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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.)

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

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.

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.

Plant roots growing through soil typically encounter considerable structural heterogeneity, and local variations in soil dry bulk density. The way the in situ architecture of root systems of different species respond to such heterogeneity is poorly understood due to challenges in visualising roots growing in soil. The objective of this study was to visualise and quantify the impact of abrupt changes in soil bulk density on the roots of three cover crop species with contrasting inherent root morphologies, viz. tillage radish (Raphanus sativus), vetch (Vicia sativa) and black oat (Avena strigosa). The species were grown in soil columns containing a two-layer compaction treatment featuring a 1.2 g cm-3 (uncompacted) zone overlaying a 1.4 g cm-3 (compacted) zone. Three-dimensional visualisations of the root architecture were generated via X-ray computed tomography, and an automated root-segmentation imaging algorithm. Three classes of behaviour were manifest as a result of roots encountering the compacted interface, directly related to the species. For radish, there was switch from a single tap-root to multiple perpendicular roots which penetrated the compacted zone, whilst for vetch primary roots were diverted more horizontally with limited lateral growth at less acute angles. Black oat roots penetrated the compacted zone with no apparent deviation. Smaller root volume, surface area and lateral growth were consistently observed in the compacted zone in comparison to the uncompacted zone across all species. The rapid transition in soil bulk density had a large effect on root morphology that differed greatly between species, with major implications for how these cover crops will modify and interact with soil structure.

Traditional methods for trait phenotyping have been a bottleneck for research in many crop species due to their intensive labor, high cost, complex implementation, lack of reproducibility and propensity to subjective bias. Recently, multiple high-throughput phenotyping platforms have been developed, but most of them are expensive, species-dependent, complex to use, and available only for major crops. To overcome such limitations, we present the open-source software GiNA, which is a simple and free tool for measuring horticultural traits such as shape- and color-related parameters of fruits, vegetables, and seeds. GiNA is multiplatform software available in both R and MATLAB® programming languages and uses conventional images from digital cameras with minimal requirements. It can process up to 11 different horticultural morphological traits such as length, width, two-dimensional area, volume, projected skin, surface area, RGB color, among other parameters. Different validation tests produced highly consistent results under different lighting conditions and camera setups making GiNA a very reliable platform for high-throughput phenotyping. In addition, five-fold cross validation between manually generated and GiNA measurements for length and width in cranberry fruits were 0.97 and 0.92. In addition, the same strategy yielded prediction accuracies above 0.83 for color estimates produced from images of cranberries analyzed with GiNA compared to total anthocyanin content (TAcy) of the same fruits measured with the standard methodology of the industry. Our platform provides a scalable, easy-to-use and affordable tool for massive acquisition of phenotypic data of fruits, seeds, and vegetables.

Banana (Musa sp.) is a vegetatively propagated, low fertility, potentially hybrid and polyploid crop. These qualities make the breeding and targeted genetic improvement of this crop a difficult and long process. The Genome-Wide Association Study (GWAS) approach is becoming widely used in crop plants and has proven efficient to detecting candidate genes for traits of interest, especially in cereals. GWAS has not been applied yet to a vegetatively propagated crop. However, successful GWAS in banana would considerably help unravel the genomic basis of traits of interest and therefore speed up this crop improvement. We present here a dedicated panel of 105 accessions of banana, freely available upon request, and their corresponding GBS data. A set of 5,544 highly reliable markers revealed high levels of admixture in most accessions, except for a subset of 33 individuals from Papua. A GWAS on the seedless phenotype was then successfully applied to the panel. By applying the Mixed Linear Model corrected for both kinship and structure as implemented in TASSEL, we detected 13 candidate genomic regions in which we found a number of genes potentially linked with the seedless phenotype (i.e. parthenocarpy combined with female sterility). An additional GWAS performed on the unstructured Papuan subset composed of 33 accessions confirmed six of these regions as candidate. Out of both sets of analyses, one strong candidate gene for female sterility, a putative orthologous gene to Histidine Kinase CKI1, was identified. The results presented here confirmed the feasibility and potential of GWAS when applied to small sets of banana accessions, at least for traits underpinned by a few loci. As phenotyping in banana is extremely space and time-consuming, this latest finding is of particular importance in the context of banana improvement.

