3D modeling and reconstruction of plants and trees: A cross-cutting review across computer graphics,vision, and plant phenotyping

This paper reviews the past and current trends of three-dimensional (3D) modeling and reconstruction of plants and trees. These topics have been studied in multiple research fields, including computer vision, graphics, plant phenotyping, and forestry. This paper, therefore, provides a cross-cutting review. Representations of plant shape and structure are first summarized, where every method for plant modeling and reconstruction is based on a shape/structure representation. The methods were then categorized into 1) creating non-existent plants (modeling) and 2) creating models from real-world plants (reconstruction). This paper also discusses the limitations of current methods and possible future directions.     

High-throughput field crop phenotyping: current status and challenges

In contrast to the rapid advances made in plant genotyping, plant phenotyping is considered a bottleneck in plant science. This has promoted high-throughput plant phenotyping (HTP) studies, resulting in an exponential increase in phenotyping-related publications. The development of HTP was originally intended for use as indoor HTP technologies for model plant species under controlled environments. However, this subsequently shifted to HTP for use in crops in fields. Although HTP in fields is much more difficult to conduct due to unstable environmental conditions compared to HTP in controlled environments, recent advances in HTP technology have allowed these difficulties to be overcome, allowing for rapid, efficient, non-destructive, non-invasive, quantitative, repeatable, and objective phenotyping. Recent HTP developments have been accelerated by the advances in data analysis, sensors, and robot technologies, including machine learning, image analysis, three dimensional (3D) reconstruction, image sensors, laser sensors, environmental sensors, and drones, along with high-speed computational resources. This article provides an overview of recent HTP technologies, focusing mainly on canopy-based phenotypes of major crops, such as canopy height, canopy coverage, canopy biomass, and canopy stressed appearance, in addition to crop organ detection and counting in the fields. Current topics in field HTP are also presented, followed by a discussion on the low rates of adoption of HTP in practical breeding programs.     

Genetic improvement for root growth angle to enhance crop production

The root system is an essential organ for taking up water and nutrients and anchoring shoots to the ground. On the other hand, the root system has rarely been regarded as breeding target, possibly because it is more laborious and time-consuming to evaluate roots (which require excavation) in a large number of plants than aboveground tissues. The root growth angle (RGA), which determines the direction of root elongation in the soil, affects the area in which roots capture water and nutrients. In this review, we describe the significance of RGA as a potential trait to improve crop production, and the physiological and molecular mechanisms that regulate RGA. We discuss the prospects for breeding to improve RGA based on current knowledge of quantitative trait loci for RGA in rice.     

Importance of individual root traits to understand crop root system in agronomic and environmental contexts

Resource acquisition, one of the major functions of roots, can contribute to crop growth and mitigating environmental impacts. The spatio-temporal distribution of roots in the soil in relation to the dynamics of the soil resources is critical in resource acquisition. Root distribution is determined by root system development. The root system consists of many individual roots of different types and ages. Each individual root has specific development, resource acquisition, and transport traits, which change with root growth. The integration of individual root traits in the root system could exhibit crop performance in the various environments via root distribution in the soil. However, the relationship between individual root traits and the pattern of root distribution is complicated. To understand this complicated relationship, we need to evaluate enormous numbers of individual root traits and understand the relationship between individual root development and root distribution as well as the integrated functions of individual root traits along with dynamics of resources in the soil.     

Including root architecture in a crop model improves predictions of spring wheat grain yield and above‐ground biomass under water limitations

Although the root length density (RLD) of crops depends on their root system architecture (RSA), the root growth modules of many 1D field crop models often ignored the RSA in the simulation of the RLD. In this study, two model set‐up scenarios were used to simulate the RLD, above‐ground biomass (AGB) and grain yield (GY) of water‐stressed spring wheat in Germany, aiming to investigate the impact of improved RLD on AGB and GY predictions. In scenario 1, SlimRoot, a root growth sub‐model that does not consider the RSA of the crop, was coupled to a Lintul5‐SlimNitrogen‐SoilCN‐Hillflow1D crop model combination. In scenario 2, SlimRoot was replaced with the Somma sub‐model which considered the RSA for simulating RLD. The simulated RLD, AGB and GY were compared with observations. Scenario 2 predicted the RLD, AGB and GY with an average root mean square error (RMSE) of 0.43 cm/cm³, 0.59 t/ha and 1.03 t/ha, respectively, against 1.03 cm/cm³, 1.20 t/ha and 2.64 t/ha for scenario 1. The lower RMSE under scenario 2 shows that, even under water‐stress conditions, predictions of GY and AGB can be improved by considering the RSA of the crop for simulating the RLD.     

