and express its physical quality. The experiments were conducted to classify the physical characteristics like size, shape, color and texture and then workout the relationship between manual observations and using image processing techniques for weight and volume of the four wheat refractions i.e. sound, damaged, shriveled and broken grains of wheat variety PBW 725. A flatbed scanner was used to acquire the images and digital image processing method was used to process the images and output of image analysis was compared with the actual measurements data using digital vernier caliper. A linear relationship was observed between the axial dimensions of refractions between manual measurement and image processing method with R 2 in the range of 0.798-0.947. The individual kernel weight and thousand grain weight of the refractions were observed to be in the range of 0.021-0.045 and 12.56-46.32 g respectively. Another linear relationship was found between individual kernel weight and projected area estimated using image processing methodology with R 2 in the range of 0.841-0.920. The sphericity of the refractions varied in the range of 0.52-0.71. Analyses of the captured images suggest ellipsoid shape with convex geometry while the same observation was recorded by physical measurements also. A linear relationship was observed between the volume of refractions derived from measured dimensions and calculated from image with R 2 in the range of 0.845-0.945. Various color and grey level co-variance matrix texture features were extracted from acquired images using the open-source Python programming language and OpenCV library which can exploit different machine and deep learning algorithms to properly classify these refractions., (© 2021. The Author(s).)

The development of crops with deeper roots holds substantial promise to mitigate the consequences of climate change. Deeper roots are an essential factor to improve water uptake as a way to enhance crop resilience to drought, to increase nitrogen capture, to reduce fertilizer inputs, and to increase carbon sequestration from the atmosphere to improve soil organic fertility. A major bottleneck to achieving these improvements is high-throughput phenotyping to quantify root phenotypes of field-grown roots. We address this bottleneck with Digital Imaging of Root Traits (DIRT)/3D, an image-based 3D root phenotyping platform, which measures 18 architecture traits from mature field-grown maize (Zea mays) root crowns (RCs) excavated with the Shovelomics technique. DIRT/3D reliably computed all 18 traits, including distance between whorls and the number, angles, and diameters of nodal roots, on a test panel of 12 contrasting maize genotypes. The computed results were validated through comparison with manual measurements. Overall, we observed a coefficient of determination of r2>0.84 and a high broad-sense heritability of Hmean2> 0.6 for all but one trait. The average values of the 18 traits and a developed descriptor to characterize complete root architecture distinguished all genotypes. DIRT/3D is a step toward automated quantification of highly occluded maize RCs. Therefore, DIRT/3D supports breeders and root biologists in improving carbon sequestration and food security in the face of the adverse effects of climate change., (© The Author(s) 2021. Published by Oxford University Press on behalf of American Society of Plant Biologists.)

Background: Leaf color variation is a common trait in plants and widely distributed in many plants. In this study, a leaf color mutation in Camellia japonica (cultivar named as Maguxianzi, M) was used as material, and the mechanism of leaf color variation was revealed by physiological, cytological, transcriptome and microbiome analyses., Results: The yellowing C. japonica (M) exhibits lower pigment content than its parent (cultivar named as Huafurong, H), especially chlorophyll (Chl) and carotenoid, and leaves of M have weaker photosynthesis. Subsequently, the results of transmission electron microscopy(TEM) exhibited that M chloroplast was accompanied by broken thylakoid membrane, degraded thylakoid grana, and filled with many vesicles. Furthermore, comparative transcriptome sequencing identified 3,298 differentially expressed genes (DEGs). KEGG annotation analysis results showed that 69 significantly enriched DEGs were involved in Chl biosynthesis, carotenoid biosynthesis, photosynthesis, and plant-pathogen interaction. On this basis, we sequenced the microbial diversity of the H and M leaves. The sequencing results suggested that the abundance of Didymella in the M leaves was significantly higher than that in the H leaves, which meant that M leaves might be infected by Didymella., Conclusions: Therefore, we speculated that Didymella infected M leaves while reduced Chl and carotenoid content by damaging chloroplast structures, and altered the intensity of photosynthesis, thereby causing the leaf yellowing phenomenon of C. japonica (M). This research will provide new insights into the leaf color variation mechanism and lay a theoretical foundation for plant breeding and molecular markers., (© 2021. The Author(s).)

Kenaf (Hibiscus cannabinus L.) is an industrial crop used as a raw material in various fields and is cultivated worldwide. Compared to high potential for its utilization, breeding sector is not vigorous partially due to laborous breeding procedure. Thus, efficient breeding methods are required for varieties that can adapt to various environments and obtain optimal production. For that, identifying kenaf's characteristics is very important during the breeding process. Here, we investigated if RGB based vegetative index (VI) could be associated with traits for biomass. We used 20 varieties and germplasm of kenaf and RGB images taken with unmanned aerial vehicles (UAVs) for field selection in early and late growth stage. In addition, measuring the stem diameter and the number of nodes confirmed whether the vegetative index value obtained from the RGB image could infer the actual plant biomass. Based on the results, it was confirmed that the individual surface area and estimated plant height, which were identified from the RGB image, had positive correlations with the stem diameter and node number, which are actual growth indicators of the rate of growth further, biomass could also be estimated based on this. Moreover, it is suggested that VIs have a high correlation with actual growth indicators; thus, the biomass of kenaf could be predicted. Interstingly, those traits showing high correlation in the late stage had very low correlations in the early stage. To sum up, the results in the current study suggest a more efficient breeding method by reducing labor and resources required for breeding selection by the use of RGB image analysis obtained by UAV. This means that considerable high-quality research could be performed even with a tight budget. Furthermore, this method could be applied to crop management, which is done with other vegetative indices using a multispectral camera., Competing Interests: No authors have competing interests

