A pulse crop dataset of agronomic traits and multispectral images from multiple environments.

Crop yield potential in breeding trials can be captured using unmanned aerial vehicle (UAV) based multispectral imagery. Several digital traits or phenotypes such as vegetation indices can represent canopy crop vigor and overall plant health, which can be used to evaluate differences in performance across varieties in crop breeding programs. This dataset contains agronomic data for named cultivars and breeding lines of spring-sown dry pea and chickpea, and over 275 multispectral images from advanced and preliminary breeding trials. The breeding trials were located at three locations in the "Palouse" region of Eastern Washington and Northern Idaho of the United States across 2017, 2018 and 2019 cropping seasons. The multispectral images were captured using a UAV integrated with a 5-band multispectral camera at multiple time points from early vegetative growth through pod development stages during each cropping season. This dataset details seed yield information from trials of dry peas and chickpea that were obtained from each location, as well as additional agronomic and phenological data recorded at one location (mostly Pullman, WA) for each cropping season. The dataset also includes 20-78 megabytes (MB) Tagged Image Format (TIF) uncalibrated stitched orthomosaic images generated from the photogrammetric software. The images can be processed using any convenient image processing algorithm to obtain vegetation indices and other useful information.

Selecting High-Performing and Stable Pea Genotypes in Multi-Environmental Trial (MET): Applying AMMI, GGE-Biplot, and BLUP Procedures.

A large amount of data on various traits is accumulated over the course of a breeding program and can be used to optimize various aspects of the crop improvement pipeline. We leveraged data from advanced yield trials (AYT) of three classes of peas (green, yellow, and winter peas) collected over ten years (2012-2021) to analyze and test key aspects fundamental to pea breeding. Six balanced datasets were used to test the predictive success of the BLUP and AMMI family models. Predictive assessment using cross-validation indicated that BLUP offered better predictive accuracy as compared to any AMMI family model. However, BLUP may not always identify the best genotype that performs well across environments. AMMI and GGE, two statistical tools used to exploit GE, could fill this gap and aid in understanding how genotypes perform across environments. AMMI's yield by environmental IPCA1, WAASB by yield plot, and GGE biplot were shown to be useful in identifying genotypes for specific or broad adaptability. When compared to the most favorable environment, we observed a yield reduction of 80-87% in the most unfavorable environment. The seed yield variability across environments was caused in part by weather variability. Hotter conditions in June and July as well as low precipitation in May and June affected seed yield negatively. In conclusion, the findings of this study are useful to breeders in the variety selection process and growers in pea production.

Remote sensing for field pea yield estimation: A study of multi-scale data fusion approaches in phenomics.

Introduction: Remote sensing using unmanned aerial systems (UAS) are prevalent for phenomics and precision agricultural applications. The high-resolution data for these applications can provide useful spectral characteristics of crops associated with performance traits such as seed yield. With the recent availability of high-resolution satellite imagery, there has been growing interest in using this technology for plot-scale remote sensing applications, particularly those related to breeding programs. This study compared the features extracted from high-resolution satellite and UAS multispectral imagery (visible and near-infrared) to predict the seed yield from two diverse plot-scale field pea yield trials (advanced breeding and variety testing) using the random forest model. Methods: The multi-modal (spectral and textural features) and multi-scale (satellite and UAS) data fusion approaches were evaluated to improve seed yield prediction accuracy across trials and time points. These approaches included both image fusion, such as pan-sharpening of satellite imagery with UAS imagery using intensity-hue-saturation transformation and additive wavelet luminance proportional approaches, and feature fusion, which involved integrating extracted spectral features. In addition, we also compared the image fusion approach to high-definition satellite data with a resolution of 0.15 m/pixel. The effectiveness of each approach was evaluated with data at both individual and combined time points. Results and discussion: The major findings can be summarized as follows: (1) the inclusion of the texture features did not improve the model performance, (2) the performance of the model using spectral features from satellite imagery at its original resolution can provide similar results as UAS imagery, with variation depending on the field pea yield trial under study and the growth stage, (3) the model performance improved after applying multi-scale, multiple time point feature fusion, (4) the features extracted from the pan-sharpened satellite imagery using intensity-hue-saturation transformation (image fusion) showed better model performance than those with original satellite imagery or high definition imagery, and (5) the green normalized difference vegetation index and transformed triangular vegetation index were identified as key features contributing to high model performance across trials and time points. These findings demonstrate the potential of high-resolution satellite imagery and data fusion approaches for plot-scale phenomics applications.

