Digital phenotyping and genotype-to-phenotype (G2P) models to predict complex traits in cereal crops

The revolution in digital phenotyping combined with the new layers of omics and envirotyping tools offers great promise to improve selection and accelerate genetic gains for crop improvement. This chapter examines the latest methods involving digital phenotyping tools to predict complex traits in cereals crops. The chapter has two parts. In the first part, entitled “Digital phenotyping as a tool to support breeding programs”, the secondary phenotypes measured by high-throughput plant phenotyping that are potentially useful for breeding are reviewed. In the second part, “Implementing complex G2P models in breeding programs”, the integration of data from digital phenotyping into genotype to phenotype (G2P) models to improve the prediction of complex traits using genomic information is discussed. The current status of statistical models to incorporate secondary traits in univariate and multivariate models, as well as how to better handle longitudinal (for example light interception, biomass accumulation, canopy height) traits, is reviewe

Using UAV-Based Imagery to Determine Volume, Groundcover, and Growth Rate Characteristics of Lentil (Lens culinaris Medik.)

Plant growth rate is an essential phenotypic parameter for crop physiologists and plant breeders to understand in order to quantify potential crop productivity based on specific stages throughout the growing season. While plant growth rate information can be attained though manual collection of biomass, this procedure is rarely performed due to the prohibitively large effort and destruction of plant material that is required. Unmanned Aerial Vehicles (UAVs) offer great potential for rapid collection of imagery which can be utilized for quantification of plant growth rate. In this study, six diverse lines of lentil were grown in three replicates of microplots with six biomass collection time-points throughout the growing season over five site-years. Aerial imagery of each biomass collection time point was collected from a UAV and utilized to produce stitched two-dimensional orthomosaics and three-dimensional point clouds. Analysis of this imagery produced quantification of groundcover and vegetation volume on an individual plot basis. Comparison with manually-measured above-ground biomass suggests strong correlation, indicating great potential for UAVs to be utilized in plant breeding programs for evaluation of groundcover and vegetation volume. Nonlinear logistic models were fit to multiple data collection points throughout the growing season. The growth rate and G50, which is the number of growing degree days (GDD) required to accumulate 50 % of maximum growth, parameters of the model are capable of quantifying growth rate, and have potential utility in plant research and plant breeding programs. Predicted maximum volume was identified as a potential proxy for whole-plot biomass measurement. Six new phenotypes have been described that can be accurately and efficiently collected from field trials with the use of UAV’s or other overhead image-collection systems. These phenotypes are; Area Growth Rate, Area G50, Area Maximum Predicted Growth, Volume Growth Rate, Volume G50, and Volume Maximum Predicted Growth

HIGH-THROUGHPUT PHENOTYPING THAT IMPROVES THE EFFICIENCY OF A COTTON PLANT BREEDING SYSTEM

Unmanned Aerial Vehicles (UAVs) play an important role in agricultural research because they facilitate high-throughput phenotyping (HTP). Cotton (Gossypium spp.) is the world’s leading natural textile fiber crop, and breeding programs that enhance the efficiency of growing the crop are important to the viability of the cotton industry. The effectiveness of plant breeding programs is improved when researchers have the ability to quickly evaluate important traits in a field environment. The ability to identify cotton plant height and boll count across a field can serve as an important tool in predicting plant growth and yield. In order to capture a three-dimensional (3D) view of field plots, which is believed to be helpful in estimating yield and crop development parameters, sensors mounted on UAVs must have access to a view of the ground. However, cotton planted in solid rows can obscure this view. Canopy closure prevents sensors from measuring plant architecture and boll-loads three dimensionally from the mid-growing season until the crop is defoliated. Therefore, this project was initiated to compare solid vs. skip-row planting patterns in terms of predicting yield and fiber quality since skip rows would allow UAV sensors to capture more accurate 3D data from plots. The purposes of this project were to (1) use UAVs to characterize genotype x row pattern interaction and how location and year affect that interaction, (2) evaluate the ability of UAVs to predict plant height and yield, (3) compare the accuracy of UAV-derived data from different planting patterns and (4) use images processed from UAVs to standardize data for every single row to predict yield performance. Two UAVs were used for red, green, and blue (RGB) data collection and multispectral data collection. Five cotton genotypes were grown in a skip versus solid row pattern at three locations in 2017 and 2018. Yield and fiber qualities were measured for all treatments. UAVs were flown across the field bi-weekly to estimate plant height, canopy cover, canopy volume, vegetation indices, open boll count and boll area over different growing stages. Without extreme weather influence, lint yield and fiber quality were not affected by Genotype X row-spacing effects. Also, year and location did not influence that interaction. In addition, yield and plant height estimations were improved when cotton was planted in a skip-row pattern. Single row rating based on orthomosaic images and 3D point cloud images correlated with yield performance. Therefore, to take full advantage of UAV data, cotton breeding programs need to plant early generation lines (progeny rows) in skip rows that allow sensors to have access to the view of the ground and capture 3D images. This can be accomplished without compromising the efficiency and accuracy of the breeding program

