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.     

Development of a high-throughput field phenotyping rover optimized for size-limited breeding fields as open-source hardware

Phenotyping is a critical process in plant breeding, especially when there is an increasing demand for streamlining a selection process in a breeding program. Since manual phenotyping has limited efficiency, high-throughput phenotyping methods are recently popularized owing to progress in sensor and image processing technologies. However, in a size-limited breeding field, which is common in Japan and other Asian countries, it is challenging to introduce large machinery in the field or fly unmanned aerial vehicles over the field. In this study, we developed a ground-based high-throughput field phenotyping rover that could be easily introduced to a field regardless of the scale and location of the field even without special facilities. We also made the field rover open-source hardware, making its system available to public for easy modification, so that anyone can build one for their own use at a low cost. The trial run of the field rover revealed that it allowed the collection of detailed remote-sensing images of plants and quantitative analyses based on the images. The results suggest that the field rover developed in this study could allow efficient phenotyping of plants especially in a small breeding field.     

Root phenotyping: important and minimum information required for root modeling in crop plants

As plants cannot relocate, they require effective root systems for water and nutrient uptake. Root development plasticity enables plants to adapt to different environmental conditions. Research on improvements in crop root systems is limited in comparison with that in shoots as the former are difficult to image. Breeding more effective root systems is proposed as the “second green revolution”. There are several recent publications on root system architecture (RSA), but the methods used to analyze the RSA have not been standardized. Here, we introduce traditional and current root-imaging methods and discuss root structure phenotyping. Some important root structures have not been standardized as roots are easily affected by rhizosphere conditions and exhibit greater plasticity than shoots; moreover, root morphology significantly varies even in the same genotype. For these reasons, it is difficult to define the ideal root systems for breeding. In this review, we introduce several types of software to analyze roots and identify important root parameters by modeling to simplify the root system characterization. These parameters can be extracted from photographs captured in the field. This modeling approach is applicable to various legacy root data stored in old or unpublished formats. Standardization of RSA data could help estimate root ideotypes.     

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.     

水稻叶片叶绿素含量与吸收光谱变量的相关性研究

采用小区试验研究了水稻叶片叶绿素含量与吸收光谱衍生变量的相关性。结果表明：拔节期、抽穗期和灌浆期是水稻叶片诊断的敏感时期;选择最佳的敏感波段组合构造衍生变量,利用光谱衍生变量反演水稻叶片叶绿素含量。发现：在抽穗期和灌浆期,对数相加模型的反演能力明显优于SPAD值的反演能力。SPAD值的反演能力仅在拔节期略优于对数相加模型的反演能力,说明用每个生育期的相应敏感光谱波段对数相加能更加准确地估测叶绿素含量。本文为进一步改进SPAD-502的测量性能提出一些探索性研究。     

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.     

杂交中稻粒肥高效施用量与齐穗期SPAD值关系研究

以杂交中稻组合Ⅱ优602为材料,通过不同基、蘖肥施氮量以塑造施粒肥当时植株营养状况的差异,在此基础上,分别设粒肥施用量处理,探明了粒肥高效施用量与齐穗期库源结构关系。粒肥施用效果与稻齐穗期植株营养水平关系密切,齐穗期剑叶SPAD值、叶片含氮量和群体单位面积的总颖花量3个因子决定粒肥高效施用量。建立了根据齐穗期剑叶SPAD值（x）预测粒肥的高效施氮量(y,kg hm^-2)的回归方程,y =－30.7980x + 1340.9,R² = 0.9114,并指出当齐穗期剑叶的SPAD值高于43.5时,植株营养充足,不需施粒肥,此为临界的苗情诊断指标。     

Pear mutagenesis: In vitro treatment with gamma-rays and field selection for vegetative form traits

In vitro shoots of four pear (Pyrus communis L.) cultivars, 'Conference', 'Doyenné d'Hiver', 'Passe Crassane' and 'Bartlett', were irradiated with gamma rays (3.5 Gy). Around 1000 microcuttings of each cultivar were treated. After three subcultures, microcuttings from both the irradiated shoots and additional non-irradiated shoots were rooted; plants obtained were used to establish a survey orchard in Ostellato (Ferrara), Italy. For the first 2 years in the field, growth and survival were observed, but no data were collected. Subsequently, field surveys were conducted to characterize the population and identify mutants for vegetative traits. Trees that showed phenotypic evidence of vegetative growth characteristics more desirable than those shown by the overall population and by control plants were selected and measured for three years. Traits used for selection were small tree size, wide branch angle and short internodes. Frequencies of variants with compact habit varied with cultivars from 0.5% to 2.7% of irradiated trees. Effect of mutagenic treatment and efficacy of the selection methods are discussed.     

