Morpho-densitometric traits for quinoa (Chenopodium quinoa Willd.) seed phenotyping by two X-ray micro-CT scanning approaches

Toward robust and high-throughput detection of seed defects in X-ray images via deep learning

BACKGROUND

The detection of internal defects in seeds via non-destructive imaging techniques is a topic of high interest to optimize the quality of seed lots. In this context, X-ray imaging is especially suited. Recent studies have shown the feasibility of defect detection via deep learning models in 3D tomography images. We demonstrate the possibility of performing such deep learning-based analysis on 2D X-ray radiography for a faster yet robust method via the X-Robustifier pipeline proposed in this article.

RESULTS

2D X-ray images of both defective and defect-free seeds were acquired. A deep learning model based on state-of-the-art object detection neural networks is proposed. Specific data augmentation techniques are introduced to compensate for the low ratio of defects and increase the robustness to variation of the physical parameters of the X-ray imaging systems. The seed defects were accurately detected (F1-score >90%), surpassing human performance in computation time and error rates. The robustness of these models against the principal distortions commonly found in actual agro-industrial conditions is demonstrated, in particular, the robustness to physical noise, dimensionality reduction and the presence of seed coating.

CONCLUSION

This work provides a full pipeline to automatically detect common defects in seeds via 2D X-ray imaging. The method is illustrated on sugar beet and faba bean and could be efficiently extended to other species via the proposed generic X-ray data processing approach (X-Robustifier). Beyond a simple proof of feasibility, this constitutes important results toward the effective use in the routine of deep learning-based automatic detection of seed defects.

Metabolome and Transcriptome Association Analysis Reveals Mechanism of Synthesis of Nutrient Composition in Quinoa (Chenopodium quinoa Willd.) Seeds

Quinoa (Chenopodium quinoa Willd.) seeds are rich in nutrition, superior to other grains, and have a high market value. However, the biosynthesis mechanisms of protein, starch, and lipid in quinoa grain are still unclear. The objective of this study was to ascertain the nutritional constituents of white, yellow, red, and black quinoa seeds and to employ a multi-omics approach to analyze the synthesis mechanisms of these nutrients. The findings are intended to furnish a theoretical foundation and technical support for the biological breeding of quinoa in China. In this study, the nutritional analysis of white, yellow, red, and black quinoa seeds from the same area showed that the nutritional contents of the quinoa seeds were significantly different, and the protein content increased with the deepening of color. The protein content of black quinoa was the highest (16.1 g/100 g) and the lipid content was the lowest (2.7 g/100 g), among which, linoleic acid was the main fatty acid. A combined transcriptome and metabolome analysis exhibited that differentially expressed genes were enriched in "linoleic acid metabolism", "unsaturated fatty acid biosynthesis", and "amino acid biosynthesis". We mainly identified seven genes involved in starch synthesis (LOC110716805, LOC110722789, LOC110738785, LOC110720405, LOC110730081, LOC110692055, and LOC110732328); five genes involved in lipid synthesis (LOC110701563, LOC110699636, LOC110709273, LOC110715590, and LOC110728838); and nine genes involved in protein synthesis (LOC110710842, LOC110720003, LOC110687170, LOC110716004, LOC110702086, LOC110724454 LOC110724577, LOC110704171, and LOC110686607). The data presented in this study based on nutrient, transcriptome, and metabolome analyses contribute to an enhanced understanding of the genetic regulation of seed quality traits in quinoa, and provide candidate genes for further genetic improvements to improve the nutritional value of quinoa seeds.