Field phenotyping for African crops: overview and perspectives

Improvements in crop productivity are required to meet the dietary demands of the rapidly-increasing African population. The development of key staple crop cultivars that are high-yielding and resilient to biotic and abiotic stresses is essential. To contribute to this objective, high-throughput plant phenotyping approaches are important enablers for the African plant science community to measure complex quantitative phenotypes and to establish the genetic basis of agriculturally relevant traits. These advances will facilitate the screening of germplasm for optimum performance and adaptation to low-input agriculture and resource-constrained environments. Increasing the capacity to investigate plant function and structure through non-invasive technologies is an effective strategy to aid plant breeding and additionally may contribute to precision agriculture. However, despite the significant global advances in basic knowledge and sensor technology for plant phenotyping, Africa still lags behind in the development and implementation of these systems due to several practical, financial, geographical and political barriers. Currently, field phenotyping is mostly carried out by manual methods that are prone to error, costly, labor-intensive and may come with adverse economic implications. Therefore, improvements in advanced field phenotyping capabilities and appropriate implementation are key factors for success in modern breeding and agricultural monitoring. In this review, we provide an overview of the current state of field phenotyping and the challenges limiting its implementation in some African countries. We suggest that the lack of appropriate field phenotyping infrastructures is impeding the development of improved crop cultivars and will have a detrimental impact on the agricultural sector and on food security. We highlight the prospects for integrating emerging and advanced low-cost phenotyping technologies into breeding protocols and characterizing crop responses to environmental challenges in field experimentation. Finally, we explore strategies for overcoming the barriers and maximizing the full potential of emerging field phenotyping technologies in African agriculture. This review paper will open new windows and provide new perspectives for breeders and the entire plant science community in Africa.BBSRC: BB/P016855/

Unmanned Aerial Vehicle-Based Phenotyping Using Morphometric and Spectral Analysis Can Quantify Responses of Wild Tomato Plants to Salinity Stress

With salt stress presenting a major threat to global food production, attention has turned to the identification and breeding of crop cultivars with improved salt tolerance. For instance, some accessions of wild species with higher salt tolerance than commercial varieties are being investigated for their potential to expand food production into marginal areas or to use brackish waters for irrigation. However, assessment of individual plant responses to salt stress in field trials is time-consuming, limiting, for example, longitudinal assessment of large numbers of plants. Developments in Unmanned Aerial Vehicle (UAV) sensing technologies provide a means for extensive, repeated and consistent phenotyping and have significant advantages over standard approaches. In this study, 199 accessions of the wild tomato species, Solanum pimpinellifolium, were evaluated through a field assessment of 600 control and 600 salt-treated plants. UAV imagery was used to: (1) delineate tomato plants from a time-series of eight RGB and two multi-spectral datasets, using an automated object-based image analysis approach; (2) assess four traits, i.e., plant area, growth rates, condition and Plant Projective Cover (PPC) over the growing season; and (3) use the mapped traits to identify the best-performing accessions in terms of yield and salt tolerance. For the first five campaigns, >99% of all tomato plants were automatically detected. The omission rate increased to 2–5% for the last three campaigns because of the presence of dead and senescent plants. Salt-treated plants exhibited a significantly smaller plant area (average control and salt-treated plant areas of 0.55 and 0.29 m2, respectively), maximum growth rate (daily maximum growth rate of control and salt-treated plant of 0.034 and 0.013 m2, respectively) and PPC (5–16% difference) relative to control plants. Using mapped plant condition, area, growth rate and PPC, we show that it was possible to identify eight out of the top 10 highest yielding accessions and that only five accessions produced high yield under both treatments. Apart from showcasing multi-temporal UAV-based phenotyping capabilities for the assessment of plant performance, this research has implications for agronomic studies of plant salt tolerance and for optimizing agricultural production under saline conditions