Apocrine Cystadenoma of the Eyelid, a Rare Neoplasm: Expanded Immunohistologic Profile.

An 83-year-old woman experienced the slow enlargement of a right lower eyelid mass. Histopathologic examination of the excised tissue showed a mucin-filled cystic tumor emanating from an apocrine bilayer that displayed bleb-like apocrine decapitation secretion. The outer flattened myoepithelial layer of the bilayer reacted with immunohistochemical stains for smooth muscle actin and calponin. In foci, the tumor exhibited a cribriform architecture with small pockets of mucin. Tumor cells were reactive for cytokeratin 7, Gross Cystic Disease Fluid Protein 15 (BRST-2), estrogen and progesterone receptors, androgen receptors, mammaglobin, epithelial membrane antigen, and GATA3. Ki67 showed a very low proliferation fraction. The lesion exemplifies the fourth instance of an eyelid apocrine cystadenoma in the literature.

Prediction of Protein Concentration in Pea (Pisum sativum L.) Using Near-Infrared Spectroscopy (NIRS) Systems.

Breeding for increased protein concentration is a priority in field peas. Having a quick, accurate, and non-destructive protein quantification method is critical for screening breeding materials, which the near-infrared spectroscopy (NIRS) system can provide. Partial least square regression (PLSR) models to predict protein concentration were developed and compared for DA7250 and FT9700 NIRS systems. The reference protein data were accurate and exhibited a wider range of variation (15.3−29.8%). Spectral pre-treatments had no clear advantage over analyses based on raw spectral data. Due to the large number of samples used in this study, prediction accuracies remained similar across calibration sizes. The final PLSR models for the DA7250 and FT9700 systems required 10 and 13 latent variables, respectively, and performed well and were comparable (R2 = 0.72, RMSE = 1.22, and bias = 0.003 for DA7250; R2 = 0.79, RMSE = 1.23, and bias = 0.055 for FT9700). Considering three groupings for protein concentration (Low: <20%, Medium: ≥20%, but ≤25%, and High: >25%), none of the entries changed from low to high or vice versa between the observed and predicted values for the DA7250 system. Only a single entry moved from a low category in the observed data to a high category in the predicted data for the FT9700 system in the calibration set. Although the FT9700 system outperformed the DA7250 system by a small margin, both systems had the potential to predict protein concentration in pea seeds for breeding purposes. Wavelengths between 950 nm and 1650 nm accounted for most of the variation in pea protein concentration.

Evaluation of Effective Class-Balancing Techniques for CNN-Based Assessment of Aphanomyces Root Rot Resistance in Pea (Pisum sativum L.).

Aphanomyces root rot (ARR) is a devastating disease that affects the production of pea. The plants are prone to infection at any growth stage, and there are no chemical or cultural controls. Thus, the development of resistant pea cultivars is important. Phenomics technologies to support the selection of resistant cultivars through phenotyping can be valuable. One such approach is to couple imaging technologies with deep learning algorithms that are considered efficient for the assessment of disease resistance across a large number of plant genotypes. In this study, the resistance to ARR was evaluated through a CNN-based assessment of pea root images. The proposed model, DeepARRNet, was designed to classify the pea root images into three classes based on ARR severity scores, namely, resistant, intermediate, and susceptible classes. The dataset consisted of 1581 pea root images with a skewed distribution. Hence, three effective data-balancing techniques were identified to solve the prevalent problem of unbalanced datasets. Random oversampling with image transformations, generative adversarial network (GAN)-based image synthesis, and loss function with class-weighted ratio were implemented during the training process. The result indicated that the classification F1-score was 0.92 ± 0.03 when GAN-synthesized images were added, 0.91 ± 0.04 for random resampling, and 0.88 ± 0.05 when class-weighted loss function was implemented, which was higher than when an unbalanced dataset without these techniques were used (0.83 ± 0.03). The systematic approaches evaluated in this study can be applied to other image-based phenotyping datasets, which can aid the development of deep-learning models with improved performance.