Current trends and prospects in quinoa research: An approach for strategic knowledge areas

Currently, the demand for healthy consumption and the use of alternatives to dairy proteins for the development of foods with good nutritional value are growing. Quinoa has received much attention because it contains a high content of proteins, essential amino acids, essential fatty acids, minerals, vitamins, dietary fibers, and bioactive compounds. Nevertheless, this content and the bioavailability of specific compounds of interest are related to the genotype, the agri-environmental conditions, and management practices where quinoa is grown and postharvest management. This article aimed to analyze the research trends for three knowledge areas: quinoa plant breeding for nutraceutical properties, plant-soil relations focused on abiotic stresses, and postharvest and value-added transformation activities. To this end, a specific methodological design based on bibliometrics and scientometrics methods was used. Through these analyses based on publications' keywords, titles, abstracts, and conclusions sections, for each knowledge area, the key research trends (scope and main topics), the classification of trends based on their development and relevance degree, and the core of knowledge were established. The trends comprise the current state of research. Finally, analyzing the conclusions, recommendations, and future research sections of key publications, a strong correlation among plant breeding research to obtain varieties with tolerance to biotic and abiotic stresses, nutritional and functional compounds of interest for food safety, and the development of products with higher added value established interest in further research on the potential bioactivity of quinoa and the verification of health benefits to humans.

Crop Seed Phenomics: Focus on Non-Destructive Functional Trait Phenotyping Methods and Applications

Seeds play a critical role in ensuring food security for the earth's 8 billion people. There is great biodiversity in plant seed content traits worldwide. Consequently, the development of robust, rapid, and high-throughput methods is required for seed quality evaluation and acceleration of crop improvement. There has been considerable progress in the past 20 years in various non-destructive methods to uncover and understand plant seed phenomics. This review highlights recent advances in non-destructive seed phenomics techniques, including Fourier Transform near infrared (FT-NIR), Dispersive-Diode Array (DA-NIR), Single-Kernel (SKNIR), Micro-Electromechanical Systems (MEMS-NIR) spectroscopy, Hyperspectral Imaging (HSI), and Micro-Computed Tomography Imaging (micro-CT). The potential applications of NIR spectroscopy are expected to continue to rise as more seed researchers, breeders, and growers successfully adopt it as a powerful non-destructive method for seed quality phenomics. It will also discuss the advantages and limitations that need to be solved for each technique and how each method could help breeders and industry with trait identification, measurement, classification, and screening or sorting of seed nutritive traits. Finally, this review will focus on the future outlook for promoting and accelerating crop improvement and sustainability.

A comprehensive characterization of agronomic and end-use quality phenotypes across a quinoa world core collection

Quinoa (Chenopodium quinoa Willd.), a pseudocereal with high protein quality originating from the Andean region of South America, has broad genetic variation and adaptability to diverse agroecological conditions, contributing to the potential to serve as a global keystone protein crop in a changing climate. However, the germplasm resources currently available to facilitate quinoa expansion worldwide are restricted to a small portion of quinoa's total genetic diversity, in part because of day-length sensitivity and issues related to seed sovereignty. This study aimed to characterize phenotypic relationships and variation within a quinoa world core collection. The 360 accessions were planted in a randomized complete block design with four replicates in each of two greenhouses in Pullman, WA during the summer of 2018. Phenological stages, plant height, and inflorescence characteristics were recorded. Seed yield, composition, thousand seed weight, nutritional composition, shape, size, and color were measured using a high-throughput phenotyping pipeline. Considerable variation existed among the germplasm. Crude protein content ranged from 11.24% to 17.81% (fixed at 14% moisture). We found that protein content was negatively correlated with yield and positively correlated with total amino acid content and days to harvest. Mean essential amino acids values met adult daily requirements but not leucine and lysine infant requirements. Yield was positively correlated with thousand seed weight and seed area, and negatively correlated with ash content and days to harvest. The accessions clustered into four groups, with one-group representing useful accessions for long-day breeding programs. The results of this study establish a practical resource for plant breeders to leverage as they strategically develop germplasm in support of the global expansion of quinoa.

Diversity of quinoa genetic resources for sustainable production: A survey on nutritive characteristics as influenced by environmental conditions

Environmental extremes and climatic variability have enhanced the changes in numerous plant stressors. Researchers have been working to improve “major” crops for several decades to make them more adaptable and tolerant to environmental stresses. However, neglected and underutilized crop species that have the potential to ensure food and nutritional security for the ever-growing global population have received little or no research attention. Quinoa is one of these crops. It is a pseudocereal, considered a rich and balanced food resource due to its protein content and protein quality, high mineral content, and health benefits. This review provides currently available information on the genetic resources of quinoa and their quality in terms of variability of economically important traits such as yield, and the content of bioactive compounds, such as protein and amino acid composition. The influence of variety and environmental conditions on selected traits is also discussed. The various types of nutrients present in the different varieties form the basis and are key for future breeding efforts and for efficient, healthy, and sustainable food production.