DCPTA (2-diethylaminoethyl-3, 4-dichlorophenylether) and CCC (2-chloroethyltrimethyl- ammonium chloride) have a great effect on maize growth, but applying DCPTA individually can promote the increase of plant height, resulting in the rise of lodging percent. Plant height and lodging percent decrease in CCC-treated plants, but the accumulation of biomass reduce, resulting in yield decrease. Based on the former experiments, the performance of a mixture which contained 40 mg DCPTA and 20 mg CCC as active ingredients per liter of solution, called PCH was tested with applying 40mg/L DCPTA and 20mg/L CCC individually. Grain yield, yield components, internode characters, leaf area per plant, plant height and lodging percent as well as chlorophyll content, chlorophyll fluorescence, enzymatic antioxidants, membranous peroxide and organic osmolyte were analyzed in two years (2011 and 2012), using maize hybrid, Zhengdan 958 (ZD 958) at density of 6.75 plants m-2. CCC, DCPTA and PCH were sprayed on the whole plant leaves at 7 expanded leaves stage and water was used as control. Compared to control, PCH significantly increased grain yield (by 9.53% and 6.68%) from 2011 to 2012. CCC significantly decreased kernel number per ear (by 6.78% and 5.69%) and thousand kernel weight (TKW) (by 8.57% and 6.55%) from 2011 to 2012. Kernel number per ear and TKW increased in DCPTA-treated and PCH-treated plants, but showed no significant difference between them. In CCC-treated and PCH-treated plants, internode length and plant height decreased, internode diameter increased, resulting in the significant decline of lodging percent. With DCPTA application, internode diameter increased, but internode length and plant height increased at the same time, resulting in the augment of lodging percent. Bending strength and puncture strength were increased by applying different plant growth regulators (PGRs). In PCH-treated plants, bending strength and puncture strength were greater than other treatments. Compared to control, the bending strength of 3rd internode was increased by 14.47% in PCH-treated plants in 2011, increased by 18.40% in 2012, and the difference was significant. Puncture strength of 1st, 3rd and 5th internode was increased by 37.25%, 29.17% and 26.09% in 2011 and 34.04%, 25% and 23.68% in 2012, compared to control. Leaf area and dry weight per plant reduced significantly in CCC-treated plants, increased in DCPTA-treated and PCH-treated plants from 2011 to 2012. Chlorophyll content and chlorophyll fluorescence improved with CCC and DCPTA application. Due to the additive effect of DCPTA and CCC, PCH showed the significant effect on chlorophyll content and chlorophyll fluorescence. Compared to control, total enzyme activity (SOD, POD, CAT, APX and GR) and soluble protein content increased, malonaldehyde (MDA) and hydrogen peroxide (H2O2) content reduced in PCH-treated plants. The transportation of soluble sugar from leaf to kernel improved significantly at the late silking stage. The research provided the way for the further use of DCPTA and CCC into the production practice.

A procedure to achieve the semi-automatic relative image normalization of multitemporal remote images of an agricultural scene called ARIN was developed using the following procedures: 1) defining the same parcel of selected vegetative pseudo-invariant features (VPIFs) in each multitemporal image; 2) extracting data concerning the VPIF spectral bands from each image; 3) calculating the correction factors (CFs) for each image band to fit each image band to the average value of the image series; and 4) obtaining the normalized images by linear transformation of each original image band through the corresponding CF. ARIN software was developed to semi-automatically perform the ARIN procedure. We have validated ARIN using seven GeoEye-1 satellite images taken over the same location in Southern Spain from early April to October 2010 at an interval of approximately 3 to 4 weeks. The following three VPIFs were chosen: citrus orchards (CIT), olive orchards (OLI) and poplar groves (POP). In the ARIN-normalized images, the range, standard deviation (s. d.) and root mean square error (RMSE) of the spectral bands and vegetation indices were considerably reduced compared to the original images, regardless of the VPIF or the combination of VPIFs selected for normalization, which demonstrates the method's efficacy. The correlation coefficients between the CFs among VPIFs for any spectral band (and all bands overall) were calculated to be at least 0.85 and were significant at P = 0.95, indicating that the normalization procedure was comparably performed regardless of the VPIF chosen. ARIN method was designed only for agricultural and forestry landscapes where VPIFs can be identified.