Frontiers in the Solicitation of Machine Learning Approaches in Vegetable Science Research

Along with essential nutrients and trace elements, vegetables provide raw materials for the food processing industry. Despite this, plant diseases and unfavorable weather patterns continue to threaten the delicate balance between vegetable production and consumption. It is critical to utilize machine learning (ML) in this setting because it provides context for decision-making related to breeding goals. Cutting-edge technologies for crop genome sequencing and phenotyping, combined with advances in computer science, are currently fueling a revolution in vegetable science and technology. Additionally, various ML techniques such as prediction, classification, and clustering are frequently used to forecast vegetable crop production in the field. In the vegetable seed industry, machine learning algorithms are used to assess seed quality before germination and have the potential to improve vegetable production with desired features significantly; whereas, in plant disease detection and management, the ML approaches can improve decision-support systems that assist in converting massive amounts of data into valuable recommendations. On similar lines, in vegetable breeding, ML approaches are helpful in predicting treatment results, such as what will happen if a gene is silenced. Furthermore, ML approaches can be a saviour to insufficient coverage and noisy data generated using various omics platforms. This article examines ML models in the field of vegetable sciences, which encompasses breeding, biotechnology, and genome sequencing

Is label-free LC-MS/MS ready for biomarker discovery?

Label-free LC-MS methods are attractive for high-throughput quantitative proteomics, as the sample processing is straightforward and can be scaled to a large number of samples. Label-free methods therefore facilitate biomarker discovery in studies involving dozens of clinical samples. However, despite the increased popularity of label-free workflows, there is a hesitance in the research community to use it in clinical proteomics studies. Therefore, we here discuss pros and cons of label free LC-MS/MS for biomarker discovery, and delineate the main prerequisites for its successful employment. Furthermore, we cite studies where label-free LC-MS/MS was successfully used to identify novel biomarkers, and foresee an increased acceptance of label-free techniques by the proteomics community in the near future. This article is protected by copyright. All rights reserved

Climate Change Impact on Wheat Performance-Effects on Vigour, Plant Traits and Yield from Early and Late Drought Stress in Diverse Lines

Global climate change is threatening wheat productivity; improved yield under drought conditions is urgent. Here, diverse spring-wheat lines (modern, old and wheat-rye introgressions) were examined in an image-based early-vigour assay and a controlled-conditions (Biotron) trial that evaluated 13 traits until maturity. Early root vigour was significantly higher in the old Swedish lines (root length 8.50 cm) and introgressed lines with 1R (11.78 cm) and 1RS (9.91 cm) than in the modern (4.20 cm) and 2R (4.67 cm) lines. No significant correlation was noted between early root and shoot vigour. A higher yield was obtained under early drought stress in the 3R genotypes than in the other genotype groups, while no clear patterns were noted under late drought. Evaluating the top 10% of genotypes in terms of the stress-tolerance index for yield showed that root biomass, grains and spikes per plant were accountable for tolerance to early drought, while 1000-grain weight and flag-leaf area were accountable for tolerance to late drought. Early root vigour was determined as an important focus trait of wheat breeding for tolerance to climate-change-induced drought. The responsible genes for the trait should be searched for in these diverse lines. Additional drought-tolerance traits determined here need further elaboration to identify the responsible genes

Unraveling the Genetic Basis of Key Agronomic Traits of Wrinkled Vining Pea (Pisum sativum L.) for Sustainable Production

Estimating the allelic variation and exploring the genetic basis of quantitatively inherited complex traits are the two foremost breeding scenarios for sustainable crop production. The current study utilized 188 wrinkled vining pea genotypes comprising historical varieties and breeding lines to evaluate the existing genetic diversity and to detect molecular markers associated with traits relevant to vining pea production, such as wrinkled vining pea yield (YTM100), plant height (PH), earliness (ERL), adult plant resistance to downy mildew (DM), pod length (PDL), numbers of pods per plant (PDP), number of peas per pod (PPD), and percent of small wrinkled vining peas (PSP). Marker-trait associations (MTAs) were conducted using 6902 quality single nucleotide polymorphism (SNP) markers generated from the diversity arrays technology sequencing (DArTseq) and Genotyping-by-sequencing (GBS) sequencing methods. The best linear unbiased prediction (BLUP) values were estimated from the two-decadeslong (1999–2020) unbalanced phenotypic data sets recorded from two private breeding programs, the Findus and the Birds eye, now owned by Nomad Foods. Analysis of variance revealed a highly significant variation between genotypes and genotype-byenvironment interactions for the ten traits. The genetic diversity and population structure analyses estimated an intermediate level of genetic variation with two optimal subgroups within the current panel. A total of 48 significant (P < 0.0001) MTAs were identified for eight different traits, including five for wrinkled vining pea yield on chr2LG1, chr4LG4, chr7LG7, and scaffolds (two), and six for adult plant resistance to downy mildew on chr1LG6, chr3LG5 (two), chr6LG2, and chr7LG7 (two). We reported several novel MTAs for different crucial traits with agronomic importance in wrinkled vining pea production for the first time, and these candidate markers could be easily validated and integrated into the active breeding programs for marker-assisted selection