Photosynthesis is not the unique useful trait for discriminating salt tolerance capacity between sensitive and tolerant quinoa varieties

Growth was not strictly linked to photosynthesis performance under salinity conditions in quinoa. Other key traits, which were varieties-specific, rather than photosynthesis explained better growth performance. Phenotyping for salinity stress tolerance in quinoa is of great interest to select traits contributing to overall salinity tolerance and to understand the response mechanisms to salinity at a whole plant level. The objective of this work was to dissect the responses of specific traits and analyse relations between these traits to better understand growth response under salinity conditions in quinoa. Growth response to salinity was mostly related to differences in basal values of biomass, being reduced the most in plants with higher basal biomass. Regarding the relationship between growth and specific traits, in Puno variety, better photosynthetic performance was related to a better maintenance of growth. Nevertheless, in the rest of the varieties other traits rather than photosynthesis could better explain growth response. In this way, the development of succulence in F-16 and Collana varieties, also the osmotic adjustment but in smaller dimensions in Pasankalla, Marisma and S-15-15 helped to maintain better growth. Besides, smaller increases of Cl^- could have caused a limited nitrate uptake reducing more growth in Vikinga. Ascorbate was considered a key trait as a noticeable fall of it was also related to higher reductions in growth in Titicaca. These results suggest that, due to the genetic variability of quinoa and the complexity of salinity tolerance, no unique and specific traits should be taken into consideration when using phenotyping for analysing salinity tolerance in quinoa.

Radiographic Imaging as a Quality Index Proxy for Brachiaria brizantha Seeds

Efficient methodologies for automated seed quality evaluations are important for the seed industry. Advanced seed technology research requires the use of adequate methods to ensure good seed performance under adverse environmental conditions; thus, providing producers with detailed, quick, and accurate information on structural seed integrity and ensuring vigorous production. To address this problem, this study aimed to determine Brachiaria brizantha (Marandu cv., Piatã cv. and Xaraés cv.) seed quality through radiographic imaging analyses associated with vigor tests and anatomical characterizations. Brachiaria seed cultivars displaying different physical and physiological attributes were selected and subjected to the 1000-seed weight test, water content determinations, X-ray analyses, germination tests, and anatomical characterizations. The X-ray analyses made it possible to establish a relationship between the X-ray images and other determined variables. Furthermore, the X-ray images can indicate evidence of internal and external damage that could later compromise germination. The Marandu and Piatã cultivars presented the highest germination percentages, germination speed indices, normal seedling development, and cellular structure preservation compared to the Xaraés cultivar. To summarize, X-ray analyses are efficient methods used for the selection of higher physical quality cultivars and can aid in the decision-making processes of companies and seed producers worldwide.

Characterisation of Grains and Flour Fractions from Field Grown Transgenic Oil-Accumulating Wheat Expressing Oat WRI1

Wheat (Triticum aestivum L.) is one of the major staple crops in the world and is used to prepare a range of foods. The development of new varieties with wider variation in grain composition could broaden their use. We characterized grains and flours from oil-accumulating transgenic wheat expressing the oat (Avena sativa L.) endosperm WRINKLED1 (AsWRI1) grown under field conditions. Lipid and starch accumulation was determined in developing caryopses of AsWRI1-wheat and X-ray microtomography was used to study grain morphology. The developing caryopses of AsWRI1-wheat grains had increased triacylglycerol content and decreased starch content compared to the control. Mature AsWRI1-wheat grains also had reduced weight, were wrinkled and had a shrunken endosperm and X-ray tomography revealed that the proportion of endosperm was decreased while that of the aleurone was increased. Grains were milled to produce two white flours and one bran fraction. Mineral and lipid analyses showed that the flour fractions from the AsWRI1-wheat were contaminated with bran, due to the effects of the changed morphology on milling. This study gives a detailed analysis of grains from field grown transgenic wheat that expresses a gene that plays a central regulatory role in carbon allocation and significantly affects grain composition.

