High Throughput Field Phenotyping for Plant Height Using UAV-Based RGB Imagery in Wheat Breeding Lines: Feasibility and Validation

Plant height (PH) is an essential trait in the screening of most crops. While in crops such as wheat, medium stature helps reduce lodging, tall plants are preferred to increase total above-ground biomass. PH is an easy trait to measure manually, although it can be labor-intense depending on the number of plots. There is an increasing demand for alternative approaches to estimate PH in a higher throughput mode. Crop surface models (CSMs) derived from dense point clouds generated via aerial imagery could be used to estimate PH. This study evaluates PH estimation at different phenological stages using plot-level information from aerial imaging-derived 3D CSM in wheat inbred lines during two consecutive years. Multi-temporal and high spatial resolution images were collected by fixed-wing (PlatFW) and multi-rotor (PlatMR) unmanned aerial vehicle (UAV) platforms over two wheat populations (50 and 150 lines). The PH was measured and compared at four growth stages (GS) using ground-truth measurements (PHground) and UAV-based estimates (PHaerial). The CSMs generated from the aerial imagery were validated using ground control points (GCPs) as fixed reference targets at different heights. The results show that PH estimations using PlatFW were consistent with those obtained from PlatMR, showing some slight differences due to image processing settings. The GCPs heights derived from CSM showed a high correlation and low error compared to their actual heights (R2 ≥ 0.90, RMSE ≤ 4 cm). The coefficient of determination (R2) between PHground and PHaerial at different GS ranged from 0.35 to 0.88, and the root mean square error (RMSE) from 0.39 to 4.02 cm for both platforms. In general, similar and higher heritability was obtained using PHaerial across different GS and years and ranged according to the variability, and environmental error of the PHground observed (0.06–0.97). Finally, we also observed high Spearman rank correlations (0.47–0.91) and R2 (0.63–0.95) of PHaerial adjusted and predicted values against PHground values. This study provides an example of the use of UAV-based high-resolution RGB imagery to obtain time-series estimates of PH, scalable to tens-of-thousands of plots, and thus suitable to be applied in plant wheat breeding trials.

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Terrestrial laser scanning for plant height measurement and biomass estimation of maize

ISPRS - International Archives of the Photogrammetry, Remote Sensing and Spatial Information Sciences ◽

10.5194/isprsarchives-xl-7-181-2014 ◽

2014 ◽

Vol XL-7 ◽

pp. 181-187 ◽

Cited By ~ 9

Author(s):

N. Tilly ◽

D. Hoffmeister ◽

H. Schiedung ◽

C. Hütt ◽

J. Brands ◽

...

Keyword(s):

Plant Height ◽

Precision Agriculture ◽

Laser Scanning ◽

Point Clouds ◽

Time Frame ◽

Coefficient Of Determination ◽

Biomass Estimation ◽

Height Measurement ◽

Growing Period ◽

Non Destructive

Over the last decades, the role of remote sensing gained in importance for monitoring applications in precision agriculture. A key factor for assessing the development of crops during the growing period is the actual biomass. As non-destructive methods of directly measuring biomass do not exist, parameters like plant height are considered as estimators. In this contribution, first results of multitemporal surveys on a maize field with a terrestrial laser scanner are shown. The achieved point clouds are interpolated to generate Crop Surface Models (CSM) that represent the top canopy. These CSMs are used for visualizing the spatial distribution of plant height differences within the field and calculating plant height above ground with a high resolution of 1 cm. In addition, manual measurements of plant height were carried out corresponding to each TLS campaign to verify the results. The high coefficient of determination (R² = 0.93) between both measurement methods shows the applicability of the presented approach. The established regression model between CSM-derived plant height and destructively measured biomass shows a varying performance depending on the considered time frame during the growing period. This study shows that TLS is a suitable and promising method for measuring plant height of maize. Moreover, it shows the potential of plant height as a non-destructive estimator for biomass in the early growing period. However, challenges are the non-linear development of plant height and biomass over the whole growing period.