Utilization of molecular markers for improving the phosphorus efficiency in crop plants

Phosphorus (P) is the second most growth limiting macronutrient after nitrogen and plays several important roles in all organisms including plants. In soil, P is available in both organic and inorganic forms. P deficiency reduces the growth and yield of several crop plants. Plants respond to P deficiency by the phenotypic changes especially by the modification of root architecture. Molecular marker‐assisted breeding (MAB) has been proposed as an important tool to identify and develop improved varieties of crop plants with efficient P‐use efficiency (PUE). Identification of quantitative trait loci (QTLs) for traits related to PUE has been considered as the first step in marker‐assisted selection (MAS) and improvement of crop yield programmes. In this review, we describe in detail on architectural changes of roots under P deficiency that are reported in various crops and discuss the efforts made to improve PUE using molecular marker tools. Details on QTLs identified for low P‐stress tolerance in various crop plants are presented. These QTLs can be used to improve PUE in crop plants through MAS and breeding, which may be beneficial to improve the yields under P‐deficient soil. Development of new and improved varieties using MAB will limit the use of non‐renewable fertilizers and improve PUE of key crop plants in low input agriculture.     

WIPPER: an accurate and efficient field phenotyping platform for large-scale applications

More accurate, rapid, and easy phenotyping tools are required to match the recent advances in high-throughput genotyping for accelerating breeding and genetic analysis. The conventional data recording in field notebooks and then inputting data to computers for further analysis is inefficient, time-consuming, laborious, and prone to human error. Here, we report WIPPER (for Wireless Plant Phenotyper), a new phenotyping platform that combines field phenotyping and data recording with the aid of Bluetooth communication, thus saving time and labor not only for field data recoding but also for inputting data to computers. Additionally, it eliminates the risk of human error associated with phenotyping and inputting data. We applied WIPPER to 100 individuals of a rice recombinant inbred line (RIL) for measuring leaf width and relative chlorophyll content (SPAD value), and were able to record an accurate data in a significantly reduced time compared with the conventional method of data collection. We are currently using WIPPER for routine management of rice germplasm including recording and documenting information on phenotypic data, seeds, and DNA for their accelerated utilization in crop breeding.     

Modulation of plant root traits by nitrogen and phosphate: transporters,long-distance signaling proteins and peptides,and potential artificial traps

As sessile organisms, plants rely on their roots for anchorage and uptake of water and nutrients. Plant root is an organ showing extensive morphological and metabolic plasticity in response to diverse environmental stimuli including nitrogen (N) and phosphorus (P) nutrition/stresses. N and P are two essential macronutrients serving as not only cell structural components but also local and systemic signals triggering root acclimatory responses. Here, we mainly focused on the current advances on root responses to N and P nutrition/stresses regarding transporters as well as long-distance mobile proteins and peptides, which largely represent local and systemic regulators, respectively. Moreover, we exemplified some of the potential pitfalls in experimental design, which has been routinely adopted for decades. These commonly accepted methods may help researchers gain fundamental mechanistic insights into plant intrinsic responses, yet the output might lack strong relevance to the real situation in the context of natural and agricultural ecosystems. On this basis, we further discuss the established—and yet to be validated—improvements in experimental design, aiming at interpreting the data obtained under laboratory conditions in a more practical view.     

Development of a plant conveyance system using an AGV and a self-designed plant-handling device: A case study of DIY plant phenotyping

Plant phenotyping technology has been actively developed in recent years, but the introduction of these technologies into the field of agronomic research has not progressed as expected, in part due to the need for flexibility and low cost. “DIY” (Do It Yourself) methodologies are an efficient way to overcome such obstacles. Devices with modular functionality are critical to DIY experimentation, allowing researchers flexibility of design. In this study, we developed a plant conveyance system using a commercial AGV (Automated Guided Vehicle) as a case study of DIY plant phenotyping. The convey module consists of two devices, a running device and a plant-handling device. The running device was developed based on a commercial AGV Kit. The plant-handling device, plant stands, and pot attachments were originally designed and fabricated by us and our associates. Software was also developed for connecting the devices and operating the system. The run route was set with magnetic tape, which can be easily changed or rerouted. Our plant delivery system was developed with low cost and having high flexibility, as a unit that can contribute to others’ DIY’ plant research efforts as well as our own. It is expected that the developed devices will contribute to diverse phenotype observations of plants in the greenhouse as well as to other important functions in plant breeding and agricultural production.     

