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

Initial steps for high-throughput phenotyping in vineyards

The evaluation of phenotypic characters of grapevines is required directly in vineyards and is strongly limited by time, costs and the subjectivity of person in charge. Sensor-based techniques are prerequisite in order to allow non-invasive phenotyping of individual plant traits, to increase the quantity of object records and to reduce error variation. Thus, a Prototype-Image-Acquisition-System (PIAS) was developed for semi-automated capture of geo-referenced images in an experimental vineyard. Different strategies were tested for image interpretation using MATLAB®. The interpretation of images from the vineyard with real background is more practice-oriented but requires the calculation of depth maps. Different image analysis tools were verified in order to enable contactless and non-invasive detection of bud burst and quantification of shoots at an early developmental stage (BBCH 10) and enable fast and accurate determination of the grapevine berry size at BBCH 89. Depending on the time of image acquisition at BBCH 10 up to 94 % of green shoots were visible in images. The mean berry size (BBCH 89) was recorded non-invasively with a precision of 1 mm.

Automatic grape bunch detection in vineyards based on affordable 3D phenotyping using a consumer webcam.

This work presents a methodology for 3-D phenotyping of vineyards based on images captured by a low cost high-definition webcamera. A novel software application integrated visual odometry and multiple-view stereo components to create dense and accurate three-dimensional points clouds for vines, properly transformed to millimeter scale. Geometrical and color features of the points were employed by a classification procedure that reached 93% of accuracy on detecting points belonging to grapes. Individual bunches were automatically delimited and their volumes estimated. The sum of the estimated volumes per vine presented a coefficient of correlation of R = 0.99 to the real grape weight observed in each vine after harvesting.SBIAgro 2017

Potential phenotyping methodologies to assess inter- and intravarietal variability and to select grapevine genotypes tolerant to abiotic stress

ReviewPlant phenotyping is an emerging science that combines multiple methodologies and protocols to measure plant traits (e.g., growth, morphology, architecture, function, and composition) at multiple scales of organization. Manual phenotyping remains as a major bottleneck to the advance of plant and crop breeding. Such constraint fostered the development of high throughput plant phenotyping (HTPP), which is largely based on imaging approaches and automatized data retrieval and processing. Field phenotyping still poses major challenges and the progress of HTPP for field conditions can be relevant to support selection and breeding of grapevine. The aim of this review is to discuss potential and current methods to improve field phenotyping of grapevine to support characterization of inter- and intravarietal diversity. Vitis vinifera has a large genetic diversity that needs characterization, and the availability of methods to support selection of plant material (polyclonal or clonal) able to withstand abiotic stress is paramount. Besides being time consuming, complex and expensive, field experiments are also affected by heterogeneous and uncontrolled climate and soil conditions, mostly due to the large areas of the trials and to the high number of traits to be observed in a number of individuals ranging from hundreds to thousands. Therefore, adequate field experimental design and data gathering methodologies are crucial to obtain reliable data. Some of the major challenges posed to grapevine selection programs for tolerance to water and heat stress are described herein. Useful traits for selection and related field phenotyping methodologies are described and their adequacy for large scale screening is discussedinfo:eu-repo/semantics/publishedVersio

High-Throughput System for the Early Quantification of Major Architectural Traits in Olive Breeding Trials Using UAV Images and OBIA Techniques

The need for the olive farm modernization have encouraged the research of more efficient crop management strategies through cross-breeding programs to release new olive cultivars more suitable for mechanization and use in intensive orchards, with high quality production and resistance to biotic and abiotic stresses. The advancement of breeding programs are hampered by the lack of efficient phenotyping methods to quickly and accurately acquire crop traits such as morphological attributes (tree vigor and vegetative growth habits), which are key to identify desirable genotypes as early as possible. In this context, an UAV-based high-throughput system for olive breeding program applications was developed to extract tree traits in large-scale phenotyping studies under field conditions. The system consisted of UAV-flight configurations, in terms of flight altitude and image overlaps, and a novel, automatic, and accurate object-based image analysis (OBIA) algorithm based on point clouds, which was evaluated in two experimental trials in the framework of a table olive breeding program, with the aim to determine the earliest date for suitable quantifying of tree architectural traits. Two training systems (intensive and hedgerow) were evaluated at two very early stages of tree growth: 15 and 27 months after planting. Digital Terrain Models (DTMs) were automatically and accurately generated by the algorithm as well as every olive tree identified, independently of the training system and tree age. The architectural traits, specially tree height and crown area, were estimated with high accuracy in the second flight campaign, i.e. 27 months after planting. Differences in the quality of 3D crown reconstruction were found for the growth patterns derived from each training system. These key phenotyping traits could be used in several olive breeding programs, as well as to address some agronomical goals. In addition, this system is cost and time optimized, so that requested architectural traits could be provided in the same day as UAV flights. This high-throughput system may solve the actual bottleneck of plant phenotyping of "linking genotype and phenotype," considered a major challenge for crop research in the 21st century, and bring forward the crucial time of decision making for breeders

A systematic literature review

Barriguinha, A., Neto, M. D. C., & Gil, A. (2021). Vineyard yield estimation, prediction, and forecasting: A systematic literature review. Agronomy, 11(9), 1-27. [1789]. https://doi.org/10.3390/agronomy11091789Purpose—knowing in advance vineyard yield is a critical success factor so growers and winemakers can achieve the best balance between vegetative and reproductive growth. It is also essential for planning and regulatory purposes at the regional level. Estimation errors are mainly due to the high inter-annual and spatial variability and inadequate or poor performance sampling methods; therefore, improved applied methodologies are needed at different spatial scales. This paper aims to identify the alternatives to traditional estimation methods. Design/methodology/approach—this study consists of a systematic literature review of academic articles indexed on four databases collected based on multiple query strings conducted on title, abstract, and keywords. The articles were reviewed based on the research topic, methodology, data requirements, practical application, and scale using PRISMA as a guideline. Findings—the methodological approaches for yield estimation based on indirect methods are primarily applicable at a small scale and can provide better estimates than the traditional manual sampling. Nevertheless, most of these approaches are still in the research domain and lack practical applicability in real vineyards by the actual farmers. They mainly depend on computer vision and image processing algorithms, data-driven models based on vegetation indices and pollen data, and on relating climate, soil, vegetation, and crop management variables that can support dynamic crop simulation models. Research limitations—this work is based on academic articles published before June 2021. Therefore, scientific outputs published after this date are not included. Originality/value—this study contributes to perceiving the approaches for estimating vineyard yield and identifying research gaps for future developments, and supporting a future research agenda on this topic. To the best of the authors’ knowledge, it is the first systematic literature review fully dedicated to vineyard yield estimation, prediction, and forecasting methods.publishersversionpublishe