High-throughput phenotyping for non-destructive estimation of soybean fresh biomass using a machine learning model and temporal UAV data.

BACKGROUND: Biomass accumulation as a growth indicator can be significant in achieving high and stable soybean yields. More robust genotypes have a better potential for exploiting available resources such as water or sunlight. Biomass data implemented as a new trait in soybean breeding programs could be beneficial in the selection of varieties that are more competitive against weeds and have better radiation use efficiency. The standard techniques for biomass determination are invasive, inefficient, and restricted to one-time point per plot. Machine learning models (MLMs) based on the multispectral (MS) images were created so as to overcome these issues and provide a non-destructive, fast, and accurate tool for in-season estimation of soybean fresh biomass (FB). The MS photos were taken during two growing seasons of 10 soybean varieties, using six-sensor digital camera mounted on the unmanned aerial vehicle (UAV). For model calibration, canopy cover (CC), plant height (PH), and 31 vegetation index (VI) were extracted from the images and used as predictors in the random forest (RF) and partial least squares regression (PLSR) algorithm. To create a more efficient model, highly correlated VIs were excluded and only the triangular greenness index (TGI) and green chlorophyll index (GCI) remained. RESULTS: More precise results with a lower mean absolute error (MAE) were obtained with RF (MAE = 0.17 kg/m2) compared to the PLSR (MAE = 0.20 kg/m2). High accuracy in the prediction of soybean FB was achieved using only four predictors (CC, PH and two VIs). The selected model was additionally tested in a two-year trial on an independent set of soybean genotypes in drought simulation environments. The results showed that soybean grown under drought conditions accumulated less biomass than the control, which was expected due to the limited resources. CONCLUSION: The research proved that soybean FB could be successfully predicted using UAV photos and MLM. The filtration of highly correlated variables reduced the final number of predictors, improving the efficiency of remote biomass estimation. The additional testing conducted in the independent environment proved that model is capable to distinguish different values of soybean FB as a consequence of drought. Assessed variability in FB indicates the robustness and effectiveness of the proposed model, as a novel tool for the non-destructive estimation of soybean FB.

Carbohydrate metabolism enzymes and phenotypic characterization of diverse lines of the climate-resilient food, feed, and bioenergy crop Camelina sativa.

Climate change poses tremendous pressure on agriculture. Camelina sativa is an ancient, low-input, high-quality oilseed crop for food, feed and industrial applications that has retained its natural stress tolerance. Its climate resilience, adaptability to different growth conditions, and the qualities of its seed oil and cake have spurred the interest in camelina. However, due to a period of neglect it has not yet undergone intensive breeding and knowledge about this multi-purpose crop is still limited. Metabolism is strongly associated with plant growth and development and little information is available on camelina primary carbohydrate metabolism. Here, eight camelina lines from different geographic and climatic regions were characterized for important growth parameters and agricultural traits. Furthermore, the activities of key enzymes of the carbohydrate metabolism were analysed in leaves, seedpods, capsules, and developing seeds. The lines differed in shoot and leaf morphology, plant height, biomass formation as well as in seed yield and seed oil and protein content. Key carbohydrate metabolism enzymes showed specific activity signatures in leaves and reproductive organs during seed development, and different lines exhibited distinct enzyme activity patterns, providing a valuable basis for developing new physiological markers for camelina breeding programs.

Spermidine and other functional phytochemicals in soybean seeds: Spatial distribution as visualized by mass spectrometry imaging.

Soybean seeds contain phytochemicals such as polyamines and isoflavones, which have been identified as functional components mediating health benefits in association with the consumption of soy foods. While a clear picture of the spatial distribution of these components within the seed is lacking, such information would be important to enhance or reduce their concentration in respective foods through processing. Thus, the objective of the present study was to visualize the most relevant components with respect to their distribution in soybean seeds. Mature soybean seeds were subject to atmospheric-pressure scanning-microprobe matrix-assisted laser desorption/ionization (AP-SMALDI) combined with a Fourier-transform orbital trapping mass spectrometer to generate high-resolution chemical images of phytochemical distribution. Based on seed cross sections, differential distributions of functional components were found between soybean cotyledon and germ (shoot, hypocotyl, root) regions. Spermidine and spermine were present in higher concentrations in the germ rather than in cotyledons with highest concentrations in root and shoot meristem tissues. Differential concentrations of spermidine and other components between the germ and cotyledon regions were confirmed by seed fractioning. In contrast to polyamines spermidine and spermine, the different types of daidzein, glycitein, and genistein isoflavones were all visualized in root parenchyma tissue exclusively. Overall, mass spectrometry imaging of soybean seeds revealed clear insights into the differential distribution of functional phytochemicals. Based on their distribution and depending on specific needs, spermidine and isoflavones can either be enriched or reduced during food processing by separating cotyledon and germ fractions.