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Automatic Evaluation of Wheat Resistance to Fusarium Head Blight Using Dual Mask-RCNN Deep Learning Frameworks in Computer Vision

Remote Sensing ◽

10.3390/rs13010026 ◽

2020 ◽

Vol 13 (1) ◽

pp. 26

Author(s):

Wen-Hao Su ◽

Jiajing Zhang ◽

Ce Yang ◽

Rae Page ◽

Tamas Szinyei ◽

...

Keyword(s):

Fusarium Head Blight ◽

Ground Truth ◽

Wheat Breeding ◽

Head Blight ◽

Detection Rates ◽

Ground Truth Data ◽

Resistant Cultivars ◽

Feature Pyramid ◽

Rater Error ◽

Wheat Lines

In many regions of the world, wheat is vulnerable to severe yield and quality losses from the fungus disease of Fusarium head blight (FHB). The development of resistant cultivars is one means of ameliorating the devastating effects of this disease, but the breeding process requires the evaluation of hundreds of lines each year for reaction to the disease. These field evaluations are laborious, expensive, time-consuming, and are prone to rater error. A phenotyping cart that can quickly capture images of the spikes of wheat lines and their level of FHB infection would greatly benefit wheat breeding programs. In this study, mask region convolutional neural network (Mask-RCNN) allowed for reliable identification of the symptom location and the disease severity of wheat spikes. Within a wheat line planted in the field, color images of individual wheat spikes and their corresponding diseased areas were labeled and segmented into sub-images. Images with annotated spikes and sub-images of individual spikes with labeled diseased areas were used as ground truth data to train Mask-RCNN models for automatic image segmentation of wheat spikes and FHB diseased areas, respectively. The feature pyramid network (FPN) based on ResNet-101 network was used as the backbone of Mask-RCNN for constructing the feature pyramid and extracting features. After generating mask images of wheat spikes from full-size images, Mask-RCNN was performed to predict diseased areas on each individual spike. This protocol enabled the rapid recognition of wheat spikes and diseased areas with the detection rates of 77.76% and 98.81%, respectively. The prediction accuracy of 77.19% was achieved by calculating the ratio of the wheat FHB severity value of prediction over ground truth. This study demonstrates the feasibility of rapidly determining levels of FHB in wheat spikes, which will greatly facilitate the breeding of resistant cultivars.

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Reference Measurements in Developing UAV Systems for Detecting Pests, Weeds, and Diseases

Remote Sensing ◽

10.3390/rs13071238 ◽

2021 ◽

Vol 13 (7) ◽

pp. 1238

Author(s):

Jere Kaivosoja ◽

Juho Hautsalo ◽

Jaakko Heikkinen ◽

Lea Hiltunen ◽

Pentti Ruuttunen ◽

...

Keyword(s):

Reference Data ◽

Measurement Techniques ◽

Synthetic Data ◽

Ground Truth ◽

Precision Farming ◽

Aerial Imaging ◽

Aerial Vehicle ◽

Uav Images ◽

Reference Measurements

The development of UAV (unmanned aerial vehicle) imaging technologies for precision farming applications is rapid, and new studies are published frequently. In cases where measurements are based on aerial imaging, there is the need to have ground truth or reference data in order to develop reliable applications. However, in several precision farming use cases such as pests, weeds, and diseases detection, the reference data can be subjective or relatively difficult to capture. Furthermore, the collection of reference data is usually laborious and time consuming. It also appears that it is difficult to develop generalisable solutions for these areas. This review studies previous research related to pests, weeds, and diseases detection and mapping using UAV imaging in the precision farming context, underpinning the applied reference measurement techniques. The majority of the reviewed studies utilised subjective visual observations of UAV images, and only a few applied in situ measurements. The conclusion of the review is that there is a lack of quantitative and repeatable reference data measurement solutions in the areas of mapping pests, weeds, and diseases. In addition, the results that the studies present should be reflected in the applied references. An option in the future approach could be the use of synthetic data as reference.