Farmers' Perceptions on Rice Varieties in Sikasso Region of Mali and their Implications for Rice Breeding

Rice is an important staple food and cash crop. Although many varieties of rice have been developed to date, few are adopted possibly because researchers did not take into account farmers’ preferences and perceptions on varieties during the development process. Because farmers increasingly rely on low-yielding landraces, production fails to meet demand. To provide an understanding of farmers’ preferences for rice cultivars and perceptions on drought stress and management practices as inputs to rice breeding research, this study was conducted in the Sikasso region of Mali in September 2005 using participatory rural appraisal approach. A total number of 125 farmers were randomly selected from 10 villages in three ecologies and interviewed individually and in groups. Results showed that farmers’ preferences, crop management practices and ranking of production constraints differed significantly across ecologies. Whereas farmers in the irrigated ecologies preferred high-yielding, long duration rice varieties, those in the upland and lowland ecologies preferred tall plants of short duration. While upland and lowland farmers preferred red and white long grains, respectively, irrigated ecologies were indifferent about grain colour. Farmers appeared willing to trade-off yield for grain quality and plant height, inconsistent with traditional breeders’ selection criteria. The high preference for tall varieties among farmers in the upland and lowland ecologies also contrasted sharply with the model of dwarf rice varieties responsible for the green revolution in Asia. The implication of these findings for rice breeders is that different plant idiotypes complemented by effective drought management practices should target different ecologies to increase impact.     

稻瘟病菌与水稻互作研究进展

为了更好的防控稻瘟病的发生,为水稻育种工作和新药研发提供科学依据,深入了解稻瘟病菌(Magnaporthe oryzae)与水稻相互作用的机制是非常必要的。本文归纳了稻瘟病菌侵染水稻的机制、水稻对稻瘟病菌侵染的信号识别及其下游反应以及识别后诱导水稻产生的防御反应机制,分析了水稻防御相关基因的表达调控以及利用分子育种手段提高水稻抗病性的相关策略。稻瘟病菌侵染水稻后,植株会通过细胞壁加厚、病程相关蛋白表达以及病原菌侵入位点细胞程序性死亡等系统免疫反应来抵御稻瘟病菌的侵染;因此指出通过基因工程手段诱导植物发生免疫反应来抵御稻瘟病菌的危害具有重要的现实意义,也是防治病害最有效和最经济的方法;而且,作为研究病原菌—植物互作的模式系统,深入了解稻瘟病菌与水稻的互作机制,也为通过诱导水稻防御基因的表达来防治其他重要真菌性病害提供了科学依据。     

Quantitative trait loci for agronomic and seed quality traits in an F2 and F4:6 soybean population

Molecular breeding is becoming more practical as better technology emerges. The use of molecular markers in plant breeding for indirect selection of important traits can favorably impact breeding efficiency. The purpose of this research is to identify quantitative trait loci (QTL) on molecular linkage groups (MLG) which are associated with seed protein concentration, seed oil concentration, seed size, plant height, lodging, and maturity, in a population from a cross between the soybean cultivars ‘Essex’ and ‘Williams.’ DNA was extracted from F₂ generation soybean leaves and amplified via polymerase chain reaction (PCR) using simple sequence repeat (SSR) markers. Markers that were polymorphic between the parents were analyzed against phenotypic trait data from the F₂ and F_4:6 generation. For the F₂ population, significant additive QTL were Satt540 (MLG M, maturity, r² = 0.11; height, r² = 0.04, seed size, r²= 0.06], Satt373 (MLG L, seed size, r² = 0.04; height, r² = 0.14), Satt50 (MLG A1, maturity r² = 0.07), Satt14 (MLG D2, oil, r² = 0.05), and Satt251 (protein r² = 0.03, oil, r² =0.04). Significant dominant QTL for the F₂ population were Satt540 (MLG M,height, r² = 0.04; seed size, r² = 0.06) and Satt14 (MLG D2, oil, r² = 0.05). In the F_4:6 generation significant additive QTL were Satt239 (MLGI, height, r² = 0.02 at Knoxville, TN and r² = 0.03 at Springfield, TN), Satt14 (MLG D2, seed size, r² = 0.14 at Knoxville, TN), Satt373 (MLG L, protein, r² = 0.04 at Knoxville, TN) and Satt251 (MLG B1, lodging r² = 0.04 at Springfield, TN). Averaged over both environments in the F_4:6 generation, significant additive QTL were identified as Satt251 (MLG B1, protein, r² = 0.03), and Satt239 (MLG I, height, r² = 0.03). The results found in this study indicate that selections based solely on these QTL would produce limited gains (based on low r² values). Few QTL were detected to be stable across environments. Further research to identify stable QTL over environments is needed to make marker-assisted approaches more widely adopted by soybean breeders. This revised version was published online in July 2006 with corrections to the Cover Date.     