Transcriptional Regulation of Quinoa Seed Quality: Identification of Novel Candidate Genetic Markers for Increased Protein Content

Quinoa (Chenopodium quinoa Willd.) is a crop that has great potential for increased cultivation in diverse climate regions. The seed protein quality obtained from this crop is high concerning the requirements to meet human nutritional needs, but the seed protein content is relatively low if compared to crops such as grain legumes. Increased seed protein content is desirable for increasing the economic viability of this crop in order for it to be used as a protein crop. In this study, we characterized three genotypes of quinoa with different levels of seed protein content. By performing RNA sequencing of developing seeds, we determined the genotype differences in gene expression and identified genetic polymorphisms that could be associated with increased protein content. Storage nutrient analyses of seeds of three quinoa genotypes (Titicaca, Pasankalla, and Regalona) from different ecoregions grown under controlled climate conditions showed that Pasankalla had the highest protein content (20%) and the lowest starch content (46%). Our seed transcriptome analyses revealed highly differentially expressed transcripts (DETs) in Pasankalla as compared to the other genotypes. These DETs encoded functions in sugar transport, starch and protein synthesis, genes regulating embryo size, and seed transcription factors. We selected 60 genes that encode functions in the central carbon metabolism and transcription factors as potential targets for the development of high-precision markers. Genetic polymorphisms, such as single nucleotide polymorphisms (SNPs) and base insertions and deletions (InDels), were found in 19 of the 60 selected genes, which can be further evaluated for the development of genetic markers for high seed protein content in quinoa. Increased cultivation of quinoa can contribute to a more diversified agriculture and support the plant protein diet shift. The identification of quinoa genotypes with contrasting seed quality can help establish a model system that can be used for the identification of precise breeding targets to improve the seed quality of quinoa. The data presented in this study based on nutrient and transcriptome analyses contribute to an enhanced understanding of the genetic regulation of seed quality traits in quinoa and suggest high-precision candidate markers for such traits.

How Does Mechanical Pearling Affect Quinoa Nutrients and Saponin Contents?

Agriculture is facing many challenges, such as climate change, drought, and salinity, which call for urgent interventions for fast adaptation and crop diversification. The introduction of high-value and stress tolerant crops such as quinoa would be a judicious solution to overcome constraints related to abiotic stress and to increase land productivity and farmers’ incomes. The implementation of quinoa in Morocco has not been supported by a full valorization program to control the quality of quinoa seeds. The novelty of this work is to assess the pearling operation as an efficient method of saponins removal as well as the determination of total residual saponins. This study aimed to evaluate the effects of several pearling durations on nutrient and saponin content of quinoa seeds of three tested varieties (Puno, Titicaca, and ICBA-Q5). Five pearling durations were tested (0, 2, 4, 6, 7, and 8 min) using a locally manufactured pearling machine. The results indicated that a pearling duration of two minutes was enough to reduce total saponin content from 0.49% to 0.09% for Puno variety, from 0.37% to 0.07% for Titicaca variety, and from 0.57% to 0.1% for ICBA-Q5 variety. Our results showed that pearling slightly reduced protein, total fat, and moisture contents for all varieties except for Puno, where total fat content slightly increased with the pearling. Puno variety had the highest seed content in terms of protein and total fat; the ICBA-Q5 variety had the lowest. Titicaca had the highest bran content in terms of protein and total fat, ICBA-Q5 had the highest bran content in terms of ash and the lowest bran content in terms of protein and total fat, and Puno had the lowest bran content in terms of ash. Pearling had no significant effect on macronutrient contents in the processed seed, but it resulted in a very highly significant difference for most of them in the bran except for Mg and S. Regarding seed content in terms of micro-nutrients, statistical analysis showed significant differences between varieties in terms of Zn, Cu, and Mn contents, but no significant difference was recorded for Fe or B. Pearling had no significant effect on seed micronutrient contents. Therefore, to retain maximum nutritional content in the quinoa and maintain quinoa integrity, it is necessary to limit the pearling duration of quinoa to two minutes, which is enough to reduce saponin content below the Codex Standard threshold (0.12%).