Background: The root distribution in the soil is one of the elements that comprise the root system architecture (RSA). In monocots, RSA comprises radicle and crown roots, each of which can be basically represented by a single curve with lateral root branches or approximated using a polyline. Moreover, RSA vectorization (polyline conversion) is useful for RSA phenotyping. However, a robust software that can enable RSA vectorization while using noisy three-dimensional (3D) volumes is unavailable., Results: We developed RSAtrace3D, which is a robust 3D RSA vectorization software for monocot RSA phenotyping. It manages the single root (radicle or crown root) as a polyline (a vector), and the set of the polylines represents the entire RSA. RSAtrace3D vectorizes root segments between the two ends of a single root. By utilizing several base points on the root, RSAtrace3D suits noisy images if it is difficult to vectorize it using only two end nodes of the root. Additionally, by employing a simple tracking algorithm that uses the center of gravity (COG) of the root voxels to determine the tracking direction, RSAtrace3D efficiently vectorizes the roots. Thus, RSAtrace3D represents the single root shape more precisely than straight lines or spline curves. As a case study, rice (Oryza sativa) RSA was vectorized from X-ray computed tomography (CT) images, and RSA traits were calculated. In addition, varietal differences in RSA traits were observed. The vector data were 32,000 times more compact than raw X-ray CT images. Therefore, this makes it easier to share data and perform re-analyses. For example, using data from previously conducted studies. For monocot plants, the vectorization and phenotyping algorithm are extendable and suitable for numerous applications., Conclusions: RSAtrace3D is an RSA vectorization software for 3D RSA phenotyping for monocots. Owing to the high expandability of the RSA vectorization and phenotyping algorithm, RSAtrace3D can be applied not only to rice in X-ray CT images but also to other monocots in various 3D images. Since this software is written in Python language, it can be easily modified and will be extensively applied by researchers in this field., (© 2021. The Author(s).)

Temperature stresses affect plant phenotypic diversity. The developmental stability of the inflorescence, required for reproductive success, is tightly regulated by the interplay of genetic and environmental factors. However, the mechanisms underpinning how plant inflorescence architecture responds to temperature are largely unknown. We demonstrate that the barley SEPALLATA MADS-box protein HvMADS1 is responsible for maintaining an unbranched spike architecture at high temperatures, while the loss-of-function mutant forms a branched inflorescence-like structure. HvMADS1 exhibits increased binding to target promoters via A-tract CArG-box motifs, which change conformation with temperature. Target genes for high-temperature-dependent HvMADS1 activation are predominantly associated with inflorescence differentiation and phytohormone signalling. HvMADS1 directly regulates the cytokinin-degrading enzyme HvCKX3 to integrate temperature response and cytokinin homeostasis, which is required to repress meristem cell cycle/division. Our findings reveal a mechanism by which genetic factors direct plant thermomorphogenesis, extending the recognized role of plant MADS-box proteins in floral development., (© 2021. The Author(s), under exclusive licence to Springer Nature Limited.)

Background: Sesame (Sesamum indicum L.) leaves, flowers, especially seeds are used in traditional medicine to prevent or cure various diseases. Its seed's market is expanding. However, the other tissues are still underexploited due to the lack of information related to metabolites distribution and variability in the plant. Herein, the metabolite profiles of five sesame tissues (leaves, fresh seeds, white and purple flowers, and fresh carpels) have been investigated using ultra-high-performance liquid chromatography-mass spectrometry (UPLC-MS/MS)-based widely targeted metabolomics analysis platform., Results: In total, 776 metabolites belonging to diverse classes were qualitatively and quantitatively identified. The different tissues exhibited obvious differences in metabolites composition. The majority of flavonoids predominantly accumulated in flowers. Amino acids and derivatives, and lipids were identified predominantly in fresh seeds followed by flowers. Many metabolites, including quinones, coumarins, tannins, vitamins, terpenoids and some bioactive phenolic acids (acteoside, isoacteoside, verbascoside, plantamajoside, etc.) accumulated mostly in leaves. Lignans were principally detected in seeds. 238 key significantly differential metabolites were filtered out. KEGG annotation and enrichment analyses of the differential metabolites revealed that flavonoid biosynthesis, amino acids biosynthesis, and phenylpropanoid biosynthesis were the main differently regulated pathways. In addition to the tissue-specific accumulation of metabolites, we noticed a cooperative relationship between leaves, fresh carpels, and developing seeds in terms of metabolites transfer. Delphinidin-3-O-(6"-O-p-coumaroyl)glucoside and most of the flavonols were up-regulated in the purple flowers indicating they might be responsible for the purple coloration., Conclusion: This study revealed that the metabolic processes in the sesame tissues are differently regulated. It offers valuable resources for investigating gene-metabolites interactions in sesame tissues and examining metabolic transports during seed development in sesame. Furthermore, our findings provide crucial knowledge that will facilitate sesame biomass valorization., (© 2021. The Author(s).)

Background: Root system architecture (RSA), which is determined by the crown root angle (CRA), crown root diameter (CRD), and crown root number (CRN), is an important factor affecting the ability of plants to obtain nutrients and water from the soil. However, the genetic mechanisms regulating crown root traits in the field remain unclear., Methods: In this study, the CRA, CRD, and CRN of 316 diverse maize inbred lines were analysed in three field trials. Substantial phenotypic variations were observed for the three crown root traits in all environments. A genome-wide association study was conducted using two single-locus methods (GLM and MLM) and three multi-locus methods (FarmCPU, FASTmrMLM, and FASTmrEMMA) with 140,421 SNP., Results: A total of 38 QTL including 126 SNPs were detected for CRA, CRD, and CRN. Additionally, 113 candidate genes within 50 kb of the significant SNPs were identified. Combining the gene annotation information and the expression profiles, 3 genes including GRMZM2G141205 (IAA), GRMZM2G138511 (HSP) and GRMZM2G175910 (cytokinin-O-glucosyltransferase) were selected as potentially candidate genes related to crown root development. Moreover, GRMZM2G141205, encoding an AUX/IAA transcriptional regulator, was resequenced in all tested lines. Five variants were identified as significantly associated with CRN in different environments. Four haplotypes were detected based on these significant variants, and Hap1 has more CRN., Conclusions: These findings may be useful for clarifying the genetic basis of maize root system architecture. Furthermore, the identified candidate genes and variants may be relevant for breeding new maize varieties with root traits suitable for diverse environmental conditions., (© 2021. The Author(s).)

Pollen apertures are an interesting model for the formation of specialized plasma-membrane domains. The plant-specific protein INP1 serves as a key aperture factor in such distantly related species as Arabidopsis, rice and maize. Although INP1 orthologues probably play similar roles throughout flowering plants, they show substantial sequence divergence and often cannot substitute for each other, suggesting that INP1 might require species-specific partners. Here, we present a new aperture factor, INP2, which satisfies the criteria for being a species-specific partner for INP1. Both INP proteins display similar structural features, including the plant-specific DOG1 domain, similar patterns of expression and mutant phenotypes, as well as signs of co-evolution. These proteins interact with each other in a species-specific manner and can restore apertures in a heterologous system when both are expressed but not when expressed individually. Our findings suggest that the INP proteins form a species-specific functional module that underlies formation of pollen apertures., (© 2021. The Author(s), under exclusive licence to Springer Nature Limited.)