High-throughput phenotyping of yield parameters for modern grapevine breeding

Weinbau wird auf 1% der deutschen Agrarfläche betrieben. Auf dieser vergleichsweise kleinen Anbaufläche wird jedoch ein Drittel aller in der deutschen Landwirtschaft verwendeten Fungizide appliziert, was auf die Einführung von Schaderregern im 19. Jahrhundert zurück zu führen ist. Für einen nachhaltigen Anbau ist eine Reduktion des Pflanzenschutzmittelaufwands dringend notwendig. Dieses Ziel kann durch die Züchtung und den Anbau neuer, pilzwiderstandsfähiger Rebsorten erreicht werden. Die Rebenzüchtung als solche ist sehr zeitaufwendig, da die Entwicklung neuer Rebsorten 20 bis 25 Jahre dauert. Der Einsatz der markergestützten Selektion (MAS) erhöht die Effizienz der Selektion in der Rebenzüchtung fortwährend. Eine weitere Effizienzsteigerung ist mit der andauernden Verbesserung der Hochdurchsatz Genotypisierung zu erwarten. Im Vergleich zu den Methoden der Genotypisierung ist die Qualität, Objektivität und Präzision der traditionellen Phänotypisierungsmethoden begrenzt. Die Effizienz in der Rebenzüchtung soll mit der Entwicklung von Hochdurchsatz Methoden zur Phänotypisierung durch sensorgestützte Selektion weiter gesteigert werden. Hierfür sind bisher vielfältige Sensortechniken auf dem Markt verfügbar. Das Spektrum erstreckt sich von RGB-Kameras über Multispektral-, Hyperspektral-, Wärmebild- und Fluoreszenz- Kameras bis hin zu 3D-Techniken und Laserscananwendungen. Die Phänotypisierung von Pflanzen kann unter kontrollierten Bedingungen in Klimakammern oder Gewächshäusern beziehungsweise im Freiland stattfinden. Die Möglichkeit einer standardisierten Datenaufnahme nimmt jedoch kontinuierlich ab. Bei der Rebe als Dauerkultur erfolgt die Aufnahme äußerer Merkmale, mit Ausnahme junger Sämlinge, deshalb auch überwiegend im Freiland. Variierende Lichtverhältnisse, Ähnlichkeit von Vorder- und Hintergrund sowie Verdeckung des Merkmals stellen aus methodischer Sicht die wichtigsten Herausforderungen in der sensorgestützen Merkmalserfassung dar. Bis heute erfolgt die Aufnahme phänotypischer Merkmale im Feld durch visuelle Abschätzung. Hierbei werden die BBCH Skala oder die OIV Deskriptoren verwendet. Limitierende Faktoren dieser Methoden sind Zeit, Kosten und die Subjektivität bei der Datenerhebung. Innerhalb des Züchtungsprogramms kann daher nur ein reduziertes Set an Genotypen für ausgewählte Merkmale evaluiert werden. Die Automatisierung, Präzisierung und Objektivierung phänotypischer Daten soll dazu führen, dass (1) der bestehende Engpass an phänotypischen Methoden verringert, (2) die Effizienz der Rebenzüchtung gesteigert, und (3) die Grundlage zukünftiger genetischer Studien verbessert wird, sowie (4) eine Optimierung des weinbaulichen Managements stattfindet. Stabile und über die Jahre gleichbleibende Erträge sind für eine Produktion qualitativ hochwertiger Weine notwendig und spielen daher eine Schlüsselrolle in der Rebenzüchtung. Der Fokus dieser Studie liegt daher auf Ertragsmerkmalen wie der Beerengröße, Anzahl der Beeren pro Traube und Menge der Trauben pro Weinstock. Die verwandten Merkmale Traubenarchitektur und das Verhältnis von generativem und vegetativem Wachstum wurden zusätzlich bearbeitet. Die Beurteilung von Ertragsmerkmalen auf Einzelstockniveau ist aufgrund der genotypischen Varianz und der Vielfältigkeit des betrachteten Merkmals komplex und zeitintensiv. Als erster Schritt in Richtung Hochdurchsatz (HT) Phänotypisierung von Ertragsmerkmalen wurden zwei voll automatische Bildinterpretationsverfahren für die Anwendung im Labor entwickelt. Das Cluster Analysis Tool (CAT) ermöglicht die bildgestützte Erfassung der Traubenlänge, -breite und -kompaktheit, sowie der Beerengröße. Informationen über Anzahl, Größe (Länge, Breite) und das Volumen der einzelnen Beeren liefert das Berry Analysis Tool (BAT). Beide Programme ermöglichen eine gleichzeitige Erhebung mehrerer, präziser phänotypischer Merkmale und sind dabei schnell, benutzerfreundlich und kostengünstig. Die Möglichkeit, den