Multi-trait genomic prediction improves selection accuracy for enhancing seed mineral concentrations in pea.

Multi-trait genomic selection (MT-GS) has the potential to improve predictive ability by maximizing the use of information across related genotypes and genetically correlated traits. In this study, we extended the use of sparse phenotyping method into the MT-GS framework by split testing of entries to maximize borrowing of information across genotypes and predict missing phenotypes for targeted traits without additional phenotyping expenditure. Using 300 advanced breeding lines from North Dakota State University (NDSU) pulse breeding program and ∼200 USDA accessions that were evaluated for 10 nutritional traits, our results show that the proposed sparse phenotyping aided MT-GS can further improve predictive ability by >12% across traits compared with univariate (UNI) genomic selection. The proposed strategy departed from the previous reports that weak genetic correlation is a limitation to the advantage of MT-GS over UNI genomic selection, which was evident in the partially balanced phenotyping-enabled MT-GS. Our results point to heritability and genetic correlation between traits as possible metrics to optimize and further improve the estimation of model parameters, and ultimately, prediction performance. Overall, our study offers a new approach to optimize the prediction performance using the MT-GS and further highlight strategy to maximize the efficiency of GS in a plant breeding program. The sparse-testing-aided MT-GS proposed in this study can be further extended to multi-environment, multi-trait GS to improve prediction performance and further reduce the cost of phenotyping and time-consuming data collection process.

We extended the use of sparse phenotyping into the multi-trait genomic selection (MT-GS) framework by split testing of entries. The sparse-phenotyping-aided MT-GS can increase predictive ability by >12% across traits. Heritability and genetic correlation are possible metrics to optimize and further improve prediction performance of MT-GS. The sparse-testing-aided MT-GS can be further extended to multi-environment, multi-trait GS framework.

Phenotypic and Genetic Characterization of the Lentil Single Plant-Derived Core Collection for Resistance to Root Rot Caused by Fusarium avenaceum.

Lentil (Lens culinaris) is a pulse crop grown for its amino acid profile, moderate drought tolerance, and ability to fix nitrogen. As the global demand for lentils expands and new production regions emerge so too have the complement of diseases that reduce yield, including the root rot complex. Although the predominant causal pathogen varies based on growing region, Fusarium avenaceum is often found to be an important contributor to disease. This study screened part of the lentil single plant-derived core collection for resistance to F. avenaceum in a greenhouse. Plants were phenotyped for disease severity using three scoring scales and the differences in biomass traits due to pathogen presence were measured. Lentil accessions varied in disease severity and differences in biomass traits were found to be correlated with each visual severity estimate (r = -0.37 to -0.63, P < 0.001), however, heritability estimates were low to moderate among traits (H2 = 0.12 to 0.43). Results of a genome-wide association study (GWAS) using single nucleotide polymorphism (SNP) markers derived from genotyping-by-sequencing revealed 11 quantitative trait loci (QTL) across four chromosomes. Two pairs of QTL colocated for two traits and were found near putative orthologs that have been previously associated with plant disease resistance. The identification of lentil accessions that did not exhibit a difference in biomass traits may serve as parental material in breeding or in the development of biparental mapping populations to further validate and dissect the genetic control of resistance to root rot caused by F. avenaceum.

Organic dry pea (Pisum sativum L.) biofortification for better human health.