Background: Raising nitrogen use efficiency of crops by improving root system architecture is highly essential not only to reduce costs of agricultural production but also to mitigate climate change. The physiological mechanisms of how biochar affects nitrogen assimilation by crop seedlings have not been well elucidated., Results: Here, we report changes in root system architecture, activities of the key enzymes involved in nitrogen assimilation, and cytokinin (CTK) at the seedling stage of cotton with reduced urea usage and biochar application at different soil layers (0-10 cm and 10-20 cm). Active root absorption area, fresh weight, and nitrogen agronomic efficiency increased significantly when urea usage was reduced by 25% and biochar was applied in the surface soil layer. Glutamine oxoglutarate amino transferase (GOGAT) activity was closely related to the application depth of urea/biochar, and it increased when urea/biochar was applied in the 0-10 cm layer. Glutamic-pyruvic transaminase activity (GPT) increased significantly as well. Nitrate reductase (NR) activity was stimulated by CTK in the very fine roots but inhibited in the fine roots. In addition, AMT1;1, gdh3, and gdh2 were significantly up-regulated in the very fine roots when urea usage was reduced by 25% and biochar was applied., Conclusion: Nitrogen assimilation efficiency was significantly affected when urea usage was reduced by 25% and biochar was applied in the surface soil layer at the seedling stage of cotton. The co-expression of gdh3 and gdh2 in the fine roots increased nitrogen agronomic efficiency. The synergistic expression of the ammonium transporter gene and gdh3 suggests that biochar may be beneficial to amino acid metabolism.

Sweet pepper ( Capsicum annuum L.) is one of the most important vegetable crops in the world because of the nutritional value of its fruits and its economic importance. Calcium (Ca) improves the quality of sweet pepper fruits, and the application of calcite nanoparticles in agricultural practice has a positive effect on the morphological, physiological, and physicochemical properties of the whole plant. The objectives of this study were to investigate the effect of commercial calcite nanoparticles on yield, chemical, physical, morphological, and multispectral properties of sweet pepper fruits using a combination of conventional and novel image-based nondestructive methods of fruit quality analysis. In the field trial, two sweet pepper cultivars, i.e., Šorokšari and Kurtovska kapija, were treated with commercial calcite nanoparticles (at a concentration of 3% and 5%, calcite-based foliar fertilizer (positive control), and water (negative control) three times during vegetation). Sweet pepper fruits were harvested at the time of technological and physiological maturity. Significant differences were observed between pepper cultivars as well as between harvests times. In general, application of calcite nanoparticles reduced yield and increased fruit firmness. However, different effects of calcite nanoparticles were observed on almost all properties depending on the cultivar. In Šorokšari, calcite nanoparticles and calcite-based foliar fertilizers significantly increased N, P, K, Mg, Fe, Zn, Mn, and Cu at technological maturity, as well as P, Ca, Mg, Fe, Zn, Mn, Cu, and N at physiological maturity. However, in Kurtovska kapija, the treatments increased only Ca at technological maturity and only P at physiological maturity. The effect of treatments on fruit morphological properties was observed only at the second harvest. In Šorokšari, calcite nanoparticles (3% and 5%) increased the fruit length, minimal circle area, and minimal circle radius, and it decreased the fruit width and convex hull compared to the positive and negative controls, respectively. In Kurtovska kapija, calcite nanoparticles increased the fruit width and convex hull compared to the controls. At physiological maturity, lower anthocyanin and chlorophyll indices were found in Kurtovska kapija in both treatments with calcite nanoparticles, while in Šorokšari, the opposite effects were observed.

Plants acclimate to shade by sensing light signals such as low photosynthetic active radiation (PAR), low blue light (BL) levels and low red-to-far red ratios (R:FR) trough plant photoreceptors cross talk. We previously demonstrated that grapevine is irresponsive to variations in R:FR and that BL-attenuation mediates morphological and architectural responses to shade increasing light interception and absorption efficiencies. However, we wondered if grapevine respond to low R:FR when BL is attenuated at the same time. Our objective was to evaluate if morphological, architectural and hydraulic acclimation to shade is mediated by low R:FR ratios and BL attenuation. To test this, we carried out experiments under natural radiation, manipulating light quality by selective sunlight exclusion and light supplementation. We grew grapevines under low PAR (LP) and four high PAR (HP) treatments: HP, HP plus FR supplementation (HP + FR), HP with BL attenuation (HP-B) and HP with BL attenuation plus FR supplementation (HP-B + FR). We found that plants grown under HP-B and HP-B + FR had similar morphological (stem and petiole length, leaf thickness and area), architectural (laminae' angles) and anatomical (stomatal density) traits than plants grown under LP. However, only LP plants presented lower stomata differentiation, lower δ 13 C and hence lower water use efficiency. Therefore, even under a BL and R:FR attenuated environment, morphological and architectural responses were modulated by BL but not by variation in R:FR. Meanwhile water relations were affected by PAR intensity but not by changes in light quality. Knowing grapevine responses to light quantity and quality are indispensable to adopt tools or design new cultural management practices that manipulate irradiance in the field intending to improve crop performance., (Copyright © 2021 Elsevier B.V. All rights reserved.)

PACLOBUTRAZOL RESISTANCE (PRE) genes code atypical HLH transcriptional regulators characterized by the absence of a DNA-binding domain but present an HLH dimerization domain. In vegetative tissues, the function of these HLH proteins has been related with cell elongation processes. In strawberry, three FaPRE genes are expressed, two of them (FaPRE2 and FaPRE3) in vegetative tissues while FaPRE1 is fruit receptacle-specific. Ubiquitous FaPRE1 accumulation produced elongated flower receptacles and plants due to the elongation of the main aerial vegetative organs, with the exception of leaves. Histological analysis clearly demonstrated that the observed phenotype was due to significant changes in the parenchymal cell's morphology. In addition, transcriptomic studies of the transgenic elongated flower receptacles allowed to identify a small group of differentially expressed genes that encode cell wall-modifying enzymes. Together, the data seem to indicate that, in the strawberry plant vegetative organs, FaPRE proteins could modulate the expression of genes related with the determination of the size and shape of the parenchymal cells., (Copyright © 2021 Elsevier B.V. All rights reserved.)