Vorder- und Hintergrund in einem Freilandbild zu unterscheiden, ist besonders in einem frühen Entwicklungsstadium der Rebe aufgrund der fehlenden Laubwand schwierig. Eine Möglichkeit, die beiden Ebenen in der Bildanalyse zu trennen, ist daher unerlässlich. Es wurde eine berührungsfreie, schnelle sowie objektive Methode zur Bestimmung des Winterschnittholzgewichts, welches das vegetative Wachstum der Rebe beschreibt, entwickelt. In einem innovativen Ansatz wurde unter Kombination von Tiefenkarten und Bildsegmentierung die sichtbare Winterholzfläche im Bild bestimmt. Im Zuge dieser Arbeit wurde die erste HT Phänotypisierungspipeline für die Rebenzüchtung aufgebaut. Sie umfasst die automatisierte Bildaufnahme im Freiland unter Einsatz des PHENObots, das Datenmanagement mit Datenanalyse sowie die Interpretation des erhaltenen phänotypischen Datensatzes. Die Basis des PHENObots ist ein automatisiert gesteuertes Raupenfahrzeug. Des Weiteren umfasst er ein Multi-Kamera- System, ein RTK-GPS-System und einen Computer zur Datenspeicherung. Eine eigens entwickelte Software verbindet die Bilddaten mit der Standortreferenz. Diese Referenz wird anschließend für das Datenmanagement in einer Datenbank verwendet. Um die Funktionalität der Phänotypisierungspipeline zu demonstrieren, wurden die Merkmale Beerengröße und -farbe im Rebsortiment des Geilweilerhofes unter Verwendung des Berries In Vineyard (BIVcolor) Programms erfasst. Im Durschnitt werden 20 Sekunden pro Weinstock für die Bildaufnahme im Feld benötigt, gefolgt von der Extraktion der Merkmale mittels automatischer, objektiver und präziser Bildauswertung. Im Zuge dieses Versuches konnten mit dem PHENObot 2700 Weinstöcke in 12 Stunden erfasst werden, gefolgt von einer automatischen Bestimmung der Merkmale Beerengröße und -farbe aus den Bildern. Damit konnte die grundsätzliche Machbarkeit bewiesen werden. Diese Pilotpipeline bietet nun die Möglichkeit zur Entwicklung weiterer innovativer Programme zur Erhebung neuer Merkmale sowie die Integration zusätzlicher Sensoren auf dem PHENObot.Grapevine is grown on about 1% of the German agricultural area requiring one third of all fungicides sprayed due to pathogens being introduced within the 19th century. In spite of this requirement for viticulture a reduction is necessary to improve sustainability. This objective can be achieved by growing fungus resistant grapevine cultivars. The development of new cultivars, however, is very time-consuming, taking 20 to 25 years. In recent years the breeding process could be increased considerably by using marker assisted selection (MAS). Further improvements of MAS applications in grapevine breeding will come along with developing of faster and more cost efficient high-throughput (HT) genotyping methods.Complementary to genotyping techniques the quality, objectivity and precision of current phenotyping methods is limited and HT phenotyping methods need to be developed to further increase the efficiency of grapevine breeding through sensor assisted selection. Many different types of sensors technologies are available ranging from visible light sensors (Red Green Blue (RGB) cameras), multispectral, hyperspectral, thermal, and fluorescence cameras to three dimensional (3D) camera and laser scan approaches. Phenotyping can either be done under controlled environments (growth chamber, greenhouse) or can take place in the field, with a decreasing level of standardization. Except for young seedlings, grapevine as a perennial plant needs ultimately to be screened in the field. From a methodological point of view a variety of challenges need to be considered like the variable light conditions, the similarity of fore- and background, and in the canopy hidden traits.The assessment of phenotypic data in grapevine breeding is traditionally done directly in the field by visual estimations. In general the BBCH scale is used to acquire and classify the stages of annual plant development or OIV descriptors are applied to assess the phenotypes into