A primary criticism of organic agriculture is its lower yield and nutritional quality compared to conventional systems. Nutritionally, dry pea (Pisum sativum L.) is a rich source of low digestible carbohydrates, protein, and micronutrients. This study aimed to evaluate dry pea cultivars and advanced breeding lines using on-farm field selections to inform the development of biofortified organic cultivars with increased yield and nutritional quality. A total of 44 dry pea entries were grown in two USDA-certified organic on-farm locations in South Carolina (SC), United States of America (USA) for two years. Seed yield and protein for dry pea ranged from 61 to 3833 kg ha-1 and 12.6 to 34.2 g/100 g, respectively, with low heritability estimates. Total prebiotic carbohydrate concentration ranged from 14.7 to 26.6 g/100 g. A 100-g serving of organic dry pea provides 73.5 to 133% of the recommended daily allowance (%RDA) of prebiotic carbohydrates. Heritability estimates for individual prebiotic carbohydrates ranged from 0.27 to 0.82. Organic dry peas are rich in minerals [iron (Fe): 1.9-26.2 mg/100 g; zinc (Zn): 1.1-7.5 mg/100 g] and have low to moderate concentrations of phytic acid (PA:18.8-516 mg/100 g). The significant cultivar, location, and year effects were evident for grain yield, thousand seed weight (1000-seed weight), and protein, but results for other nutritional traits varied with genotype, environment, and interactions. "AAC Carver," "Jetset," and "Mystique" were the best-adapted cultivars with high yield, and "CDC Striker," "Fiddle," and "Hampton" had the highest protein concentration. These cultivars are the best performing cultivars that should be incorporated into organic dry pea breeding programs to develop cultivars suitable for organic production. In conclusion, organic dry pea has potential as a winter cash crop in southern climates. Still, it will require selecting diverse genetic material and location sourcing to develop improved cultivars with a higher yield, disease resistance, and nutritional quality.

A Case for the Use of Artificial Intelligence in Glaucoma Assessment.

We hypothesize that artificial intelligence (AI) applied to relevant clinical testing in glaucoma has the potential to enhance the ability to detect glaucoma. This premise was discussed at the recent Collaborative Community on Ophthalmic Imaging meeting, "The Future of Artificial Intelligence-Enabled Ophthalmic Image Interpretation: Accelerating Innovation and Implementation Pathways," held virtually September 3-4, 2020. The Collaborative Community on Ophthalmic Imaging (CCOI) is an independent self-governing consortium of stakeholders with broad international representation from academic institutions, government agencies, and the private sector whose mission is to act as a forum for the purpose of helping speed innovation in healthcare technology. It was 1 of the first 2 such organizations officially designated by the Food and Drug Administration in September 2019 in response to their announcement of the collaborative community program as a strategic priority for 2018-2020. Further information on the CCOI can be found online at their website (https://www.cc-oi.org/about). Artificial intelligence for glaucoma diagnosis would have high utility globally, because access to care is limited in many parts of the world and half of all people with glaucoma are unaware of their illness. The application of AI technology to glaucoma diagnosis has the potential to broadly increase access to care worldwide, in essence flattening the Earth by providing expert-level evaluation to individuals even in the most remote regions of the planet.

Crop Performance Evaluation of Chickpea and Dry Pea Breeding Lines Across Seasons and Locations Using Phenomics Data.

The Pacific Northwest is an important pulse production region in the United States. Currently, pulse crop (chickpea, lentil, and dry pea) breeders rely on traditional phenotyping approaches to collect performance and agronomic data to support decision making. Traditional phenotyping poses constraints on data availability (e.g., number of locations and frequency of data acquisition) and throughput. In this study, phenomics technologies were applied to evaluate the performance and agronomic traits in two pulse (chickpea and dry pea) breeding programs using data acquired over multiple seasons and locations. An unmanned aerial vehicle-based multispectral imaging system was employed to acquire image data of chickpea and dry pea advanced yield trials from three locations during 2017-2019. The images were analyzed semi-automatically with custom image processing algorithm and features were extracted, such as canopy area and summary statistics associated with vegetation indices. The study demonstrated significant correlations (P < 0.05) between image-based features (e.g., canopy area and sum normalized difference vegetation index) with yield (r up to 0.93 and 0.85 for chickpea and dry pea, respectively), days to 50% flowering (r up to 0.76 and 0.85, respectively), and days to physiological maturity (r up to 0.58 and 0.84, respectively). Using image-based features as predictors, seed yield was estimated using least absolute shrinkage and selection operator regression models, during which, coefficients of determination as high as 0.91 and 0.80 during model testing for chickpea and dry pea, respectively, were achieved. The study demonstrated the feasibility to monitor agronomic traits and predict seed yield in chickpea and dry pea breeding trials across multiple locations and seasons using phenomics tools. Phenomics technologies can assist plant breeders to evaluate the performance of breeding materials more efficiently and accelerate breeding programs.

Chickpea Seed Rot and Damping-Off Caused by Metalaxyl-Resistant Pythium ultimum and Its Management with Ethaboxam.