Comparison of the Chemical and Technological Characteristics of Wholemeal Flours Obtained from Amaranth (Amaranthus sp.), Quinoa (Chenopodium quinoa) and Buckwheat (Fagopyrum sp.) Seeds

A sound fundamental knowledge of the seed and flour characteristics of pseudocereals is crucial to be able to promote their industrial use. As a first step towards a more efficient and successful application, this study focuses on the seed characteristics, chemical composition and technological properties of commercially available pseudocereals (amaranth, quinoa, buckwheat). The levels of starch, fat, dietary fiber and minerals were comparable for amaranth and quinoa seeds but the protein content is higher in amaranth. Due to the high amount of starch, buckwheat seeds are characterised by the lowest amounts of fat, dietary fibre and minerals. Its protein content ranged between that of amaranth and quinoa. Buckwheat seeds were larger but easily reduced in size. The lipid fraction of the pseudocereals mostly contained unsaturated fatty acids, with the highest prevalence of linoleic and oleic acid. Palmitic acid is the most abundant unsaturated fatty acid. Moreover, high levels of P, K and Mg were found in these pseudocereals. The highest phenolic content was found in buckwheat. Amaranth WMF (wholemeal flour) had a high swelling power but low shear stability. The pasting profile strongly varied among the different quinoa WMFs. Buckwheat WMFs showed high shear stability and rate of retrogradation.

Amaranth, quinoa and chia bioactive peptides: a comprehensive review on three ancient grains and their potential role in management and prevention of Type 2 diabetes

Worldwide prevalence of Type 2 Diabetes (T2D) has become a major concern with several implications for public health, economy, and social well-being, especially in developing countries. Conventional pharmacological management of T2D have proved effective, but possess underlying side effects, leading the scientific community to research alternative compounds that exert beneficial effects on current therapeutic targets of T2D. Bioactive peptides (BAPs) from food sources, have shown relative advantages in this matter, moreover, BAPs have proved to impart anti-diabetic activity through one or more mechanisms such as enzymatic inhibition of α-glucosidase, α-amylase and DPP-IV. Several plants and animal have been used as protein sources of anti-diabetic BAPs, in the sense of this matter, the pseudo-cereals amaranth and quinoa, along with the ancestral grain chia, have gained attention. Due, to their high protein content and balanced amino-acid composition, along with proved anti-diabetic features, the three seeds are top choices for the obtention of anti-diabetic BAPs. With a comprehensive overview of the most recent reported in silico and in vitro anti-diabetic studies in relation to biomarkers α-glucosidase, α-amylase and DPP-IV, the present review aims to examine the current knowledge of amaranth, quinoa and chia derived anti-diabetic BAPs and their effects on T2D therapeutic markers.

3D imaging of bean seeds: Correlations between hilum region structures and hydration kinetics

X-ray micro-CT imaging has been applied successfully in food science and seed research due to its capacity to provide very small details of seed traits that are very complex to score. The micropyle and the tissues of the hilum region of bean seeds are recognized as structures which play an important role in hydration process. This latter influences, in turn, not only germination but also the cooking and industrial processing. Nevertheless, the role of each structure of the bean seeds is yet to be fully understood. Moreover such traits are never been quantified by using 3D imaging approaches. In this work, seeds of four ancient Italian landraces of beans have been scanned by X-ray microCT with a twofold approach: bulk scans for whole seed imaging and single seed scans for internal traits measurements. Then water uptake tests have been performed. The different structures composing the hilum region of the beans have been imaged and characterized. The two-dimensional and the three-dimensional morphometric traits have been correlated with parameters of hydration models by Principal Component Analysis (PCA) and Pearson coefficients. Micropyle groove area was the trait most influencing the very initial hydration rates while the hilum groove area was the best correlated with the overall infiltration behavior. The internal free space was the trait best correlated with the moisture at equilibrium. Moreover, strophiole shape resulted the most suitable internal trait for univocal identification of the four landraces. Overall results give a contribution to the understanding of the role of hilum region structures in bean seeds hydration process and show novel morphological traits useful for identification of local bean landraces.