The rapid and responsive growth of a pollen tube requires delicate coordination of membrane receptor signaling, Rho-of-Plants (ROP) GTPase activity switching, and actin cytoskeleton assembly. The tomato ( Solanum lycopersicum ) kinase partner protein (KPP), is a ROP guanine nucleotide exchange factor (GEF) that activates ROP GTPases and interacts with the tomato pollen receptor kinases LePRK1 and LePRK2. It remains unclear how KPP relays signals from plasma membrane-localized LePRKs to ROP switches and other cellular machineries to modulate pollen tube growth. Here, we biochemically verified KPP's activity on ROP4 and showed that KPP RNA interference transgenic pollen tubes grew slower while KPP -overexpressing pollen tubes grew faster, suggesting that KPP functions as a rheostat for speed control in LePRK2-mediated pollen tube growth. The N terminus of KPP is required for self-inhibition of its ROPGEF activity, and expression of truncated KPP lacking the N terminus caused pollen tube tip enlargement. The C-terminus of KPP is required for its interaction with LePRK1 and LePRK2, and the expression of a truncated KPP lacking the C-terminus triggered pollen tube bifurcation. Furthermore, coexpression assays showed that self-associated KPP recruited actin-nucleating Actin-Related Protein2/3 (ARP2/3) complexes to the tip membrane. Interfering with ARP2/3 activity reduced the pollen tube abnormalities caused by overexpressing KPP fragments. In conclusion, KPP plays a key role in pollen tube speed and shape control by recruiting the branched actin nucleator ARP2/3 complex and an actin bundler to the membrane-localized receptors LePRK1 and LePRK2., (© 2020 American Society of Plant Biologists. All Rights Reserved.)

Nonstomatal water loss by transpiration through the hydrophobic cuticle is ubiquitous in land plants, but the pathways along which this occurs have not been identified. Tomato ( Solanum lycopersicum ) provides an excellent system in which to study this phenomenon, as its fruit are astomatous and a major target for desiccation resistance to enhance shelf life. We screened a tomato core collection of 398 accessions from around the world and selected seven cultivars that collectively exhibited the lowest and highest degrees of transpirational water loss for a more detailed study. The transpirational differences between these lines reflected the permeances of their isolated cuticles, but this did not correlate with various measures of cuticle abundance or composition. Rather, we found that fruit cuticle permeance has a strong dependence on the abundance of microscopic polar pores. We further observed that these transcuticular pores are associated with trichomes and are exposed when the trichomes are dislodged, revealing a previously unreported link between fruit trichome density and transpirational water loss. During postharvest storage, limited self-sealing of the pores was detected for certain cultivars, in contrast with the stem scar, which healed relatively rapidly. The abundance of trichome-associated pores, together with their self-sealing capacity, presents a promising target for breeding or engineering efforts to reduce fruit transpirational water loss., (© 2020 American Society of Plant Biologists. All Rights Reserved.)

Cereal crop yield comprises interrelated components, among which the number of tillers is highly responsive to nitrogen fertilization. We addressed the hypothesis of whether the supply of different nitrogen forms can be employed to manipulate the tiller number in cereal crops. Relative to urea or ammonium, exclusive supply of nitrate increased tiller number in hydroponically-grown barley plants. Thereby, tiller number correlated positively with the root-to-shoot translocation rate of endogenous cytokinins. External supply of a synthetic cytokinin analog further stimulated tillering in nitrate-containing but not in urea-containing nutrient solution. When the cytokinin analog 6-benzylaminopurine riboside was externally supplied to roots, its translocation to shoots was 2.5 times higher in presence of nitrate than in presence of urea or ammonium, suggesting that cytokinin loading into the xylem is affected by different nitrogen forms. We then translated this finding to field scale, cultivated winter wheat in four environments, and confirmed that nitrate fertilization significantly increased tiller number in a dose-dependent manner. As assessed in 22 winter wheat cultivars, nitrogen form-dependent tiller formation was subject to substantial genotypic variation. We conclude that cytokinin-mediated signaling effects of fertilizer nitrogen forms can be employed as a management tool to regulate the tiller number in cereal crops.

Background: Stalk fracture caused by strong wind can severely reduce yields in maize. Stalks with higher stiffness and flexibility will exhibit stronger lodging resistance. However, stalk flexibility is rarely studied in maize. Stalk fracture of the internode above the ear before tasseling will result in the lack of tassel and pollen, which is devastating for pollination in seed production. In this study, we focused on stalk lodging before tasseling in two maize inbred lines, JING724 and its improved line JING724A1 and their F 2:3 population., Results: JING724A1 showed a larger stalk fracture angle than JING724, indicating higher flexibility. In addition, compared to JING724, JING724A1 also had longer and thicker stalks, with a conical, frustum-shaped internode above the ear. Microscopy and X-ray microcomputed tomography of the internal stalk architecture revealed that JING724A1 had more vascular bundles and thicker sclerenchyma tissue. Furthermore, total soluble sugar content of JING724A1, especially the glucose component, was substantially higher than in JING724. Using an F 2:3 population derived from a JING724 and JING724A1 cross, we performed bulk segregant analysis for stalk fracture angle and detected one QTL located on Chr3: 14.00-19.28 Mb. Through transcriptome data analysis and ∆ (SNP-index), we identified two candidate genes significantly associated with high stalk fracture angle, which encode a RING/U-box superfamily protein (Zm00001d039769) and a MADS-box transcription factor 54 (Zm00001d039913), respectively. Two KASP markers designed from these two candidate genes also showed significant correlations with stalk fracture angle., Conclusions: The internode shape and glucose content are possibly correlated with stalk flexibility in maize. Two genes in the detected QTL are potentially associated with stalk fracture angle. These novel phenotypes and associated loci will provide a theoretical foundation for understanding the genetic mechanisms of lodging, and facilitate the selection of maize varieties with improved flexibility and robust lodging resistance.

Tiller angle largely determines plant architecture, which in turn substantially influences crop production by affecting planting density. A recent study revealed that HEAT STRESS TRANSCRIPTION FACTOR2D ( HSFA2D ) acts upstream of LAZY1 ( LA1 ) to regulate tiller angle establishment in rice ( Oryza sativa ). However, the mechanisms underlying transcriptional regulation of HSFA2D remain unknown. In this study, two class II homeodomain-Leu zipper genes, OsHOX1 and OsHOX28 , were identified as positive regulators of tiller angle by affecting shoot gravitropism. OsHOX1 and OsHOX28 showed strong transcriptional suppressive activity in rice protoplasts and formed intricate self- and mutual-transcriptional negative feedback loops. Moreover, OsHOX1 and OsHOX28 bound to the pseudopalindromic sequence CAAT(C/G)ATTG within the promoter of HSFA2D , thus suppressing its expression. In contrast to HSFA2D and LA1 , OsHOX1 and OsHOX28 attenuated lateral auxin transport, thus repressing the expression of WUSCHEL-RELATED HOMEOBOX 6 ( WOX6 ) and WOX11 in the lower side of the shoot base of plants subjected to gravistimulation. Genetic analysis further confirmed that OsHOX1 and OsHOX28 act upstream of HSFA2D Additionally, both OsHOX1 and OsHOX28 inhibit the expression of multiple OsYUCCA genes and decrease auxin biosynthesis. Taken together, these results demonstrated that OsHOX1 and OsHOX28 regulate the local distribution of auxin, and thus tiller angle establishment, through suppression of the HSFA2D - LA1 pathway and reduction of endogenous auxin content. Our finding increases the knowledge concerning fine tuning of tiller angles to optimize plant architecture in rice., (© 2020 American Society of Plant Biologists. All Rights Reserved.)