Metalaxyl and its isomer mefenoxam have been the primary fungicides used as seed treatments in managing Pythium seed rot and damping-off of chickpea (Cicer arietinum). However, outbreaks of seed rot and damping-off of metalaxyl-treated chickpea seeds were found in the dryland agriculture regions of southeastern Washington and northern Idaho. Pythium spp. isolated from rotten seeds and associated soils showed high levels of resistance to metalaxyl. Large proportions (31 to 91%) of Pythium isolates resistant to metalaxyl were detected in areas where severe chickpea damping-off occurred and were observed in commercial chickpea fields over several years. All metalaxyl-resistant (MR) isolates were identified as Pythium ultimum var. ultimum. The metalaxyl resistance trait measured by EC50 values was stable over 10 generations in the absence of metalaxyl, and no observable fitness costs were associated with metalaxyl resistance. Under controlled conditions, metalaxyl treatments failed to protect chickpea seeds from seed rot and damping-off after inoculation with MR Pythium isolates. In culture, ethaboxam inhibited mycelial growth of both MR and metalaxyl-sensitive isolates. Greenhouse and field tests showed that ethaboxam is effective in managing MR Pythium. Ethaboxam in combination with metalaxyl is commonly applied as seed treatments in commercial chickpea production.

Harnessing Genetic Diversity in the USDA Pea Germplasm Collection Through Genomic Prediction.

Phenotypic evaluation and efficient utilization of germplasm collections can be time-intensive, laborious, and expensive. However, with the plummeting costs of next-generation sequencing and the addition of genomic selection to the plant breeder's toolbox, we now can more efficiently tap the genetic diversity within large germplasm collections. In this study, we applied and evaluated genomic prediction's potential to a set of 482 pea (Pisum sativum L.) accessions-genotyped with 30,600 single nucleotide polymorphic (SNP) markers and phenotyped for seed yield and yield-related components-for enhancing selection of accessions from the USDA Pea Germplasm Collection. Genomic prediction models and several factors affecting predictive ability were evaluated in a series of cross-validation schemes across complex traits. Different genomic prediction models gave similar results, with predictive ability across traits ranging from 0.23 to 0.60, with no model working best across all traits. Increasing the training population size improved the predictive ability of most traits, including seed yield. Predictive abilities increased and reached a plateau with increasing number of markers presumably due to extensive linkage disequilibrium in the pea genome. Accounting for population structure effects did not significantly boost predictive ability, but we observed a slight improvement in seed yield. By applying the best genomic prediction model (e.g., RR-BLUP), we then examined the distribution of genotyped but nonphenotyped accessions and the reliability of genomic estimated breeding values (GEBV). The distribution of GEBV suggested that none of the nonphenotyped accessions were expected to perform outside the range of the phenotyped accessions. Desirable breeding values with higher reliability can be used to identify and screen favorable germplasm accessions. Expanding the training set and incorporating additional orthogonal information (e.g., transcriptomics, metabolomics, physiological traits, etc.) into the genomic prediction framework can enhance prediction accuracy.

Dissecting the Genetic Architecture of Aphanomyces Root Rot Resistance in Lentil by QTL Mapping and Genome-Wide Association Study.

Lentil (Lens culinaris Medikus) is an important source of protein for people in developing countries. Aphanomyces root rot (ARR) has emerged as one of the most devastating diseases affecting lentil production. In this study, we applied two complementary quantitative trait loci (QTL) analysis approaches to unravel the genetic architecture underlying this complex trait. A recombinant inbred line (RIL) population and an association mapping population were genotyped using genotyping by sequencing (GBS) to discover novel single nucleotide polymorphisms (SNPs). QTL mapping identified 19 QTL associated with ARR resistance, while association mapping detected 38 QTL and highlighted accumulation of favorable haplotypes in most of the resistant accessions. Seven QTL clusters were discovered on six chromosomes, and 15 putative genes were identified within the QTL clusters. To validate QTL mapping and genome-wide association study (GWAS) results, expression analysis of five selected genes was conducted on partially resistant and susceptible accessions. Three of the genes were differentially expressed at early stages of infection, two of which may be associated with ARR resistance. Our findings provide valuable insight into the genetic control of ARR, and genetic and genomic resources developed here can be used to accelerate development of lentil cultivars with high levels of partial resistance to ARR.