Pear mutagenesis: In vitro treatment with gamma-rays and field selection for productivity and fruit traits

In vitro shoots of six pear (Pyrus communis L.) cultivars, ‘Conference’, ‘Doyennéd'Hiver’, ‘Passe Crassane’, ‘Bartlett’, ‘AbbéFetel’ and ‘Butirra Precoce Morettini’ were irradiated with gamma rays (3.5 Gy). After three subcultures, microcuttings from the irradiated shoots and from additional non-irradiated microcuttings were rooted to establish plants for survey orchards. All trees were individually observed for variation in fruit traits and for productivity. Trees were selected for improved characters related to production such as early bearing and consistent productivity. Variations observed in fruit appearance concerned degree of russeting, fruit shape and size. The frequencies of the observed variations in fruit traits depended on the cultivar, ranging from 0.81% in ‘Doyennéd'Hiver’ to 3.64% in ‘Passe Crassane’. Of the 97 variants selected, only two showed chimeral behavior. This revised version was published online in July 2006 with corrections to the Cover Date.     

玉米杂交种选育专家系统的设计与实现

“玉米杂交种选育专家系统”是根据我国著名玉米遗传育种学家经验建立的，以Turbo-Prolog、C语言实现。可在长城、Super、AST、Compaq等微机上运行，能协助育种工作者进行自交系亲本选择、组合配置，事实库管理和杂交种综合评价。 本文介绍了系统的基本结构、主要功能、实现系统的主要技术和应用情况     

Collaborative and consultative participatory plant breeding of rice for the rainfed uplands of eastern India

We describe a participatory plant breeding (PPB) programme in rice for the rainfed uplands of eastern India. Collaborative participation (farmers grew and selected in segregating materials in their fields) and consultative participation (farmers selected among progenies in researchers' plots) were used. The PPB was started with only two crosses and, of these, Kalinga III/IR64 was the most successful and produced two released varieties: Ashoka 200F from collaborative breeding and Ashoka 228 from consultative breeding. Both yielded significantly more than control varieties, including Kalinga III, in research trials and in participatory trials in farmers' fields. Qualitative data from participatory trials was highly informative, statistically analysable, and cheaper to obtain than quantitative data. In low-yielding research-station and on-farm trials the two new upland varieties showed no significant genotype × environment interaction with the check varieties. However, in higher-yielding All India Coordinated Rice Improvement Project trials, both varieties were more adapted to low yielding environments than the national check variety. Farmers liked the varieties for their early maturity, improved lodging resistance, higher fodder and grain yield, long-slender grains and excellent cooking quality. Before certified seed production, farmer groups have produced large quantities of seed that have spread widely through informal channels. The returns from PPB, compared to conventional breeding, were higher because it cost less, the genetic gains per year were higher, and the benefits to farmers were realised earlier. This revised version was published online in August 2006 with corrections to the Cover Date.     

Breeding for insect resistance in oilseed rape: Challenges,current knowledge and perspectives

Dealing with insect pests is one of the biggest challenges facing the cultivation of oilseed rape (Brassica napus, OSR). Insect pests are usually controlled using insecticides, but the increasing occurrence of insecticide‐resistant populations and the socio‐economic context argue against the sole use of these substances. Plant resistance is a classical and proven alternative crop protection strategy that is the basic tool of integrated pest management. However, no insect‐resistant OSR cultivar is currently available on the market. Here, I review some of the constraints that make phenotyping for insect resistance particularly challenging with OSR and give perspectives to develop this resistance. Some studies have proved that breeding OSR for insect resistance could be achieved, and three strategies have been considered: introducing resistance transgenes into the OSR genome, exploiting natural variation in resistance already present in B. napus and introgressing resistance from other brassicaceous species. The white mustard, Sinapis alba, seems a particularly promising source of resistance against most of the OSR insect pests.     