classes. Phenotyping is strongly limited by time, costs and the subjectivity of records. Therefore, only a comparably small set of genotypes is evaluated for certain traits within the breeding process. Due to that limitation, automation, precision and objectivity of phenotypic data evaluation is crucial in order to (1) reduce the existing phenotyping bottleneck, (2) increase the efficiency of grapevine breeding, (3) assist further genetic studies and (4) ensure improved vineyard management. In this theses emphasis was put on the following aspects: Balanced and stable yields are important to ensure a high quality wine production playing a key role in grapevine breeding. Therefore, the main focus of this study is on phenotyping different parameters of yield such as berry size, number of berries per cluster, and number of clusters per vine. Additionally, related traits like cluster architecture and vine balance (relation between vegetative and generative growth) were considered. Quantifying yield parameters on a single vine level is challenging. Complex shapes and slight variations between genotypes make it difficult and very time-consuming.As a first step towards HT phenotyping of yield parameters two fully automatic image interpretation tools have been developed for an application under controlled laboratory conditions to assess individual yield parameters. Using the Cluster Analysis Tool (CAT) four important phenotypic traits can be detected in one image: Cluster length, cluster width, berry size and cluster compactness. The utilization of the Berry Analysis Tool (BAT) provides information on number, size (length and width), and volume of grapevine berries. Both tools offer a fast, user-friendly and cheap procedure to provide several precise phenotypic features of berries and clusters at once with dimensional units in a shorter period of time compared to manual measurements.The similarity of fore- and background in an image captured under field conditions is especially difficult and crucial for image analysis at an early grapevine developmental stage due to the missing canopy. To detect the dormant pruning wood weight, partly determining vine balance, a fast and non-invasive tool for objective data acquisition in the field was developed. In an innovative approach it combines depth map calculation and image segmentation to subtract the background of the vine obtaining the pruning area visible in the image. For the implementation of HT field phenotyping in grapevine breeding a phenotyping pipeline has been set up. It ranges from the automated image acquisition directly in the field using the PHENObot, to data management, data analysis and the interpretation of obtained phenotypic data for grapevine breeding aims. The PHENObot consists of an automated guided tracked vehicle system, a calibrated multi camera system, a Real-Time-Kinematic GPS system and a computer for image data handling. Particularly developed software was applied in order to acquire geo referenced images directly in the vineyard. The geo-reference is afterwards used for the post-processing data management in a database. As phenotypic traits to be analysed within the phenotyping pipeline the detection of berries and the determination of the berry size and colour were considered. The highthroughput phenotyping pipeline was tested in the grapevine repository at Geilweilerhof to extract the characteristics of berry size and berry colour using the Berries In Vineyards (BIVcolor) tool. Image data acquisition took about 20 seconds per vine, which afterwards was followed by the automatic image analysis to extract objective and precise phenotypic data. In was possible to capture images of 2700 vines within 12 hours using the PHENObot and subsequently automatic analysis of the images and extracting berry size and berry colour. With this analysis proof of principle was demonstrated. The pilot pipeline providesthe basis for further development of additional evaluation modules as well as the integration of other sensors