Specalyzer—an interactive online tool to analyze spectral reflectance measurements

Low-cost phenotyping using proximal sensors is increasingly becoming popular in plant breeding. As these techniques generate a large amount of data, analysis pipelines that do not require expertise in computer programming can benefit a broader user base. In this work, a new online tool Specalyzer is presented that allows interactive analysis of the spectral reflectance data generated by proximal spectroradiometers. Specalyzer can be operated from any web browser allowing data uploading, analysis, interactive plots and exporting by point and click using a simple graphical user interface. Specalyzer is evaluated with case study data from a winter wheat fertilizer trial with two fertilizer treatments. Specalyzer can be accessed online at http://www.specalyzer.org

Genetic Engineering of Energy Crops to Reduce Recalcitrance and Enhance Biomass Digestibility

Bioenergy, biofuels, and a range of valuable chemicals may be extracted from the abundantly available lignocellulosic biomass. To reduce the recalcitrance imposed by the complex cell wall structure, genetic engineering has been proposed over the years as a suitable solution to modify the genes, thereby, controlling the overall phenotypic expression. The present review provides a brief description of the plant cell wall structure and its compositional array i.e., lignin, cellulose, hemicellulose, wall proteins, and pectin, along with their effect on biomass digestibility. Also, this review discusses the potential to increase biomass by gene modification. Furthermore, the review highlights the potential genes associated with the regulation of cell wall structure, which can be targeted for achieving energy crops with desired phenotypes. These genetic approaches provide a robust and assured method to bring about the desired modifications in cell wall structure, composition, and characteristics. Ultimately, these genetic modifications pave the way for achieving enhanced biomass yield and enzymatic digestibility of energy crops, which is crucial for maximizing the outcomes of energy crop breeding and biorefinery applications

Phenocave: An Automated, Standalone, and Affordable Phenotyping System for Controlled Growth Conditions

Controlled plant growth facilities provide the possibility to alter climate conditions affecting plant growth, such as humidity, temperature, and light, allowing a better understanding of plant responses to abiotic and biotic stresses. A bottleneck, however, is measuring various aspects of plant growth regularly and non-destructively. Although several high-throughput phenotyping facilities have been built worldwide, further development is required for smaller custom-made affordable systems for specific needs. Hence, the main objective of this study was to develop an affordable, standalone and automated phenotyping system called "Phenocave" for controlled growth facilities. The system can be equipped with consumer-grade digital cameras and multispectral cameras for imaging from the top view. The cameras are mounted on a gantry with two linear actuators enabling XY motion, thereby enabling imaging of the entire area of Phenocave. A blueprint for constructing such a system is presented and is evaluated with two case studies using wheat and sugar beet as model plants. The wheat plants were treated with different irrigation regimes or high nitrogen application at different developmental stages affecting their biomass accumulation and growth rate. A significant correlation was observed between conventional measurements and digital biomass at different time points. Post-harvest analysis of grain protein content and composition corresponded well with those of previous studies. The results from the sugar beet study revealed that seed treatment(s) before germination influences germination rates. Phenocave enables automated phenotyping of plants under controlled conditions, and the protocols and results from this study will allow others to build similar systems with dimensions suitable for their custom needs

GWAS-Assisted Genomic Prediction to Predict Resistance to Septoria Tritici Blotch in Nordic Winter Wheat at Seedling Stage

Septoria tritici blotch (STB) disease caused by Zymoseptoria tritici is one of the most damaging diseases of wheat causing significant yield losses worldwide. Identification and employment of resistant germplasm is the most cost-effective method to control STB. In this study, we characterized seedling stage resistance to STB in 175 winter wheat landraces and old cultivars of Nordic origin. The study revealed significant (p < 0.05) phenotypic differences in STB severity in the germplasm. Genome-wide association analysis (GWAS) using five different algorithms identified ten significant markers on five chromosomes. Six markers were localized within a region of 2 cM that contained seven candidate genes on chromosome 1B. Genomic prediction (GP) analysis resulted in a model with an accuracy of 0.47. To further improve the prediction efficiency, significant markers identified by GWAS were included as fixed effects in the GP model. Depending on the number of fixed effect markers, the prediction accuracy improved from 0.47 (without fixed effects) to 0.62 (all non-redundant GWAS markers as fixed effects), respectively. The resistant genotypes and single-nucleotide polymorphism (SNP) markers identified in the present study will serve as a valuable resource for future breeding for STB resistance in wheat. The results also highlight the benefits of integrating GWAS with GP to further improve the accuracy of GP

Mutagenesis as a Tool in Plant Genetics, Functional Genomics, and Breeding

Plant mutagenesis is rapidly coming of age in the aftermath of recent developments in high-resolution molecular and biochemical techniques. By combining the high variation of mutagenised populations with novel screening methods, traits that are almost impossible to identify by conventional breeding are now being developed and characterised at the molecular level. This paper provides a comprehensive overview of the various techniques and workflows available to researchers today in the field of molecular breeding, and how these tools complement the ones already used in traditional breeding. Both genetic (Targeting Induced Local Lesions in Genomes; TILLING) and phenotypic screens are evaluated. Finally, different ways of bridging the gap between genotype and phenotype are discussed