Conventional and contemporary approaches for drought tolerance rice breeding: Progress and prospects

Drought is becoming a major threat to rice farming across the globe owing to the depletion of water tables in rice-growing belts. Drought affects rice plants at multiple stages, causing damage at morphological and physio-biochemical levels, leading to severe losses that exceed losses from all other stresses. The amalgamation of conventional breeding methods with modern molecular biology tools and biometrical methods could help accelerate the genetic gain for drought tolerance in rice. Many drought-tolerance traits with genetic determinants have been identified and exploited for tolerance rice variety breeding. The integration of genome-wide association study and genomic selection tools with speed breeding shortened the breeding cycle and aided in rapid improvement of genetic gain. In this review, we emphasized the progress made through classical breeding as well as the limitations and usefulness of current genomic methods in improving drought tolerance. We briefly addressed methods for identifying genetic determinants for drought tolerance and deploying them through genomics-assisted breeding programmes to develop high-yielding drought-tolerant rice cultivars.     

Osmotic potential at full turgor: an easily measurable trait to help breeders select for drought tolerance in wheat

This study investigated the relationship between osmotic potential at full hydration (π₁₀₀) and turgor loss point (Ψ_TLP) in wheat (Triticum aestivum) to determine the potential of using π₁₀₀ to predict Ψ_TLP under well‐watered (WW) and drought (WS) conditions. Two methods for determining π₁₀₀ were tested: pressure–volume (PV) analysis and freezing point osmometry. The study also measured π₁₀₀ in a range of 38 field‐grown wheat cultivars to determine whether there is genetic variation in π₁₀₀ under field conditions. π₁₀₀ correlated with Ψ_TLP using both methods under both water treatments, particularly WS. Genetic variation of π₁₀₀ in the field, under rainfed conditions, was greater than controlled conditions and ranged from ?0.94 to ?1.95 MPa. Overall, the evidence supports development of π₁₀₀ as a novel tool for plant breeders to screen large populations of wheat and identify genotypes with lower Ψ_TLP, an integrative trait that is related to drought tolerance.     

Improving participatory varietal selection processes: participatory varietal selection and the role of informal seed diffusion mechanisms for upland rice in Ghana

This paper considers the process of Participatory Varietal Selection (PVS) and presents approaches and ideas based on PVS activities conducted on upland rice throughout Ghana between 1997 and 2003. In particular the role of informal seed systems in PVS is investigated and implications for PVS design are identified. PVS programmes were conducted in two main agroecological zones, Forest and Savannah, with 1,578 and 1,143 mm of annual rainfall, respectively, and between 40 and 100 varieties tested at each site. In the Savannah zone IR12979-24-1 was officially released and in the Forest zone IDSA 85 was widely accepted by farmers. Two surveys were conducted in an area of the Forest zone to study mechanisms of spread. Here small amounts (1–2 kg) of seed of selected varieties had been given to 94 farmers. In 2002, 37% of 2,289 farmers in communities surveyed had already grown a PVS variety and had obtained seed via informal mechanisms from other farmers, i.e. through gift, exchange or purchase. A modified approach for PVS is presented which enables important issues identified in the paper to be accommodated. These issues include: utilising existing seed spread mechanisms; facilitating formal release of acceptable varieties; assessing post-harvest traits, and; the need for PVS to be an ongoing and sustainable process.     

Local adjustment method for field experiments. 2. Application in experiments with and without replications

Summary Presented are the results of an application of the local adjustment Field-method in the analysis of the real field experiments without replications and in experiments with pseudo- and random replications. It was found that the local adjustment allowed a more precise estimation of the real values of genotypes in all kinds of experiments over a wide interval of spatial heterogeneity. The results obtained indicate that by simply using up to 5 random replications the decrease of the spatial effects is inadequate for fields with medium and high soil heterogeneity or with unsuccessful randomization. The Field-method which has sufficient precision in evaluating spatial heterogeneity, considerably increases the reliability of estimates in experiments even with a small number of replications or with unsuccessful randomization. Therefore, for all field experiments that have fulfilled the necessary requirements the Field-method is recommended as an obligatory statistical procedure for a prior data analysis as it allows an accurate estimation of the real character expression of genotypes, as well as the random variance in experiments without replication and the parameters of ANOVA in ones with pseudo- and random replications.