Anther cuticle and pollen exine are two physical barriers protecting plant reproductive cells against environmental stresses; defects in either often cause male sterility. Here, we report the characterization of a male-sterile mutant irregular pollen exine2 ( ipe2 ) of maize ( Zea mays ), which displays shrunken anthers and no starch accumulation in mature pollen grains. We cloned the causal gene IPE2 and confirmed its role in male fertility in maize with a set of complementary experiments. IPE2 is specifically expressed in maize developing anthers during stages 8 to 9 and encodes an endoplasmic-reticulum-localized GDSL lipase. Dysfunction of IPE2 resulted in delayed degeneration of tapetum and middle layer, leading to defective formation of anther cuticle and pollen exine, and complete male sterility. Aliphatic metabolism was greatly altered, with the contents of lipid constituents, especially C16/C18 fatty acids and their derivatives, significantly reduced in ipe2 developing anthers. Our study elucidates GDSL function in anther and pollen development and provides a promising genetic resource for breeding hybrid maize., (© 2020 American Society of Plant Biologists. All Rights Reserved.)

Advancements in phenotyping techniques capable of rapidly and nondestructively detecting impacts of drought on crops are necessary to meet the 21st-century challenge of food security. Here, we describe the use of hyperspectral reflectance to predict variation in physiological and anatomical leaf traits related with water status under varying water availability in six maize ( Zea mays ) hybrids that differ in yield stability under drought. We also assessed relationships among traits and collections of traits with yield stability. Measurements were collected in both greenhouse and field environments, with plants exposed to different levels of water stress or to natural water availability, respectively. Leaf spectral measurements were paired with a number of physiological and anatomical reference measurements, and predictive spectral models were constructed using a partial least-squares regression approach. All traits were relatively well predicted by spectroscopic models, with external validation (i.e. by applying partial least-squares regression coefficients on a dataset distinct from the one used for calibration) goodness-of-fit ( R 2 ) ranging from 0.37 to 0.89 and normalized error ranging from 12% to 21%. Correlations between reference and predicted data were statistically similar for both greenhouse and field data. Our findings highlight the capability of vegetation spectroscopy to rapidly and nondestructively identify a number of foliar functional traits affected by drought that can be used as indicators of plant water status. Although we did not detect trait coordination with yield stability in the hybrids used in this study, expanding the range of functional traits estimated by hyperspectral data can help improve trait-based breeding approaches., (© 2020 American Society of Plant Biologists. All Rights Reserved.)

Background: Leaf size and shape, which affect light capture, and chlorophyll content are important factors affecting photosynthetic efficiency. Genetic variation of these components significantly affects yield potential and seed quality. Identification of the genetic basis for these traits and the relationship between them is of great practical significance for achieving ideal plant architecture and high photosynthetic efficiency for improved yield., Results: Here, we undertook a large-scale linkage mapping study using three mapping populations to determine the genetic interplay between soybean leaf-related traits and chlorophyll content across two environments. Correlation analysis revealed a significant negative correlation between leaf size and shape, while both traits were positively correlated with chlorophyll content. This phenotypic relationship was verified across the three mapping populations as determined by principal component analysis, suggesting that these traits are under the control of complex and interrelated genetic components. The QTLs for leaf-related traits and chlorophyll are partly shared, which further supports the close genetic relationship between the two traits. The largest-effect major loci, q20, was stably identified across all population and environments and harbored the narrow leaflet gene Gm-JAG1 (Ln/ln), which is a key regulator of leaflet shape in soybean., Conclusion: Our results uncover several major QTLs (q4-1, q4-2, q11, q13, q18 and q20) and its candidate genes specific or common to leaf-related traits and chlorophyll, and also show a complex epistatic interaction between the two traits. The SNP markers closely linked to these valuable QTLs could be used for molecular design breeding with improved plant architecture, photosynthetic capacity and even yield.

The introduction of transgenic cotton (Bt-cotton) for controlling bollworms has resulted in increased production; however, the residual effects of mulches from Bt-cotton are poorly understood. Therefore, the current study evaluated the impact of Bt and non-Bt cotton mulches on soil properties, weed dynamics and yield of winter crops sown after cotton. Three different winter crops, i.e., wheat (Triticum aestivum L.), canola (Brassica napus L.) and Egyptian clover (Trifolium alexandrinum L.) and two mulch types, i.e., Bt mulch (obtained from Bt-cotton cultivars, i.e., 'CIM-616' and 'GH-Mubarik') and non-Bt mulch (obtained from non-Bt cultivars, i.e., 'CIM-620' and 'N-414') were included in the study. The mulches were applied at a rate of 2 t ha-1 before planting the winter crops. The Bt and non-Bt mulches differentially affected soil properties, weed dynamics and productivity of winter crops. The non-Bt mulches decreased the soil bulk density and penetration resistance, while increased the soil porosity. Wheat crop increased the soil porosity, pH, available N and soil organic matter content. Overall, non-Bt mulches improved the productivity of winter crops compared with Bt mulches. The toxins released by Bt mulches lowered the weed density; however, it negatively influenced soil properties (bulk density and available nitrogen) and productivity of winter crops. Therefore, appropriate crop rotation measures may be opted for the soils cultivated with Bt-cotton to conserve soil and achieve yield sustainability for the crops sown after cotton. Nonetheless, non-Bt mulches can be used for improving soil properties and productivity of winter crops., Competing Interests: The authors have declared that no competing interests exist.