Identification of mega-environments in Europe and effect of allelic variation at maturity E loci on adaptation of European soybean.

Soybean cultivation holds great potential for a sustainable agriculture in Europe, but adaptation remains a central issue. In this large mega-environment (MEV) study, 75 European cultivars from five early maturity groups (MGs 000-II) were evaluated for maturity-related traits at 22 locations in 10 countries across Europe. Clustering of the locations based on phenotypic similarity revealed six MEVs in latitudinal direction and suggested several more. Analysis of maturity identified several groups of cultivars with phenotypic similarity that are optimally adapted to the different growing regions in Europe. We identified several haplotypes for the allelic variants at the E1, E2, E3 and E4 genes, with each E haplotype comprising cultivars from different MGs. Cultivars with the same E haplotype can exhibit different flowering and maturity characteristics, suggesting that the genetic control of these traits is more complex and that adaptation involves additional genetic pathways, for example temperature requirement. Taken together, our study allowed the first unified assessment of soybean-growing regions in Europe and illustrates the strong effect of photoperiod on soybean adaptation and MEV classification, as well as the effects of the E maturity loci for soybean adaptation in Europe.

Development of soybeans with low P34 allergen protein concentration for reduced allergenicity of soy foods.

BACKGROUND: In soybean, at least 16 seed proteins have been identified as causing allergenic reactions in sensitive individuals. As a soybean genebank accession low in the immunodominant protein P34 (Gly m Bd 30K) has recently been found, introgression of the low-P34 trait into adapted soybean germplasm has been attempted in order to improve the safety of food products containing soybean protein. Therefore, marker-assisted selection and proteomics were applied to identify and characterize low-P34 soybeans. RESULTS: In low-P34 lines selected from a cross-population, concentrations of the P34 protein as identified with a polyclonal antibody were reduced by 50-70% as compared to P34-containing controls. Using 2D electrophoresis and immunoblotting, the reduction of P34 protein was verified in low-P34 lines. This result was confirmed by liquid chromatographic-tandem mass spectrometric analysis, which revealed either a reduction or complete absence of the authentic P34 protein as suggested from presence or absence of a unique peptide useful for discriminating between conventional and low-P34 lines. CONCLUSION: Marker-assisted selection proved useful for identifying low-P34 soybean lines for the development of hypoallergenic soy foods. The status of the P34 protein in low-P34 lines needs further characterization. In addition, the food safety relevance of low-P34 soybeans should be tested in clinical studies. © 2016 Society of Chemical Industry.

Female preferences for male traits and territory characteristics in the cichlid fish Tropheus moorii.

Female mate preferences for male traits and resource characteristics affect trait evolution and diversification. Here, we test the effects of male body traits and territory characteristics on within-population female preferences and on population-assortative mating in the cichlid Tropheus moorii. Within-population preferences of females were independent of male body size, coloration and territory size but were strongly dependent on territory quality and co-varied with male courtship activity. Courtship activity of individual males was contingent on the quality of their assigned territory, and therefore, courtship may not only indicate intrinsic male quality. On the basis of these results we suggest that female preferences for high-quality territories reinforce the outcome of malemale competition and ensure male mating success. Mating preferences of females for males of their own color variant (ascertained in a previous experiment) were not overturned when males of another color variant were presented in a superior territory, indicating that within- and between-population mate preferences of females depend on different cues.

Editorial: Sustainable production of renewable energy from non-food crops.

