Editorial: Spectroscopy for Crop and Product Phenotyping

Spectroscopy is a viable technique for exploring plant biochemistry in an efficient, accurate and typically non-destructive manner (Schie et al., 2018). By taking advantage of the properties of plant biomolecules and metabolites in different regions of the electromagnetic spectrum, advances have been made that allow for investigations into previously inaccessible aspects of biology in real-time (Akhgar et al., 2020). Other important advances involve disease diagnostics, early stress detection and plant product quality assessment (Gemperline et al., 2016). High-throughput technologies for nucleotide sequence analysis and detection of sequence variation have been increasingly used for plant genotyping and other fields of genetic testing. Polymerase chain reaction (PCR) is a simple and rapid method that can detect molecular genetic polymorphisms in basic and applied research applications. An important prospective use of PCR-based genotyping assays is to perform large-scale phenotyping analyses (Suyama and Matsuki, 2015), mutant screens, and comparative physiological analyses for Marker Assisted Breeding. This Research Topic highlights novel and innovative applications of all spectroscopic techniques that aim for characterization in plants in order to understand plant growth and productivity. Studies featuring impactful and innovative applications of well-established methodologies such as Raman spectroscopy, Near-infrared spectroscopy, Fluorescence resonance energy transfer, hyperspectral imaging, or a novel combination of spectrometric measurement techniques and novel spectrometric techniques were invited, resulting in 8 published articles. Infrared and Near-infrared spectroscopy (NIR) spectroscopy Infrared spectroscopy (Gillie et al., 2000) is becoming an increasingly popular and promising technology in agricultural and agri-food industries to measure intact, fresh, and unfrozen samples directly. The field of infrared spectroscopy is complex and comprehensive and could lead to specialized solutions for the agricultural sector in general, and for the viticultural industry in particular. Wyngaard et al., show that infrared spectroscopy is implemented for continuous monitoring of key metabolites in grapevine organs throughout the growing season. The observed spectral changes led to the classification of grapevine organs, providing individualized calibrations to compensate for the heterogeneity in grapevines, as well as developing more robust prediction models. Near-infrared spectroscopy is a non-destructive, fast, and low-cost method to measure the biochemicals for screening plant samples. Armstrong et al., investigate the feasibility of single kernel NIR spectroscopy for rapid determination of protein, oil, and weight in intact single sorghum seeds, highlighting the use of this non-destructive and quick method for screening these traits in sorghum breeding and industry applications. In the work of Ejaz et al., biochemical components of sorghum were predicted for enhancing grain sorting efficiency for food, feed, and fuel, using Fourier-transform NIR spectroscopy. Raman Spectroscopy-based Plant Pathology Diagnostics Raman spectroscopy (RS) is a label-free, non-invasive, non-destructive spectroscopic technique that is effective for studying the chemical structure of analyzed samples (Cialla-May et al., 2022). This technique has been widely used among biochemists, and has now found applications in agronomy, plant pathology and physiology for analysis of plant health status. Changes in plant biochemistry can be probed by Raman spectroscopy, allowing its use in confirmatory diagnosis of plant pathology. Dou et al., use RS to develop the diagnosis of Huanglongbing, a devastating disease caused by Candidatus Liberibacter spp. (Ca. L. asiaticus). By using a combination of HPLC and image studies of leaves, they created a ground truth concept demonstrating that a given signature in RS corresponds to increased p-coumaric acid and decreased lutein in infected grapefruit leaves. Since Raman spectroscopy can be used to resolve stress-induced changes in plant biochemistry on the molecular level, it represents a prospective and rapid technique for agronomy and plant pathology. Farber et al., show that RS can be used for highly accurate identification of stalk rot caused by Colletotrichum graminicola in maize at both early and late stages of disease progression, via spectroscopic analysis of both leaves and stalks. High-Resolution Microscopy and Spectrometry Approach The rhizosphere is a hotspot for microbial activity, organic carbon input, and carbon turnover in soils (Ilhardt et al., 2019). Several stand-alone and combinatorial methods have been developed to investigate the chemistry and the role of microbes in soil and the rhizosphere. Bandara et al., present a novel approach that allows simultaneous microbial identification and chemical analysis of the rhizosphere at a spatial resolution ranging from micro- to nanometers. This new method allows for comprehensive study of the spatio-temporal organization of nutrients and microbes in the rhizosphere at an unprecedented scale and provides a platform for a mechanistic understanding of complex patterns of interactions between roots, the microbiome and soil using a correlative microscopy approach. Lohse et al., present a novel workflow using laser desorption ionization combined with mass spectrometric imaging to directly analyze plant metabolites in a complex soil matrix. The target metabolites were detected with a spatial resolution of 25 μm in the root and surrounding soil, based on accurate masses using ultra-high mass resolution laser desorption ionization Fourier-transform ion cyclotron resonance mass spectrometry. Direct molecular imaging allows a non-targeted or targeted analysis of plant metabolites in undisturbed soil samples, paving the way to study the turnover of root-derived organic carbon in the rhizosphere with high chemical and spatial resolution. PCR genotyping Single-nucleotide polymorphisms (SNPs) represent the smallest type of genetic differences in DNA between biological samples (Campbell et al., 2015). SNP analysis has emerged as one of the most powerful tools employed over a wide range of research, from small-scale student-led investigations of specific SNPs to high-throughput microarray technologies to analyze thousands of SNPs simultaneously. Kalendar et al., propose a modification to improve the version of the existing Allele-specific PCR method that is similar to the Kompetitive allele specific PCR (KASP) technique for genotyping SNPs based on fluorescence resonance energy transfer (FRET). This new technique is based on the simultaneous presence of two components in the PCR: an allele-specific mixture (allele-specific and common primers), and a template-independent detector mixture that contains two to four universal probes and a single universal quencher oligonucleotide (Kalendar et al., 2022). The SNP site is positioned preferably at a penultimate base in each allele-specific primer, which increases the reaction specificity and allele discrimination. The proposed method was used for SNP genotyping in barley genes HvSAP16 and HvSAP8, and is suitable for bi-allelic uniplex, 3- or 4-allelic variants, or different SNPs in a multiplex format that can be used in a range of applications including medical, forensic, or any study involving SNP genotyping. Overall, the research collected on this Research Topic highlights innovative and promising applications of all spectroscopic techniques for characterizing plants to understand plant growth, productivity, and disease resistance, and for PCR-based genotyping to perform large-scale mutant screens, comparative analysis for Marker Assisted Breeding.Non peer reviewe