Image-Based Phenotyping of Flowering Intensity in Cool-Season Crops.

The timing and duration of flowering are key agronomic traits that are often associated with the ability of a variety to escape abiotic stress such as heat and drought. Flowering information is valuable in both plant breeding and agricultural production management. Visual assessment, the standard protocol used for phenotyping flowering, is a low-throughput and subjective method. In this study, we evaluated multiple imaging sensors (RGB and multiple multispectral cameras), image resolution (proximal/remote sensing at 1.6 to 30 m above ground level/AGL), and image processing (standard and unsupervised learning) techniques in monitoring flowering intensity of four cool-season crops (canola, camelina, chickpea, and pea) to enhance the accuracy and efficiency in quantifying flowering traits. The features (flower area, percentage of flower area with respect to canopy area) extracted from proximal (1.6-2.2 m AGL) RGB and multispectral (with near infrared, green and blue band) image data were strongly correlated (r up to 0.89) with visual rating scores, especially in pea and canola. The features extracted from unmanned aerial vehicle integrated RGB image data (15-30 m AGL) could also accurately detect and quantify large flowers of winter canola (r up to 0.84), spring canola (r up to 0.72), and pea (r up to 0.72), but not camelina or chickpea flowers. When standard image processing using thresholds and unsupervised machine learning such as k-means clustering were utilized for flower detection and feature extraction, the results were comparable. In general, for applicability of imaging for flower detection, it is recommended that the image data resolution (i.e., ground sampling distance) is at least 2-3 times smaller than that of the flower size. Overall, this study demonstrates the feasibility of utilizing imaging for monitoring flowering intensity in multiple varieties of evaluated crops.

Pulse Crop Effects on Gut Microbial Populations, Intestinal Function, and Adiposity in a Mouse Model of Diet-Induced Obesity.

The dietary fiber gap that is present in many countries co-exists with a low intake of grain legumes (pulses) that have 2-3 times more dietary fiber than cereal grains that are commonly recommended to increase fiber intake. Given the relationships among dietary fiber, gut health and chronic disease risk, a study was undertaken in a preclinical mouse model for obesity to examine how commonly consumed pulses, i.e., chickpea, common bean, dry pea and lentil, would impact gut microbes, intestinal function, and adiposity. Pulses were fed to C57BL/6 mice at similar levels of protein and fiber. Bacterial count in the cecum was elevated 3-fold by pulse consumption. At the phylum level, a 2.2- to 5-fold increase in Bacteriodetes relative to Firmicutes was observed. For Akkermansia muciniphila, a health-beneficial bacterium, differential effects were detected among pulses ranging from no effect to a 49-fold increase. Significant differences among pulses in biomarkers of intestinal function were not observed. Pulses reduced accumulation of lipid in adipose tissue with a greater reduction in the subcutaneous versus visceral depots. Metabolomics analysis indicated that 108 metabolites were highly different among pulse types, and several compounds are hypothesized to influence the microbiome. These results support recent recommendations to increase consumption of pulse-based foods for improved health, although all pulses were not equal in their effects.

Generalized Linear Model with Elastic Net Regularization and Convolutional Neural Network for Evaluating Aphanomyces Root Rot Severity in Lentil.

Phenomics technologies allow quantitative assessment of phenotypes across a larger number of plant genotypes compared to traditional phenotyping approaches. The utilization of such technologies has enabled the generation of multidimensional plant traits creating big datasets. However, to harness the power of phenomics technologies, more sophisticated data analysis methods are required. In this study, Aphanomyces root rot (ARR) resistance in 547 lentil accessions and lines was evaluated using Red-Green-Blue (RGB) images of roots. We created a dataset of 6,460 root images that were annotated by a plant breeder based on the disease severity. Two approaches, generalized linear model with elastic net regularization (EN) and convolutional neural network (CNN), were developed to classify disease resistance categories into three classes: resistant, partially resistant, and susceptible. The results indicated that the selected image features using EN models were able to classify three disease categories with an accuracy of up to 0.91 ± 0.004 (0.96 ± 0.005 resistant, 0.82 ± 0.009 partially resistant, and 0.92 ± 0.007 susceptible) compared to CNN with an accuracy of about 0.84 ± 0.009 (0.96 ± 0.008 resistant, 0.68 ± 0.026 partially resistant, and 0.83 ± 0.015 susceptible). The resistant class was accurately detected using both classification methods. However, partially resistant class was challenging to detect as the features (data) of the partially resistant class often overlapped with those of resistant and susceptible classes. Collectively, the findings provided insights on the use of phenomics techniques and machine learning approaches to provide quantitative measures of ARR resistance in lentil.

