Mapping of a Quantitative Trait Locus for Stay-Green Trait in Common Wheat

The stay-green (SG) trait enhances photosynthetic activity during the late grain-filling period, benefiting grain yield under drought and heat stresses. CH7034 is a wheat breeding line with SG. To clarify the SG loci carried by CH7034 and obtain linked molecular markers, in this study, a recombinant inbred line (RIL) population derived from the cross between CH7034 and non-SG SY95-71 was genotyped using the Wheat17K single-nucleotide polymorphism (SNP) array, and a high-density genetic map covering 21 chromosomes and consisting of 2159 SNP markers was constructed. Then, the chlorophyll content of flag leaf from each RIL was estimated for mapping, and one QTL for SG on chromosome 7D was identified, temporarily named QSg.sxau-7D, with the maximum phenotypic variance explained of 8.81~11.46%. A PCR-based diagnostic marker 7D-16 for QSg.sxau-7D was developed, and the CH7034 allele of 7D-16 corresponded to the higher flag leaf chlorophyll content, while the 7D-16 SY95-71 allele corresponded to the lower value, which confirmed the genetic effect on SG of QSg.sxau-7D. QSg.sxau-7D located in the 526.4~556.2 Mbp interval is different from all the known SG loci on chromosome 7D, and 69 high-confidence annotated genes within the interval expressed throughout the entire period of flag leaf senescence. Moreover, results of an association analysis based on the diagnostic marker showed that there is a positive correlation between QSg.sxau-7D and thousand-grain weight. Our results revealed a novel QTL QSg.sxau-7D whose CH7034 allele had a strong effect on SG, which can be applied in further wheat molecular breeding.

Performing whole-genome association analysis of winter wheat plant height using the 55K chip

Plant height is a critical agronomic that affects both plant architecture and yield. To decipher the genetic mechanisms underlying winter wheat plant height and identify candidate genes associated with this trait, we conducted phenotypic analysis on 239 wheat varieties (lines) collected from around the world. This analysis was complemented by genotyping using the wheat 55K SNP chip. A Wholegenome association analysis (GWAS) of wheat plant height was conducted utilizing the MLM (Q+K) model within TASSLE software. The results revealed significant phenotypic variation in wheat plant height across different years, with coefficients of variation ranging from 0.96% to 1.97%. Additionally, there was a strong correlation in plant height measurements between different years. GWAS identified 44 SNP markers significantly associated with wheat plant height across various environments (P ≤ 0.00001), predominantly distributed on chromosomes 1B, 1D, 2A, 2B, 2D, 3B, 3D, 4A, 4B, 6B, 6D, and 7D, explaining individual phenotypic variance rates ranging from 5.00% to 11.11%. Further, by mining association loci with substantial phenotypic effects and stability across multiple environments, seven candidate genes related to wheat plant height have been identified. This study provides new genetic markers and resources for improving wheat plant height.

Enhancing Winter Wheat Soil-Plant Analysis Development Value Prediction through Evaluating Unmanned Aerial Vehicle Flight Altitudes, Predictor Variable Combinations, and Machine Learning Algorithms

Monitoring winter wheat Soil-Plant Analysis Development (SPAD) values using Unmanned Aerial Vehicles (UAVs) is an effective and non-destructive method. However, predicting SPAD values during the booting stage is less accurate than other growth stages. Existing research on UAV-based SPAD value prediction has mainly focused on low-altitude flights of 10-30 m, neglecting the potential benefits of higher-altitude flights. The study evaluates predictions of winter wheat SPAD values during the booting stage using Vegetation Indices (VIs) from UAV images at five different altitudes (i.e., 20, 40, 60, 80, 100, and 120 m, respectively, using a DJI P4-Multispectral UAV as an example, with a resolution from 1.06 to 6.35 cm/pixel). Additionally, we compare the predictive performance using various predictor variables (VIs, Texture Indices (TIs), Discrete Wavelet Transform (DWT)) individually and in combination. Four machine learning algorithms (Ridge, Random Forest, Support Vector Regression, and Back Propagation Neural Network) are employed. The results demonstrate a comparable prediction performance between using UAV images at 120 m (with a resolution of 6.35 cm/pixel) and using the images at 20 m (with a resolution of 1.06 cm/pixel). This finding significantly improves the efficiency of UAV monitoring since flying UAVs at higher altitudes results in greater coverage, thus reducing the time needed for scouting when using the same heading overlap and side overlap rates. The overall trend in prediction accuracy is as follows: VIs + TIs + DWT > VIs + TIs > VIs + DWT > TIs + DWT > TIs > VIs > DWT. The VIs + TIs + DWT set obtains frequency information (DWT), compensating for the limitations of the VIs + TIs set. This study enhances the effectiveness of using UAVs in agricultural research and practices.