Plant Breeding and Management Strategies to Minimize the Impact of Water Scarcity and Biotic Stress in Cereal Crops under Mediterranean Conditions

Wheat and rice are two main staple food crops that may suffer from yield losses due to drought episodes that are increasingly impacted by climate change, in addition to new epidemic outbreaks. Sustainable intensification of production will rely on several strategies, such as efficient use of water and variety improvement. This review updates the latest findings regarding complementary approaches in agronomy, genetics, and phenomics to cope with climate change challenges. The agronomic approach focuses on a case study examining alternative rice water management practices, with their impact on greenhouse gas emissions and biodiversity for ecosystem services. The genetic approach reviews in depth the latest technologies to achieve fungal disease resistance, as well as the use of landraces to increase the genetic diversity of new varieties. The phenomics approach explores recent advances in high-throughput remote sensing technologies useful in detecting both biotic and abiotic stress effects on breeding programs. The complementary nature of all these technologies indicates that only interdisciplinary work will ensure significant steps towards a more sustainable agriculture under future climate change scenarios.info:eu-repo/semantics/publishedVersio

Mehitamata õhusõiduki rakendamine põllukultuuride saagikuse ja maa harimisviiside tuvastamisel

A Thesis for applying for the degree of Doctor of Philosophy in Environmental Protection.Väitekiri filosoofiadoktori kraadi taotlemiseks keskkonnakaitse erialal.This thesis aims to examine how machine learning (ML) technologies have aided significant advancements in image analysis in the area of precision agriculture. These multimodal computing technologies extend the use of machine learning to a broader spectrum of data collecting and selection for the advancement of agricultural practices (Nawar et al., 2017) These techniques will assist complicated cropping systems with more informed decisions with less human intervention, and provide a scalable framework for incorporating expert knowledge of the PA system. (Chlingaryan et al., 2018). Complexity, on the other hand, can be seen as a disadvantage in crop trials, as machine learning models require training/testing databases, limited areas with insignificant sampling sizes, time and space-specificity, and environmental factor interventions, all of which complicate parameter selection and make using a single empirical model for an entire region impractical. During the early stages of writing this thesis, we used a relatively traditional machine learning method to address the regression problem of crop yield and biomass prediction [(i.e., random forest regression (RFR), support vector regression (SVR), and artificial neural network (ANN)] to predicted dry matter (DM) yields of red clover. It obtained favourable results, however, the choosing of hyperparameters, the lengthy algorithms selection process, data cleaning, and redundant collinearity issues significantly limited the way of the machine learning application. We will further discuss the recent trend of automated machine learning (AutoML) that has been driving further significant technological innovation in the application of artificial intelligence from its automated algorithm selection and hyperparameter optimization of the deployable pipeline model for unravelling substance problems. However, a present knowledge gap exists in the integration of machine learning (ML) technology with unmanned aerial systems (UAS) and hyperspectral-based imaging data categorization and regression applications. In this thesis, we explored a state-of-the-art (SOTA) and entirely open-source AutoML framework, Auto-sklearn, which was built on one of the most frequently used machine learning systems, Scikit-learn. It was integrated with two unique AutoML visualization tools to examine the recognition and acceptance of multispectral vegetation indices (VI) data collected from UAS and hyperspectral narrow-band VIs across a varied spectrum of agricultural management practices (AMP). These procedures incorporate