Exploiting High-Throughput Indoor Phenotyping to Characterize the Founders of a Structured B. napus Breeding Population

Applications of synchrotron light in seed research: an array of x-ray and infrared imaging methodologies

Synchrotron radiation (SR) provides a wide spectrum of bright light that can be tailored to test myriad research questions. SR provides avenues to illuminate structure and composition across scales, making it ideally suited to the study of plants and seeds. Here, we present an array of methodologies and the data outputs available at a light source facility. Datasets feature seed and grain from a range of crop species including Citrullus sp. (watermelon), Brassica sp. (canola), Pisum sativum (pea), and Triticum durum (wheat), to demonstrate the power of SR for advancing plant science. The application of SR micro-computed tomography (SR-µCT) imaging revealed internal seed microstructures and their three-dimensional morphologies in exquisite detail, without the need for destructive sectioning. Spectroscopy in the infrared spectrum probed sample biochemistry, detailing the spatial distribution of seed macronutrients such as lipid, protein and carbohydrate in the embryo, endosperm and seed coat. Methods using synchrotron X-rays, including X-ray absorption spectroscopy (XAS) and X-ray fluorescence (XRF) imaging revealed elemental distributions, to spatially map micronutrients in seed subcompartments and to determine their speciation. Synchrotron spectromicroscopy (SM) allowed chemical composition to be resolved at the nano-scale level. Diverse crop seed datasets showcase the range of structural and chemical insights provided by five beamlines at the Canadian Light Source, and the potential for synchrotron imaging for informing plant and agricultural research.

Drought induced metabolic shifts and water loss mechanisms in canola: role of cysteine, phenylalanine and aspartic acid

Drought conditions severely curtail the ability of plants to accumulate biomass due to the closure of stomata and the decrease of photosynthetic assimilation rate. Additionally, there is a shift in the plant's metabolic processes toward the production of metabolites that offer protection and aid in osmoadaptation, as opposed to those required for development and growth. To limit water loss via non-stomatal transpiration, plants adjust the load and composition of cuticle waxes, which act as an additional barrier. This study investigates the impact of soil water deficit on stomatal and epicuticular water losses, as well as metabolic adjustments in two canola (Brassica napus L.) cultivars-one drought-tolerant and the other drought-sensitive. Specifically, we examined the effect of a drought treatment, which involved reducing water holding capacity to 40%, on the levels of cysteine, sucrose, and abscisic acid (ABA) in the leaves of both cultivars. Next, we looked for potential differences in night, predawn, and early morning transpiration rates and the epicuticular wax load and composition in response to drought. A substantial rise in leaf cysteine was observed in both canola cultivars in response to drought, and a strong correlation was found between cysteine, ABA, and stomatal conductance, indicating that cysteine and sulfur may play a role in controlling stomatal movement during drought stress. Attributes related to CO2 diffusion (stomatal and mesophyll conductance) and photosynthetic capacity were different between the two canola cultivars suggesting a better management of water relations under stress by the drought-tolerant cultivar. Epicuticular waxes were found to adjust in response to drought, acting as an additional barrier against water loss. Surprisingly, both canola cultivars responded similarly to the metabolites (cysteine, sucrose, and ABA) and epicuticular waxes, indicating that they were not reliable stress markers in our test setup. However, the higher level of phenylalanine in the drought-tolerant canola cultivar is suggestive that this amino acid is important for adaptation to drier climates. Furthermore, a multitrait genotype-ideotype distance index (MGIDI) revealed the likely role of aspartic acid in sustaining nitrogen and carbon for immediate photosynthetic resumption after drought episodes. In conclusion, leveraging amino acid knowledge in agriculture can enhance crop yield and bolster resistance to environmental challenges.

An Overview of High-Throughput Crop Phenotyping: Platform, Image Analysis, Data Mining, and Data Management

In this chapter, we explore the application of high-throughput crop phenotyping facilities for phenotype data acquisition and the extraction of significant information from the collected data through image processing and data mining methods. Additionally, the construction and outlook of crop phenotype databases are introduced and the need for global cooperation and data sharing is emphasized. High-throughput crop phenotyping significantly improves accuracy and efficiency compared to traditional measurements, making significant contributions to overcoming bottlenecks in the phenotyping field and advancing crop genetics.

Seasonal pigment fluctuation in diploid and polyploid Arabidopsis revealed by machine learning-based phenotyping method PlantServation

Long-term field monitoring of leaf pigment content is informative for understanding plant responses to environments distinct from regulated chambers but is impractical by conventional destructive measurements. We developed PlantServation, a method incorporating robust image-acquisition hardware and deep learning-based software that extracts leaf color by detecting plant individuals automatically. As a case study, we applied PlantServation to examine environmental and genotypic effects on the pigment anthocyanin content estimated from leaf color. We processed >4 million images of small individuals of four Arabidopsis species in the field, where the plant shape, color, and background vary over months. Past radiation, coldness, and precipitation significantly affected the anthocyanin content. The synthetic allopolyploid A. kamchatica recapitulated the fluctuations of natural polyploids by integrating diploid responses. The data support a long-standing hypothesis stating that allopolyploids can inherit and combine the traits of progenitors. PlantServation facilitates the study of plant responses to complex environments termed "in natura".