Prediction of wheat SPAD using integrated multispectral and support vector machines

Rapidly obtaining the chlorophyll content of crop leaves is of great significance for timely diagnosis of crop health and effective field management. Multispectral imagery obtained from unmanned aerial vehicles (UAV) is being used to remotely sense the SPAD (Soil and Plant Analyzer Development) values of wheat crops. However, existing research has not yet fully considered the impact of different growth stages and crop populations on the accuracy of SPAD estimation. In this study, 300 materials from winter wheat natural populations in Xinjiang, collected between 2020 to 2022, were analyzed. UAV multispectral images were obtained in the experimental area, and vegetation indices were extracted to analyze the correlation between the selected vegetation indices and SPAD values. The input variables for the model were screened, and a support vector machine (SVM) model was constructed to estimate SPAD values during the heading, flowering, and filling stages under different water stresses. The aim was to provide a method for the rapid acquisition of winter wheat SPAD values. The results showed that the SPAD values under normal irrigation were higher than those under water restriction. Multiple vegetation indices were significantly correlated with SPAD values. In the prediction model construction of SPAD, the different models had high estimation accuracy under both normal irrigation and water limitation treatments, with correlation coefficients of predicted and measured values under normal irrigation in different environments the value of r from 0.59 to 0.81 and RMSE from 2.15 to 11.64, compared to RE from 0.10% to 1.00%; and under drought stress in different environments, correlation coefficients of predicted and measured values of r was 0.69-0.79, RMSE was 2.30-12.94, and RE was 0.10%-1.30%. This study demonstrated that the optimal combination of feature selection methods and machine learning algorithms can lead to a more accurate estimation of winter wheat SPAD values. In summary, the SVM model based on UAV multispectral images can rapidly and accurately estimate winter wheat SPAD value.

Multispectral Phenotyping and Genetic Analyses of Spring Appearance in Greening Plant, Phedimus spp

The change in appearance during the seasonal transitions in ornamental greening plants is an important characteristic. In particular, the early onset of green leaf color is a desirable trait for a cultivar. In this study, we established a method for phenotyping leaf color change by multispectral imaging and performed genetic analysis based on the phenotypes to clarify the potential of the approach in breeding greening plants. We performed multispectral phenotyping and quantitative trait locus (QTL) analysis of an F₁ population derived from 2 parental lines of Phedimus takesimensis, known to be a drought and heat-tolerant rooftop plant species. The imaging was conducted in April of 2019 and 2020 when dormancy breakage occurs and growth extension begins. Principal component analysis of 9 different wavelength values showed a high contribution from the first principal component (PC1), which captured variation in the visible light range. The high interannual correlation in PC1 and in the intensity of visible light indicated that the multispectral phenotyping captured genetic variation in the color of leaves. We also performed restriction site-associated DNA sequencing and obtained the first genetic linkage map of Phedimus spp. QTL analysis revealed 2 QTLs related to early dormancy breakage. Based on the genotypes of the markers underlying these 2 QTLs, the F₁ phenotypes with early (late) dormancy break, green (red or brown) leaves, and a high (low) degree of vegetative growth were classified. The results suggest the potential of multispectral phenotyping in the genetic dissection of seasonal leaf color changes in greening plants.