Leaf angle (LA), defined as the angle between the plant stem and leaf adaxial side of the blade, generally shapes the plant architecture into a loosen or dense structure, and thus influences the light interception and competition between neighboring plants in natural settings, ultimately contributing to the crop yield and productivity. It has been elucidated that brassinosteroid (BR) plays a dominant role in determining LA, and other phytohormones also positively or negatively participate in regulating LA. Accumulating evidences have revealed that these phytohormones interact with each other in modulating various biological processes. However, the comprehensive discussion of how the phytohormones and their interaction involved in shaping LA is relatively lack. Here, we intend to summarize the advances in the LA regulation mediated by the phytohormones and their crosstalk in different plant species, mainly in rice and maize, hopefully providing further insights into the genetic manipulation of LA trait in crop breeding and improvement in regarding to overcoming the challenge from the continuous demands for food under limited arable land area.

To test the hypothesis that multiple integrated root phenotypes would co-optimize drought tolerance, we phenotyped the root anatomy and architecture of 400 mature maize ( Zea mays ) genotypes under well-watered and water-stressed conditions in the field. We found substantial variation in all 23 root phenes measured. A phenotypic bulked segregant analysis revealed that bulks representing the best and worst performers in the field displayed distinct root phenotypes. In contrast to the worst bulk, the root phenotype of the best bulk under drought consisted of greater cortical aerenchyma formation, more numerous and narrower metaxylem vessels, and thicker nodal roots. Partition-against-medians clustering revealed several clusters of unique root phenotypes related to plant performance under water stress. Clusters associated with improved drought tolerance consisted of phene states that likely enable greater soil exploration by reallocating internal resources to greater root construction (increased aerenchyma content, larger cortical cells, fewer cortical cell files), restrict uptake of water to conserve soil moisture (reduced hydraulic conductance, narrow metaxylem vessels), and improve penetrability of hard, dry soils (thick roots with a larger proportion of stele, and smaller distal cortical cells). We propose that the most drought-tolerant-integrated phenotypes merit consideration as breeding ideotypes., (© 2020 American Society of Plant Biologists. All Rights Reserved.)

Chemicals used to assure agricultural production and the feasibility of planting sites often end up in bodies of water used for crop irrigation. In a pot study, we investigated the consequences associated with the irrigation of maize with water contaminated by ciprofloxacin (Cipro; 0, 0.2, 0.8, 1.4 and 2.0 μg l -1 ) and/or glyphosate (0, 5, 25 and 50 mg l -1 ) on yields and food safety. Glyphosate in concentrations ≥25 mg l -1 prevented plant establishment, regardless of Cipro presence. Evaluations made at the V5 stage of plants reveal that Cipro concentrations ≥0.8 μg l -1 and glyphosate decreased photosynthesis and induced changes in leaf anatomy and stem biophysical properties that may contribute to decreased kernel yields. When those chemicals were applied together, kernel yield reductions were accentuated, evidencing their interactive effects. Irrigation with contaminated water resulted in accumulations of Cipro and glyphosate (as well as its metabolite, aminomethylphosphonic acid) in plant tissues. Accumulation of these chemicals in plant tissues such as leaves and kernels is a problem, since they are used to feed animals and humans. Moreover, these chemicals are of potential toxicological concern, principally due to residue accumulations in the food chain. Specially, the antibiotic residue accumulations in maize tissues can assist the induction of antibiotic resistance in dangerous bacteria. Therefore, we point out the urgency of monitoring the quality of water used for crop irrigation to avoid economic and food-quality losses., Competing Interests: Declaration of interests The authors declare no conflit of interest.Stephen.duke@ars.usda.gov Krishna.reddy@usda.gov, (Copyright © 2020 Elsevier Inc. All rights reserved.)

Background: Citrus is one of the most important fruit crops worldwide. Fluazinam is a fungicide that is used to control fungal diseases, and its dissipation and residue in citrus fruits should be studied., Results: A Quick, Easy, Cheap, Effective, Rugged and Safe (QuEChERS) procedure combined with gas chromatography with an electron capture detector (GC-ECD) has been developed. The fortified recoveries ranged from 82.1% to 105.9%, with relative standard deviations (RSDs) of less than 5.7%. Fluazinam dissipated relatively quickly following first-order kinetics, with a half-life of 8.5-9.5 days. The experiments on the terminal residue of fluazinam in citrus were conducted at six locations in China, and the risk quotient (RQ) method was applied to citrus fruits for dietary exposure risk assessment based on the terminal residue test. The RQs of fluazinam at three preharvest intervals (PHIs) (21, 28, and 35 days) were all less than 100%, which is an acceptable level for human consumption. The present study provides a reference for the establishment of maximum residue limit (MRL) for fluazinam in citrus., Conclusions: The dissipation and residues of fluazinam in citrus were monitored. The half-life of less than 10 days showed that fluazinam could degrade relatively easily in citrus. The risk assessment also indicated the intake safety of fluazinam in citrus. © 2019 Society of Chemical Industry., (© 2019 Society of Chemical Industry.)

The timing and duration of flowering are key agronomic traits that are often associated with the ability of a variety to escape abiotic stress such as heat and drought. Flowering information is valuable in both plant breeding and agricultural production management. Visual assessment, the standard protocol used for phenotyping flowering, is a low-throughput and subjective method. In this study, we evaluated multiple imaging sensors (RGB and multiple multispectral cameras), image resolution (proximal/remote sensing at 1.6 to 30 m above ground level/AGL), and image processing (standard and unsupervised learning) techniques in monitoring flowering intensity of four cool-season crops (canola, camelina, chickpea, and pea) to enhance the accuracy and efficiency in quantifying flowering traits. The features (flower area, percentage of flower area with respect to canopy area) extracted from proximal (1.6-2.2 m AGL) RGB and multispectral (with near infrared, green and blue band) image data were strongly correlated ( r up to 0.89) with visual rating scores, especially in pea and canola. The features extracted from unmanned aerial vehicle integrated RGB image data (15-30 m AGL) could also accurately detect and quantify large flowers of winter canola ( r up to 0.84), spring canola ( r up to 0.72), and pea ( r up to 0.72), but not camelina or chickpea flowers. When standard image processing using thresholds and unsupervised machine learning such as k-means clustering were utilized for flower detection and feature extraction, the results were comparable. In general, for applicability of imaging for flower detection, it is recommended that the image data resolution (i.e., ground sampling distance) is at least 2-3 times smaller than that of the flower size. Overall, this study demonstrates the feasibility of utilizing imaging for monitoring flowering intensity in multiple varieties of evaluated crops.