Since the world faced the petroleum crisis in the 1970s and people started to realize the limitation of fossil energy resources coupled with concerns over the effects of increasing carbon dioxide in the atmosphere, major efforts were devoted to the search for alternative energy sources.

Camelina as a sustainable oilseed crop: contributions of plant breeding and genetic engineering.

Camelina is an underutilized Brassicaceae oilseed plant with a considerable agronomic potential for biofuel and vegetable oil production in temperate regions. In contrast to most Brassicaceae, camelina is resistant to alternaria black spot and other diseases and pests. Sequencing of the camelina genome revealed an undifferentiated allohexaploid genome with a comparatively large number of genes and low percentage of repetitive DNA. As there is a close relationship between camelina and the genetic model plant Arabidopsis, this review aims at exploring the potential of translating basic Arabidopsis results into a camelina oilseed crop for food and non-food applications. Recently, Arabidopsis genes for drought resistance or increased photosynthesis and overall productivity have successfully been expressed in camelina. In addition, gene constructs affecting lipid metabolism pathways have been engineered into camelina for synthesizing either long-chain polyunsaturated fatty acids, hydroxy fatty acids or high-oleic oils in particular camelina strains, which is of great interest in human food, industrial or biofuel applications, respectively. These results confirm the potential of camelina to serve as a biotechnology platform in biorefinery applications thus justifying further investment in breeding and genetic research for combining agronomic potential, unique oil quality features and biosafety into an agricultural production system.

The relationship between N isotopic fractionation within soybean and N2 fixation during soybean development.

The contribution of N(2) fixation to overall soybean N uptake has most commonly been quantified by N isotope-based methods, which rely on isotopic differences in plant N between legumes and non-fixing reference plants. The choice of non-fixing reference plants is critical for the accuracy of isotope-based methods, and mismatched reference plants remain a potential source of error. Accurate estimates of soybean N(2) fixation also require information on N isotopic fractionation within soybean. On the basis of a previous observation of a close correlation between an expression of N fractionation within soybean and the proportion of plant N derived from atmosphere (%Ndfa) determined by (15) N natural abundance, this field study aimed at assessing the relationship between various expressions describing intraplant (15) N or N partitioning and %Ndfa during soybean development. Starting from a late vegetative stage until beginning senescence, the N content and N isotopic composition of shoots, roots and nodules of nodulated and non-nodulated soybeans was determined at eight different developmental stages. Regression analysis showed that %Ndfa most closely correlated with the difference in the N isotopic composition of shoot N minus that of root including nodule N, and that this relationship was similar to that obtained in a previous multi-site field study. We therefore consider this expression to hold promise as a means of quantifying %Ndfa independent of a reference plant, which would avoid some of the external sources of error introduced by the use of reference plants in determining %Ndfa.

Genetic relationships and evolution in Cucurbita pepo (pumpkin, squash, gourd) as revealed by simple sequence repeat polymorphisms.

Genetic relationships among 104 accessions of Cucurbita pepo were assessed from polymorphisms in 134 SSR (microsatellite) and four SCAR loci, yielding a total of 418 alleles, distributed among all 20 linkage groups. Genetic distance values were calculated, a dendrogram constructed, and principal coordinate analyses conducted. The results showed 100 of the accessions as distributed among three clusters representing each of the recognized subspecies, pepo, texana, and fraterna. The remaining four accessions, all having very small, round, striped fruits, assumed central positions between the two cultivated subspecies, pepo and texana, suggesting that they are relicts of undescribed wild ancestors of the two domesticated subspecies. In both, subsp. texana and subsp. pepo, accessions belonging to the same cultivar-group (fruit shape) associated with one another. Within subsp. pepo, accessions grown for their seeds or that are generalists, used for both seed and fruit consumption, assumed central positions. Specialized accessions, grown exclusively for consumption of their young fruits, or their mature fruit flesh, or seed oil extraction, tended to assume outlying positions, and the different specializations radiated outward from the center in different directions. Accessions of the longest-fruited cultivar-group, Cocozelle, radiated bidirectionally, indicating independent selection events for long fruits in subsp. pepo probably driven by a common desire to consume the young fruits. Among the accessions tested, there was no evidence for crossing between subspecies after domestication.