Migrating from Invasive to Noninvasive Techniques for Enhanced Leaf Chlorophyll Content Estimations Efficiency

Leaf chlorophyll is vital for plants because it helps them get energy through the process of photosynthesis. The present review thus examines various leaf chlorophyll content estimation techniques in laboratories and outdoor field conditions. The review consists of two sections: (1) destructive and (2) nondestructive methods for chlorophyll estimation. Through this review, we could find that Arnon's spectrophotometry method is the most popular and simplest method for the estimation of leaf chlorophyll under laboratory conditions. While android-based applications and portable equipment for the quantification of chlorophyll content are useful for onsite utilities. The algorithm used in these applications and equipment is trained for specific plants rather than being generalized across all plants. In the case of hyperspectral remote sensing, more than 42 hyperspectral indices were observed for chlorophyll estimations, and among these red-edge-based indices were found to be more appropriate. This review recommends that hyperspectral indices such as the three-band hyperspectral vegetation index, Chlgreen, Triangular Greenness Index, Wavelength Difference Index, and Normalized Difference Chlorophyll are generic and can be used for chlorophyll estimations of various plants. It was also observed that Artificial Intelligence (AI) and Machine Learning (ML)-based algorithms such as Random Forest, Support Vector Machine, and Artificial Neural Network regressions are the most suited and widely applied algorithms for chlorophyll estimation using the above hyperspectral data. It was also concluded that comparative studies are required in order to understand the advantages and disadvantages of reflectance-based vegetation indices and chlorophyll fluorescence imaging methods for chlorophyll estimations to comprehend their efficiency.

Dynamic UAV Phenotyping for Rice Disease Resistance Analysis Based on Multisource Data

Bacterial blight poses a threat to rice production and food security, which can be controlled through large-scale breeding efforts toward resistant cultivars. Unmanned aerial vehicle (UAV) remote sensing provides an alternative means for the infield phenotype evaluation of crop disease resistance to relatively time-consuming and laborious traditional methods. However, the quality of data acquired by UAV can be affected by several factors such as weather, crop growth period, and geographical location, which can limit their utility for the detection of crop disease and resistant phenotypes. Therefore, a more effective use of UAV data for crop disease phenotype analysis is required. In this paper, we used time series UAV remote sensing data together with accumulated temperature data to train the rice bacterial blight severity evaluation model. The best results obtained with the predictive model showed an R _p ² of 0.86 with an RMSE_p of 0.65. Moreover, model updating strategy was used to explore the scalability of the established model in different geographical locations. Twenty percent of transferred data for model training was useful for the evaluation of disease severity over different sites. In addition, the method for phenotypic analysis of rice disease we built here was combined with quantitative trait loci (QTL) analysis to identify resistance QTL in genetic populations at different growth stages. Three new QTLs were identified, and QTLs identified at different growth stages were inconsistent. QTL analysis combined with UAV high-throughput phenotyping provides new ideas for accelerating disease resistance breeding.

Identifying and Counting Tobacco Plants in Fragmented Terrains Based on Unmanned Aerial Vehicle Images in Beipanjiang, China

Refined tobacco plant information extraction is the basis of efficient yield estimation. Tobacco planting in mountainous plateau areas in China is characterized by scattered distribution, uneven growth, and mixed/intercropping crops. Thus, it is difficult to accurately extract information on the tobacco plants. The study area is Beipanjiang topographic fracture area in China, using the smart phantom 4 Pro v2.0 quadrotor unmanned aerial vehicle to collect the images of tobacco planting area in the study area. By screening the visible light band, Excess Green Index, Normalized Green Red Difference Vegetation Index, and Excess Green Minus Excess Red Index were used to obtain the best color index calculation method for tobacco plants. Low-pass filtering was used to enhance tobacco plant information and suppress noise from weeds, corn plants, and rocks. Combined with field measurements of tobacco plant data, the computer interactive interpretation method performed gray-level segmentation on the enhanced image and extracted tobacco plant information. This method is suitable for identifying tobacco plants in mountainous plateau areas. The detection rates of the test and verification areas were 96.61% and 97.69%, and the completeness was 95.66% and 96.53%, respectively. This study can provide fine data support for refined tobacco plantation management in the terrain broken area with large exposed rock area and irregular planting land.