Background: Weeds are a major cause of low agricultural productivity. Some weeds have morphological features similar to crops, making them difficult to discriminate., Results: We propose a novel method using a combination of filtered features extracted by combined Local Binary Pattern operators and features extracted by plant-leaf contour masks to improve the discrimination rate between broadleaf plants. Opening and closing morphological operators were applied to filter noise in plant images. The images at 4 stages of growth were collected using a testbed system. Mask-based local binary pattern features were combined with filtered features and a coefficient k. The classification of crops and weeds was achieved using support vector machine with radial basis function kernel. By investigating optimal parameters, this method reached a classification accuracy of 98.63% with 4 classes in the "bccr-segset" dataset published online in comparison with an accuracy of 91.85% attained by a previously reported method., Conclusions: The proposed method enhances the identification of crops and weeds with similar appearance and demonstrates its capabilities in real-time weed detection., (© The Author(s) 2020. Published by Oxford University Press.)

All plants must allocate limited resources to survival, growth, and reproduction. In natural species, allocation strategies reflect trade-offs between survivorship risk and subsequent fitness benefits and are therefore central to a species' ecology. Artificial selection on allocation has generated high-yielding crops that often invest the bare minimum in defense or longevity. Ecological, genetic, and evolutionary analyses of plant life history - particularly with respect to longevity and resource allocation along an axis from annual to perennial species - provides a framework to evaluate trade-offs in plant-environment interactions in natural and managed systems. Recent efforts to develop new model plant systems for research and to increase agricultural resilience and efficiency by developing herbaceous perennial crops motivates our critical assessment of traditional assumptions regarding differences between annual and perennial plant species. Here, we review our present understanding of the genetic basis of physiological, developmental, and anatomical differences in wild and crop species and reach two broad conclusions. First, that perenniality and annuality should be considered syndromes comprised of many interacting traits, and that elucidating the genetic basis of these traits is required to assess models of evolution and to develop successful breeding strategies. Modern phenomic and biotechnology tools will facilitate these enquiries. Second, many classic assumptions about the difference between the two syndromes are supported by limited evidence. Throughout this Review, we highlight key knowledge gaps in the proximate and ultimate mechanisms driving life history variation, and suggest empirical approaches to parameterize trade-offs and to make progress in this critical area of direct relevance to ecology and plant performance in a changing world., (Copyright © 2020 Elsevier Ltd. All rights reserved.)

Background: The genus Elaeis has two species of economic importance for the oil palm agroindustry: Elaeis oleifera (O), native to the Americas, and Elaeis guineensis (G), native to Africa. This work provides to our knowledge, the first association mapping study in an interspecific OxG oil palm population, which shows tolerance to pests and diseases, high oil quality, and acceptable fruit bunch production., Results: Using genotyping-by-sequencing (GBS), we identified a total of 3776 single nucleotide polymorphisms (SNPs) that were used to perform a genome-wide association analysis (GWAS) in 378 OxG hybrid population for 10 agronomic traits. Twelve genomic regions (SNPs) were located near candidate genes implicated in multiple functional categories, such as tissue growth, cellular trafficking, and physiological processes., Conclusions: We provide new insights on genomic regions that mapped on candidate genes involved in plant architecture and yield. These potential candidate genes need to be confirmed for future targeted functional analyses. Associated markers to the traits of interest may be valuable resources for the development of marker-assisted selection in oil palm breeding.

Main Conclusion: The variability in nutrient content and morphology in Gynandropsis gynandra is associated with the geographic origin of the accessions and provides a basis for breeding for higher levels of vitamin C, carotenoids or tocopherols in higher-yielding cultivars. We examined the variation in carotenoids, tocopherols and ascorbic acid as well as morphological traits in a worldwide germplasm of 76 accessions of the orphan leafy vegetable Gynandropsis gynandra (Cleomaceae) using greenhouse experiments and high-performance liquid chromatography analysis. The levels of carotenoids and tocopherols accumulating in the leaves varied significantly across accessions and were linked with the geographical origin and morphological variation. The main carotenoids included lutein, β-carotene, α-carotene and violaxanthin. A twofold to threefold variation was observed for these compounds. The main tocopherols detected were α-tocopherol and γ-tocopherol with a 20-fold variation. A ninefold variation in vitamin C concentration and independent of geographical origin was observed. Overall, the accessions were grouped into three clusters based on variation in nutrient content and morphology. West African accessions were short plants with small leaves and with high tocopherol contents and relatively low carotenoid contents, Asian accessions were short plants with broad leaves and with relatively low carotenoid and high tocopherol contents, while East-Southern African plants were tall with high contents of both carotenoids and chlorophylls and low tocopherol contents. Carotenoids were positively correlated with plant height as well as foliar and floral traits but negatively correlated with tocopherols. The absence of a significant correlation between vitamin C and other traits indicated that breeding for high carotenoids or tocopherols content may be coupled with improved leaf yield and vitamin C content. Our study provides baseline information on the natural variation available for traits of interest for breeding for enhanced crop yield and nutrient content in Gynandropsis gynandra.

Background: High-quality plant phenotyping and climate data lay the foundation for phenotypic analysis and genotype-environment interaction, providing important evidence not only for plant scientists to understand the dynamics between crop performance, genotypes, and environmental factors but also for agronomists and farmers to closely monitor crops in fluctuating agricultural conditions. With the rise of Internet of Things technologies (IoT) in recent years, many IoT-based remote sensing devices have been applied to plant phenotyping and crop monitoring, which are generating terabytes of biological datasets every day. However, it is still technically challenging to calibrate, annotate, and aggregate the big data effectively, especially when they were produced in multiple locations and at different scales., Findings: CropSight is a PHP Hypertext Pre-processor and structured query language-based server platform that provides automated data collation, storage, and information management through distributed IoT sensors and phenotyping workstations. It provides a two-component solution to monitor biological experiments through networked sensing devices, with interfaces specifically designed for distributed plant phenotyping and centralized data management. Data transfer and annotation are accomplished automatically through an hypertext transfer protocol-accessible RESTful API installed on both device side and server side of the CropSight system, which synchronize daily representative crop growth images for visual-based crop assessment and hourly microclimate readings for GxE studies. CropSight also supports the comparison of historical and ongoing crop performance while different experiments are being conducted., Conclusions: As a scalable and open-source information management system, CropSight can be used to maintain and collate important crop performance and microclimate datasets captured by IoT sensors and distributed phenotyping installations. It provides near real-time environmental and crop growth monitoring in addition to historical and current experiment comparison through an integrated cloud-ready server system. Accessible both locally in the field through smart devices and remotely in an office using a personal computer, CropSight has been applied to field experiments of bread wheat prebreeding since 2016 and speed breeding since 2017. We believe that the CropSight system could have a significant impact on scalable plant phenotyping and IoT-style crop management to enable smart agricultural practices in the near future., (© The Author(s) 2019. Published by Oxford University Press.)