Phylogeny of Abildgaardieae (Cyperaceae) Inferred from ITS and trnL–F Data

Within the tribe Abildgaardieae, the relationships between Fimbristylis and its relatives have not been certain, and the limits of Fimbristylis have been unclear, with Bulbostylis and Abildgaardia variously combined with it and each other. The relationships and limits of tribes Abildgaardieae and Arthrostylideae and their genera were evaluated across 49 representative species using parsimony and maximum likelihood analyses of ITS (nuclear ribosomal) and trnL–F (plastid) DNA sequence data separately and combined. The evolutionary reconstructions derived from sequences of cpDNA and nrDNA disagree about the position of tribe Arthrostylideae relative to Abildgaardieae; Arthrostylis and Actinoschoenus are either nested within Abildgaardieae (trnL–F data) or very closely related to this tribe (ITS data). The reconstructions also disagree about the monophyly of genus Abildgaardia (excluding A. vaginata). Crosslandia and A. vaginata form a clade that is nested within Fimbristylis. Bulbostylis is monophyletic and clearly separated from Fimbristylis. Further sampling of taxa and characters is needed to resolve and/or strengthen support for some of these ‘‘deep’’ and fine-scale relationships

Review:New sensors and data-driven approaches—A path to next generation phenomics

At the 4th International Plant Phenotyping Symposium meeting of the International Plant Phenotyping Network (IPPN) in 2016 at CIMMYT in Mexico, a workshop was convened to consider ways forward with sensors for phenotyping. The increasing number of field applications provides new challenges and requires specialised solutions. There are many traits vital to plant growth and development that demand phenotyping approaches that are still at early stages of development or elude current capabilities. Further, there is growing interest in low-cost sensor solutions, and mobile platforms that can be transported to the experiments, rather than the experiment coming to the platform. Various types of sensors are required to address diverse needs with respect to targets, precision and ease of operation and readout. Converting data into knowledge, and ensuring that those data (and the appropriate metadata) are stored in such a way that they will be sensible and available to others now and for future analysis is also vital. Here we are proposing mechanisms for “next generation phenomics” based on our learning in the past decade, current practice and discussions at the IPPN Symposium, to encourage further thinking and collaboration by plant scientists, physicists and engineering experts

Phylogeny of Cyperaceae Based on DNA Sequence Data–a New rbcL Analysis

Since the Monocots II meeting in 1998, significant new data have been published that enhance our systematic knowledge of Cyperaceae. Phylogenetic studies in the family have also progressed steadily. For this study, a parsimony analysis was carried out using all rbcL sequences currently available for Cyperaceae, including data for two new genera. One of the four subfamilies (Caricoideae) and seven of the 14 tribes (Bisboeckelereae, Cariceae, Cryptangieae, Dulichieae, Eleocharideae, Sclerieae, Trilepideae) are monophyletic. Subfamily Mapanioideae and tribe Chrysitricheae are monophyletic if, as the evidence suggests, Hellmuthia is considered a member of Cypereae. Some other features of our analysis include: well-supported Trilepideae and Sclerieae–Bisboeckelereae clades; a possible close relationship between Cryptangieae and Schoeneae; polyphyletic tribes Schoeneae and Scirpeae; the occurrence of Cariceae within the Dulichieae–Scirpeae clade, and a strongly supported clade, representing Cyperus and allied genera in Cypereae, sister to a poorly supported Ficinia–Hellmuthia– Isolepis–Scirpoides clade. Such patterns are consistent with other studies based on DNA sequence data. One outcome may be that only two subfamilies, Mapanioideae and Cyperoideae, are recognized. Much further work is needed, with efforts carefully coordinated among researchers. The work should focus on obtaining morphological and molecular data for all genera in the family

Phylogeny Of Abildgaardieae (Cyperaceae) Inferred From ITS And 'trn'L -F Data

Within the tribe Abildgaardieae, the relationships between 'Fimbristylis' and its relatives have not been certain, and the limits of 'Fimbristylis' have been unclear, with 'Bulbostylis' and 'Abildgaardia' variously combined with it and each other. The relationships and limits of tribes Abildgaardieae and Arthrostylideae and their genera were evaluated across 49 representative species using parsimony and maximum likelihood analyses of ITS (nuclear ribosomal) and 'trn'L–F (plastid) DNA sequence data separately and combined. The evolutionary reconstructions derived from sequences of cpDNA and nrDNA disagree about the position of tribe Arthrostylideae relative to Abildgaardieae; 'Arthrostylis' and 'Actinoschoenus' are either nested within Abildgaardieae ('trn'L–F data) or very closely related to this tribe (ITS data). The reconstructions also disagree about the monophyly of genus 'Abildgaardia' (excluding 'A. vaginata'). 'Crosslandia' and 'A. vaginata' form a clade that is nested within 'Fimbristylis'. 'Bulbostylis' is monophyletic and clearly separated from 'Fimbristylis'. Further sampling of taxa and characters is needed to resolve and/or strengthen support for some of these "deep" and fine-scale relationships