小麦种子根结构及胚芽鞘长度的QTL分析

为探讨小麦种子根结构及胚芽鞘长度的遗传基础,以小麦DH群体(旱选10号×鲁麦14)的150个株系为材料,利用凝胶室培养幼苗,测定种子根的数目和最大根长、胚芽鞘长度、根苗干重比等性状,并通过扫描仪测定幼苗种子根的总长度、根直径及角度。利用已经构建的DH群体遗传连锁图谱,采用基于混合线性模型的复合区间作图法分析上述性状的QTL。在1A、1B、2B、2D、3B、4A、4D、5A、5B、6A、7A和7B共12条染色体上检测到12个加性效应QTL和7对加性×加性互作效应QTL。QTL的加性效应值在0.02~8.45之间,对表型变异的贡献率为5.64%~12.37%。7对加性×加性互作效应QTL分布在1A–2B(2)、1A–6A、1B–2D、5B–6A、6A–7A和6A–7B等6对染色体之间,其互作效应值为0.20~7.45,对表型变异的贡献率为8.70%~15.90%。在染色体3B和7A上各检测到1个种子根结构相关性状的QTL簇。     

The Influence of Soil Volume on Root and Shoot Parameters in Container-grown Oilseed Rape

Oilseed rape was grown under irrigated conditions at equal plant density per unit area in PVC cylinders of 1 m length with different diameter (0.11, 0.16 and 0.20m). The influence of soil volume, expressed as cylinder diameter, was found not to be significant on root dry weight, root length, root surface area or the shoot: root ratio. However, a significant influence was found on shoot and seed dry weights. It was concluded that cylinders with a length of 1 m and a diameter of a minimum of 0.11 m are appropriate for the study of container-grown root systems.     

Heritability and gene effects for root characteristics in peas measured at flowering

Summary Heritability and gene effects for root weight, root volume and root to shoot weight ratio were determined in peas (Pisum sativum L.) at flowering. The populations used were developed from four crosses between lines and cultivars differing in size of the root systems. Broad-sense heritability was between 0.41 and 0.81 for root weight, and between 0.44 and 0.77 for root volume. Additive and dominance effects were important in the genetic control of root weight and volume in all populations, while epistatic effects were important only in two populations. The importance of the genetic parameters in the control of root to shoot weight ratio was unclear. Assuming high correlations between root growth in soil-filled pots in the greenhouse and growth in the field, with the presence of large additive effects and high heritability estimates for root weight and volume, selection for superior pure lines with large root systems should be effective.     

Genetic variation for maize root architecture in response to drought stress at the seedling stage

Although the root system is indispensable for absorption of nutrients and water, it is poorly studied in maize owing to the difficulties of direct measurement of roots. Here, 103 maize lines were used to compare root architectures under well-watered and water-stressed conditions. Significant genetic variation, with medium to high heritability and significant correlations, was observed for root traits. Total root length (TRL) and total root surface area (TSA) had high phenotypical diversity, and TRL was positively correlated with TSA, root volume, and root forks. The first two principal components explained 94.01% and 91.15% of total root variation in well-watered and water-stressed conditions, respectively. Thus, TRL and TSA, major contributors to root variation, can be used as favorable selection criteria at the seedling stage. We found that stiff stalk and non-stiff stalk groups (temperate backgrounds) showed relatively higher mean values for root morphological diversity than the TST group (tropical/subtropical background). Of the tested lines, 7, 42, 45, and 9 were classified as drought sensitive, moderately sensitive, moderately drought tolerant, and highly drought tolerant, respectively. Seven of the 9 extremely drought tolerant lines were from the TST group, suggesting that TST germplasms harbor valuable genetic resources for drought tolerance that could be used in breeding to improve abiotic stress tolerance in maize.     