Breeding for Fusarium head blight (FHB) resistance in durum wheat is complicated by the quantitative trait expression and narrow genetic diversity of available resources. High-density mapping of the FHB resistance quantitative trait loci (QTL), evaluation of their co-localization with plant height and maturity QTL and the interaction among the identified QTL are the objectives of this study. Two doubled haploid (DH) populations, one developed from crosses between Triticum turgidum ssp. durum lines DT707 and DT696 and the other between T. turgidum ssp. durum cv. Strongfield and T. turgidum ssp. carthlicum cv. Blackbird were genotyped using the 90K Infinium iSelect chip and evaluated phenotypically at multiple field FHB nurseries over years. A moderate broad-sense heritability indicated a genotype-by-environment interaction for the expression of FHB resistance in both populations. Resistance QTL were identified for the DT707 × DT696 population on chromosomes 1B, 2B, 5A (two loci) and 7A and for the Strongfield × Blackbird population on chromosomes 1A, 2A, 2B, 3A, 6A, 6B and 7B with the QTL on chromosome 1A and those on chromosome 5A being more consistently expressed over environments. FHB resistance co-located with plant height and maturity QTL on chromosome 5A and with a maturity QTL on chromosome 7A for the DT707 × DT696 population. Resistance also co-located with plant height QTL on chromosomes 2A and 3A and with maturity QTL on chromosomes 1A and 7B for the Strongfield × Blackbird population. Additive × additive interactions were identified, for example between the two FHB resistance QTL on chromosome 5A for the DT707 × DT696 population and the FHB resistance QTL on chromosomes 1A and 7B for the Strongfield × Blackbird population. Application of the Single Nucleotide Polymorphic (SNP) markers associated with FHB resistance QTL identified in this study will accelerate combining genes from the two populations., Competing Interests: The authors have declared that no competing interests exist.

With climate change and an ever-increasing human population threatening food security, developing a better understanding of the genetic basis of crop performance under stressful conditions has become increasingly important. Here, we used genome-wide association studies to genetically dissect variation in seedling growth traits in cultivated sunflower (Helianthus annuus L.) under well-watered and water-limited (i.e., osmotic stress) conditions, with a particular focus on root morphology. Water limitation reduced seedling size and produced a shift toward deeper rooting. These effects varied across genotypes, and we identified 13 genomic regions that were associated with traits of interest across the two environments. These regions varied in size from a single marker to 186.2 Mbp and harbored numerous genes, some of which are known to be involved in the plant growth/development as well as the response to osmotic stress. In many cases, these associations corresponded to growth traits where the common allele outperformed the rare variant, suggesting that selection for increased vigor during the evolution of cultivated sunflower might be responsible for the relatively high frequency of these alleles. We also found evidence of pleiotropy across multiple traits, as well as numerous environmentally independent genetic effects. Overall, our results indicate the existence of genetic variation in root morphology and allocation and further suggest that the majority of alleles associated with these traits have consistent effects across environments., Competing Interests: The authors have declared that no competing interests exist.

Root systems that improve resource uptake and penetrate compacted soil (hardpan) are important for improving soybean (Glycine max L. Merr.) productivity in optimal and sub-optimal environments. The objectives of this research were to evaluate a soybean germplasm collection of 49 genotypes for root traits, determine whether root traits are related with plant height, shoot dry weight, chlorophyll index, and seed size, and identify genotypes that can penetrate a hardpan. Plants were maintained under optimal growth conditions in a greenhouse. Single plants were grown in mesocosms, constructed of two stacked columns (top and bottom columns had 25 and 46 cm height, respectively, and 15 cm inside diameter) with a 2-cm thick wax layer (synthetic hardpan; penetration resistance, 1.5 MPa at 30°C) in between. Plants were harvested at 42 days after planting. Significant genetic variability was observed for root traits in the soybean germplasm collection, and genotypes that penetrated the synthetic hardpan were identified. Genotypes NTCPR94-5157, NMS4-1-83, and N09-13128 were ranked high and PI 424007 and R01-581F were ranked low for most root traits. Shoot dry weight and chlorophyll index were positively related with total root length, surface area, and volume, and fine root length (Correlation coefficient, r ≥ 0.60 and P-value < 0.0001 for shoot dry weight and r ≥ 0.37 and P-value < 0.01 for chlorophyll index]. Plant height was negatively correlated with total root surface area, total root volume, and average root diameter (|r| ≥ 0.29, P-value < 0.05). Seed size was not correlated with any root traits. The genetic variability identified in this research for root traits and penetration are critical for soybean improvement programs in choosing genotypes with improved root characteristics to increase yield in stressful or optimum environments., Competing Interests: The authors have declared that no competing interests exist.

False banana /Ensete ventricosum [Welw.] Cheesman/ is exploited as a food crop in Ethiopia where it represents an important staple food. The plant is harvested and large amounts of biomass residues are originated, mainly from the pseudo stem (i.e., fiber bundles obtained from the leaf sheaths after being scrapped to produce starchy food) and the inflorescence stalk. These materials were studied in relation to their summative chemical composition, composition of lignin, lipophilic and polar extracts. Moreover, their structural characteristics, in view of their valorization, were scrutinized. The analytical studies were performed with the aid of FTIR, GC/MS, Py-GC/MS and SEM. The fiber bundles are aggregates of mainly long and slender fibers with low ash, extractives and lignin contents (3.8%. 4.4% and 10.5% respectively) and high holocellulose and α-cellulose contents (87.5% and 59.6% respectively). The hemicelluloses in the fibers are mostly highly acetylated xylans and the lignin is of the H-type (H:G:S, 1:0.7:0.8). This lignin composition is in line with the FTIR peaks at 1670 cm-1 and 1250 cm-1.The inflorescence stalk has high ash content (12.3% in the main stalk and 24.6% in fines) with a major proportion of potassium, high extractives (25.9%), and low lignin and α-cellulose contents (5.8% and 17.9% respectively). The stalk includes numerous starch granules in the cellular structure with the predominant presence of parenchyma. The potential valorization routes for these materials are clearly different. The fiber bundles could be used as a fiber source for paper pulp production with the possibility of a prior hemicelluloses removal while the inflorescence stalk has nutritional value for food and fodder. Furthermore, it can also be used for sugar fermentation products., Competing Interests: The authors have declared that no competing interests exist.