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Evaluation of a Novel Molecular Marker Associated with the Tan Spot Disease Response in Wheat

Agriculture ◽

10.3390/agriculture11060513 ◽

2021 ◽

Vol 11 (6) ◽

pp. 513

Author(s):

Pao Theen See ◽

Caroline S. Moffat

Keyword(s):

Molecular Marker ◽

Hexaploid Wheat ◽

Wheat Breeding ◽

Tan Spot ◽

Growth Stages ◽

Disease Score ◽

Wheat Varieties ◽

Disease Response ◽

Spot Disease ◽

Tan Spot Disease

After nearly 40 years of DNA molecular marker development in plant breeding, the wheat research community has amassed an extensive collection of molecular markers which have been widely and successfully used for selection of agronomic, physiological and disease resistance traits in wheat breeding programs. Tan spot is a major fungal disease of wheat and a significant global economic challenge and is caused by the necrotrophic fungal pathogen Pyrenophora tritici-repentis (Ptr). Here, the potential for using a PCR-based marker (Ta1AS3422) present on the short arm of wheat chromosome 1A, was evaluated for effectiveness in distinguishing tan spot disease susceptibility. The marker was initially screened against 40 commercial Australian hexaploid wheat varieties, and those that amplified the marker had an overall lower disease score (2.8 ± 0.7 for seedlings and 2.4 ± 0.4 for plants at the tillering stage), compared to those lacking the marker which exhibited a higher disease score (3.6 ± 0.8 for both growth stages). The potential of Ta1AS3422 as a marker for the tan spot disease response was further assessed against a panel of 100 commercial Australian hexaploid wheat varieties. A significant association was observed between marker absence/presence and tan spot disease rating (Pearson’s chi-squared test, χ2 (6) = 20.53, p = 0.002), with absence of Ta1AS3422 associated with susceptibility. This simple and cost-effective PCR-based marker may be useful for varietal improvement against tan spot, although further work is required to validate its effectiveness.

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Soybean Sensitivity to Florpyrauxifen-benzyl during Reproductive Growth and the Impact on Subsequent Progeny

Weed Technology ◽

10.1017/wet.2017.108 ◽

2017 ◽

Vol 32 (2) ◽

pp. 135-140 ◽

Cited By ~ 3

Author(s):

M. Ryan Miller ◽

Jason K. Norsworthy

Keyword(s):

Plant Height ◽

Field Studies ◽

Yield Reduction ◽

Growth Stages ◽

Soybean Plant ◽

Reproductive Growth ◽

Similar Reduction ◽

Structural Class ◽

Soybean Plants ◽

The Impact

AbstractTo address recent concerns related to auxin herbicide drift onto soybean, a study was developed to understand the susceptibility of the reproductive stage of soybean to a new auxin herbicide compared with dicamba. Florpyrauxifen-benzyl is under development as the second herbicide in a new structural class of synthetic auxins, the arylpicolinates. Field studies were conducted to (1) evaluate and compare reproductive soybean injury and yield following applications of florpyrauxifen-benzyl or dicamba across various concentrations and reproductive growth stages and (2) determine whether low-rate applications of florpyrauxifen-benzyl or dicamba to soybean in reproductive stages would have similar effect on the progeny of the affected plants. Soybean were treated with 0, 1/20, or 1/160, of the 1X rate of florpyrauxifen-benzyl (30 g ai ha−1) or dicamba (560 g ae ha−1) at R1, R2, R3, R4, or R5 growth stage. Soybean plant height and yield was reduced from 1/20X dicamba across all reproductive stages. High drift rates (1/20X) of florpyrauxifen-benzyl also reduced soybean plant height >25% and yield across R1 to R4 stages. Germination, stand, plant height, and yield of the offspring of soybean plants treated with dicamba and florpyrauxifen-benzyl were significantly affected. Dicamba applied at a rate of 1/20X at R4 and R5 resulted in 20% and 35% yield reduction for the offspring, respectively. A similar reduction occurred from florpyrauxifen-benzyl applied at R4 and R5 at the 1/20X rate, resulting in 15% to 24% yield reduction for the offspring, respectively. Based on these findings, it is suggested that growers use caution when applying these herbicides in the vicinity of reproductive soybean.