Protoplast technology in relation to crop plants: Progress and problems

Summary The ready availability of isolated plant protoplasts, and the ability of these naked plant cells to fuse together, has greatly stimulated interest in the production of plant somatic hybrids. This new protoplast technology may enable interspecies hybrids to be obtained which are otherwise not possible. Many such interspecies hybrids are required amongst the crop plants, but application of this new technology to these species in presently prevented by our inability to culture cells of many of these species in vitro, and to regenerate plants reproducibly from cultured tissue.Agricultural Research Council Group, Department of Botany, University of Nottingham, U.K.     

甜菜根腐病的发生及防治研究进展

甜菜根腐病是甜菜产区的主要病害之一,也是世界上较难防治的植物病害。为进一步研究甜菜根腐病有效的防治措施,综述了70余篇文献,特别是甜菜根腐病的症状、病原物、发病因素和防治措施的研究进展,发现有关甜菜根腐病症状类型描述及病原种群鉴定的研究比较系统,而关于发病因素和防治措施的研究还存在不足。今后还需进一步研究甜菜根腐病的发病因素,实现对甜菜根腐病的预测预报,从而科学地指导防治,继续挖掘甜菜根腐病拮抗菌群及完善生防制剂地制备和应用,充分发挥生物防治的作用。     

免耕对水稻根系活力和产量性状的影响

对早稻进行了免耕与常耕栽培对比试验。研究结果表明：与常耕栽培水稻相比,免耕水稻,根系活力高7.4%~34.9%,各生育期的干物质占黄熟期干物质之比高。有效穗数、每穗实粒数、千粒重和实际产量分别高1.1%、5.1%、0.6%和10.0%。产量与根系活力和干物质积累的相关分别达到0.9和0.87以上。     

泰州市郊区土壤与作物施肥信息系统研究与开发

运用农业信息技术原理与方法,结合泰州市郊区实际,开发出了功能全面、内容丰富、现势性强、图形生产力高、界面友好、易于操作的基于Visual Basic 6.0和MapObjects 2.3的泰州市郊区土壤与作物施肥信息系统V1.0。该系统涵盖了数据查询检索、空间分析、精确施肥决策、学习辅助等功能。经试用,系统的功能可用性、功能可靠性、易用性、可扩充性较强,用户满意度较高,可为该地推广应用土壤管理与水稻、小麦精确施肥技术提供辅助决策与智能学习优质平台。     

山西省小麦苗期根系性状及抗旱特性分析

小麦苗期根系形态是成株期根系分布的基础,与抗逆和产量密切相关,全面认识苗期根系及抗旱特性,对于抗旱优异种质的利用和早期筛选具有重要意义。采用239份山西省小麦品种(系)在土培条件下,研究了苗期根系性状及对水分胁迫的响应。结果表明,正常生长下山西小麦苗期根系性状多样性丰富,地方种变异最大;不同年代品种中,除最大根长随年代略下降外,其他性状均呈先升后降的趋势;不同根系性状对水分胁迫响应存在差异,总根长对水分最敏感,其次为根表面积、根体积和根生物量,最大根长和平均根数不敏感。苗期根系综合抗旱能力随年代呈先降后升的趋势,地方种和20世纪70年代品种多为中抗,80和90年代的品种抗旱性较低,2000年以后审定品种的抗性较高,其中旱地品种抗性最好。苗期根系抗旱特性与产量性状相关分析发现,最大根长、总根长、根体积和根生物量与雨养条件下的千粒重和产量显著正相关,最大根长和根生物量与成株期抗旱性也显著正相关。因此苗期最大根长和根生物量可作为半干旱地区旱地育种过程中抗旱性和产量的早期筛选指标。     

小麦不同磷效率基因型的子母盆栽试验

本研究以小麦磷效率典型基因型为材料,以磷酸三钙为磷源,以水平分根试验为基本方法研究麦对难溶态磷酸直斩活化、吸收机理。当磷酸三钙置于营养液时,磷和基因型洛夫林１０号的吸钙量为磷低产和基因型,“中国春”和８０－５５和２．７和３．６倍。其磷素净活化,吸收量分别较之高３０％和７７％。当磷酸三钙置于石英砂中,两类基因型对钙的吸收或对磷的活化,积累保持着类似的趋势。在这种情况下,“中国春”和８０－５５都不能完