soil tillage method (STM), cultivation method (CM), and manure application (MA), and are classified as four-crop combination fields (i.e., red clover-grass mixture, spring wheat, pea-oat mixture, and spring barley). Additionally, they have not been thoroughly evaluated and lack characteristics that are accessible in agriculture remote sensing applications. This thesis further explores the existing gaps in the knowledge base for several critical crop categories and cultivation management methods referring to biomass and yield analysis, as well as to gain a better understanding of the potential for remotely sensed solutions to field-based and multifunctional platforms to meet precision agriculture demands. To overcome these knowledge gaps, this research introduces a rapid, non-destructive, and low-cost framework for field-based biomass and grain yield modelling, as well as the identification of agricultural management practices. The results may aid agronomists and farmers in establishing more accurate agricultural methods and in monitoring environmental conditions more effectively.Doktoritöö eesmärk oli uurida, kuidas masinõppe (MÕ) tehnoloogiad võimaldavad edusamme täppispõllumajanduse valdkonna pildianalüüsis. Multimodaalsed arvutustehnoloogiad laiendavad masinõppe kasutamist põllumajanduses andmete kogumisel ja valimisel (Nawar et al., 2017). Selline täpsemal informatsioonil põhinev tehnoloogia võimaldab keerukate viljelussüsteemide puhul teha otsuseid inimese vähema sekkumisega, ja loob skaleeritava raamistiku täppispõllumajanduse jaoks (Chlingaryan et al., 2018). Põllukultuuride katsete korral on komplekssete masinõppemudelite kasutamine keerukas, sest alad on piiratud ning valimi suurus ei ole piisav; vaja on testandmebaase, kindlaid aja- ja ruumitingimusi ning keskkonnategureid. See komplitseerib parameetrite valikut ning muudab ebapraktiliseks ühe empiirilise mudeli kasutamise terves piirkonnas. Siinse uurimuse algetapis rakendati suhteliselt traditsioonilist masinõppemeetodit, et lahendada saagikuse ja biomassi prognoosimise regressiooniprobleem (otsustusmetsa regression, tugivektori regressioon ja tehisnärvivõrk) punase ristiku prognoositava kuivaine saagikuse suhtes. Saadi sobivaid tulemusi, kuid hüperparameetrite valimine, pikk algoritmide valimisprotsess, andmete puhastamine ja kollineaarsusprobleemid takistasid masinõpet oluliselt. Automatiseeritud masinõppe (AMÕ) uusimate suundumustena rakendatakse tehisintellekti, et lahendada põhiprobleemid automatiseeritud algoritmi valiku ja rakendatava pipeline-mudeli hüperparameetrite optimeerimise abil. Seni napib teadmisi MÕ tehnoloogia integreerimiseks mehitamata õhusõidukite ning hüperspektripõhiste pildiandmete kategoriseerimise ja regressioonirakendustega. Väitekirjas uuriti nüüdisaegset ja avatud lähtekoodiga AMÕ tehnoloogiat Auto-sklearn, mis on ühe enimkasutatava masinõppesüsteemi Scikit-learn edasiarendus. Süsteemiga liideti kaks unikaalset AMÕ visualiseerimisrakendust, et uurida mehitamata õhusõidukiga kogutud andmete multispektraalsete taimkatteindeksite ja hüperspektraalsete kitsaribaandmete taimkatteindeksite tuvastamist ja rakendamist põllumajanduses. Neid võtteid kasutatakse mullaharimisel, kultiveerimisel ja sõnnikuga väetamisel nelja kultuuriga põldudel (punase ristiku rohusegu, suvinisu, herne-kaera segu, suvioder). Neid ei ole põhjalikult hinnatud, samuti ei hõlma need omadusi, mida kasutatatakse põllumajanduses kaugseire rakendustes. Uurimus käsitleb biomassi ja saagikuse seni uurimata analüüsivõimalusi oluliste põllukultuuride ja viljelusmeetodite näitel. Hinnatakse ka kaugseirelahenduste potentsiaali põllupõhiste ja multifunktsionaalsete platvormide kasutamisel täppispõllumajanduses. Uurimus tutvustab kiiret, keskkonna suhtes kahjutut ja mõõduka hinnaga tehnoloogiat põllupõhise biomassi ja teraviljasaagi modelleerimiseks, et leida sobiv viljelusviis. Töö tulemused võimaldavad põllumajandustootjatel ja agronoomidel tõhusamalt valida põllundustehnoloogiaid ning arvestada täpsemalt keskkonnatingimustega.Publication of this thesis is supported by the Estonian University of Life Scieces and by the Doctoral School of Earth Sciences and Ecology created under the auspices of the European Social Fund