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Referencing laser and ultrasonic height measurements of barleycultivars by using a herbometre as standard

Crop and Pasture Science ◽

10.1071/cp16238 ◽

2016 ◽

Vol 67 (12) ◽

pp. 1215 ◽

Cited By ~ 10

Author(s):

Gero Barmeier ◽

Bodo Mistele ◽

Urs Schmidhalter

Keyword(s):

Plant Height ◽

Spring Barley ◽

Operating Time ◽

Reference Method ◽

Fold Increase ◽

Barley Cultivars ◽

Coefficients Of Variation ◽

Field Phenotyping ◽

High Throughput Phenotyping ◽

Distance Sensor

Assessment of plant height is an important factor for agronomic and breeder decisions; however, current field phenotyping, such as visual scoring or using a ruler, is time consuming, labour intensive, costly and subjective. For agronomists and plant breeders, the most common method used to measure plant height is still a meter stick. In a 3-year study, we have adopted a herbometre similar to a rising plate meter as a reference method to obtain the weighted plant height of barley cultivars and to evaluate vehicle-based ultrasonic and laser distance sensors. Sets of 30 spring barley cultivars and 14 and 60 winter barley cultivars were tested in 2013, 2014 and 2015, respectively. The herbometre was well suited as a reference method allowing for an increased area and was easy to handle. The herbometre measurements within a plot showed very low coefficients of variation. Good and close relationships (R2 = 0.59, 0.76, 0.80) between the herbometre and the ultrasonic distance sensor measurements were observed in the years 2013, 2014 and 2015, respectively, demonstrating also increased values of heritability. Hence, both sensors were able to differentiate among barley cultivars in standard breeding trials. For the sensors, we observed a 4-fold faster operating time and 6-fold increase of measurement points compared with the herbometre measurement. Based on these results, we conclude that distance sensors represent a powerful and economical high-throughput phenotyping tool for breeders and plant scientists to estimate plant height and to differentiate cultivars for agronomic decisions and breeding activities potentially being also applicable in other small grain cereals with dense crop stands. Particularly, ultrasonic distance sensors may reflect an agronomically and physiologically relevant plant height information.

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Distribution of dwarfing genes (Rht-B1b and Rht-D1b) in Martonvásár wheat breeding materials

Acta Agronomica Hungarica ◽

10.1556/aagr.59.2011.3.8 ◽

2011 ◽

Vol 59 (3) ◽

pp. 249-254 ◽

Cited By ~ 3

Author(s):

G. Gulyás ◽

Z. Bognár ◽

L. Láng ◽

M. Rakszegi ◽

Z. Bedő

Keyword(s):

Triticum Aestivum ◽

Molecular Markers ◽

Plant Height ◽

Wheat Breeding ◽

Minor Role ◽

Dwarfing Genes ◽

Breeding Programmes ◽

A Minor ◽

Positive Results ◽

Marker Information

A total of 266 Martonvásár (Mv) wheat (Triticum aestivum L.) accessions, including varieties and advanced lines, were examined using the “Perfect” molecular markers to detect the Rht-B1b (formerly Rht1) and Rht-D1b (formerly Rht2) semi-dwarfing genes. The gene Rht-B1b was detected in a total of 221 (83.5%) accessions. The Rht-D1b allele was found in fewer accessions. Overall 24 genotypes (9%) contained this allele. The analysis of the development date of the genotypes revealed that the introduction of the dwarfing genes into Martonvásár breeding programmes started in the early 1970s, and they were widely utilized from the 1980s. The Rht-B1b allele was the main source for reducing plant height, while the Rht-D1b allele played only a minor role in the Martonvásár breeding programme.Characterizing accessions using various molecular markers allows us to create a database offering relevant marker information about genotypes. Such a database could be very helpful for selection, allowing breeders to include varieties giving positive results in specific breeding programmes.

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