Comprehensive epigenome characterization reveals diverse transcriptional regulation across human vascular endothelial cells.

BACKGROUND: Endothelial cells (ECs) make up the innermost layer throughout the entire vasculature. Their phenotypes and physiological functions are initially regulated by developmental signals and extracellular stimuli. The underlying molecular mechanisms responsible for the diverse phenotypes of ECs from different organs are not well understood. RESULTS: To characterize the transcriptomic and epigenomic landscape in the vascular system, we cataloged gene expression and active histone marks in nine types of human ECs (generating 148 genome-wide datasets) and carried out a comprehensive analysis with chromatin interaction data. We developed a robust procedure for comparative epigenome analysis that circumvents variations at the level of the individual and technical noise derived from sample preparation under various conditions. Through this approach, we identified 3765 EC-specific enhancers, some of which were associated with disease-associated genetic variations. We also identified various candidate marker genes for each EC type. We found that the nine EC types can be divided into two subgroups, corresponding to those with upper-body origins and lower-body origins, based on their epigenomic landscape. Epigenomic variations were highly correlated with gene expression patterns, but also provided unique information. Most of the deferentially expressed genes and enhancers were cooperatively enriched in more than one EC type, suggesting that the distinct combinations of multiple genes play key roles in the diverse phenotypes across EC types. Notably, many homeobox genes were differentially expressed across EC types, and their expression was correlated with the relative position of each organ in the body. This reflects the developmental origins of ECs and their roles in angiogenesis, vasculogenesis and wound healing. CONCLUSIONS: This comprehensive analysis of epigenome characterization of EC types reveals diverse transcriptional regulation across human vascular systems. These datasets provide a valuable resource for understanding the vascular system and associated diseases.

Genome-Wide Association Mapping for Agronomic and Seed Quality Traits of Field Pea (Pisum sativum L.).

Genome-wide association study (GWAS) was conducted to identify loci associated with agronomic (days to flowering, days to maturity, plant height, seed yield and seed weight), seed morphology (shape and dimpling), and seed quality (protein, starch, and fiber concentrations) traits of field pea (Pisum sativum L.). A collection of 135 pea accessions from 23 different breeding programs in Africa (Ethiopia), Asia (India), Australia, Europe (Belarus, Czech Republic, Denmark, France, Lithuania, Netherlands, Russia, Sweden, Ukraine and United Kingdom), and North America (Canada and USA), was used for the GWAS. The accessions were genotyped using genotyping-by-sequencing (GBS). After filtering for a minimum read depth of five, and minor allele frequency of 0.05, 16,877 high quality SNPs were selected to determine marker-trait associations (MTA). The LD decay (LD1/2max,90) across the chromosomes varied from 20 to 80 kb. Population structure analysis grouped the accessions into nine subpopulations. The accessions were evaluated in multi-year, multi-location trials in Olomouc (Czech Republic), Fargo, North Dakota (USA), and Rosthern and Sutherland, Saskatchewan (Canada) from 2013 to 2017. Each trait was phenotyped in at least five location-years. MTAs that were consistent across multiple trials were identified. Chr5LG3_566189651 and Chr5LG3_572899434 for plant height, Chr2LG1_409403647 for lodging resistance, Chr1LG6_57305683 and Chr1LG6_366513463 for grain yield, Chr1LG6_176606388, Chr2LG1_457185, Chr3LG5_234519042 and Chr7LG7_8229439 for seed starch concentration, and Chr3LG5_194530376 for seed protein concentration were identified from different locations and years. This research identified SNP markers associated with important traits in pea that have potential for marker-assisted selection towards rapid cultivar improvement.

Author Correction: Arsenic accumulation in lentil (Lens culinaris) genotypes and risk associated with the consumption of grains.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.