Genome Wide Association Mapping of Root Traits in the Andean Genepool of Common Bean (Phaseolus vulgaris L.) Grown With and Without Aluminum Toxicity

Common bean is one of the most important grain legumes for human diets but is produced on marginal lands with unfavorable soil conditions; among which Aluminum (Al) toxicity is a serious and widespread problem. Under low pH, stable forms of Al dissolve into the soil solution and as phytotoxic ions inhibit the growth and function of roots through injury to the root apex. This results in a smaller root system that detrimentally effects yield. The goal of this study was to evaluate 227 genotypes from an Andean diversity panel (ADP) of common bean and determine the level of Al toxicity tolerance and candidate genes for this abiotic stress tolerance through root trait analysis and marker association studies. Plants were grown as seedlings in hydroponic tanks at a pH of 4.5 with a treatment of high Al concentration (50 μM) compared to a control (0 μM). The roots were harvested and scanned to determine average root diameter, root volume, root surface area, number of root links, number of root tips, and total root length. Percent reduction or increase was calculated for each trait by comparing treatments. Genome wide association study (GWAS) was conducted by testing phenotypic data against single nucleotide polymorphism (SNP) marker genotyping data for the panel. Principal components and a kinship matrix were included in the mixed linear model to correct for population structure. Analyses of variance indicated the presence of significant difference between genotypes. The heritability of traits ranged from 0.67 to 0.92 in Al-treated and reached similar values in non-treated plants. GWAS revealed significant associations between root traits and genetic markers on chromosomes Pv01, Pv04, Pv05, Pv06, and Pv11 with some SNPs contributing to more than one trait. Candidate genes near these loci were analyzed to explain the detected association and included an Al activated malate transporter gene and a multidrug and toxic compound extrusion gene. This study showed that polygenic inheritance was critical to aluminum toxicity tolerance in common beans roots. Candidate genes found suggested that exudation of malate and citrate as organic acids would be important for Al tolerance. Possible cross-talk between mechanisms of aluminum tolerance and resistance to other abiotic stresses are discussed

Phenotypic Variability for Root Traits in Andean Common Beans Grown with and without Aluminum Stress Conditions

Genetic variation in wild relatives, GenBank accessions, landraces, and cultivars can unlock key alleles for the traits of interest for breeding programs. Breeding programs often utilize different strategies to quantify the source of heritable variation for target traits. One neglected area of study is the root traits of diverse genotypes, and this is especially the case for aluminum toxicity effects on legumes such as the common bean, which is the most used pulse for direct human consumption. This study evaluated 267 genotypes of common bean that were part of the global Andean Diversity Panel (ADP), consisting mainly of genotypes assembled from public and private breeding programs in Africa and North America, as well as elite lines and land races from the USDA. The ADP was evaluated for root traits at the seedling stage in the Tennessee State University (TSU) greenhouse using a hydroponic system with a standard nutrient solution with and without aluminum (Al). The recorded data on the roots per trial were fit to a linear mixed model for the analysis of variance in order to test for the genotype differences. Adjusted means considered replication and blocks within replication as random effects and genotypes as fixed effects. These were then used for Pearson correlation tests and for principal component analysis (PCA), where the first two vectors accounted for 94.5% and 93% of the explained variation under the control and Al-treatment conditions, respectively. Genotypes were clustered based on the morphology of roots in response to Al-toxicity treatment using the Euclidean distance and Ward’s hierarchical agglomerative clustering method, identifying four distinctive groups significant at p \u3c 0.01. The intra-cluster distance was lower than the inter-cluster distances, which indicated a heterogeneous and homogeneous nature between and within clusters, respectively. The results suggest that crossing between accessions from two of the clusters would result in the maximum genetic segregation. One cluster was found to have a higher Al-toxicity tolerance than the others

Genetic variability and genome-wide association analysis of flavor and texture in cooked beans (Phaseolus vulgaris L.)

Key message Cooked bean flavor and texture vary within and across 20 Andean seed types; SNPs are significantly associated with total flavor, beany, earthy, starchy, bitter, seed-coat perception, and cotyledon texture. Abstract Common dry beans are a nutritious food recognized as a staple globally, but their consumption is low in the USA. Improving bean flavor and texture through breeding has the potential to improve consumer acceptance and suitability for new end-use products. Little is known about genetic variability and inheritance of bean sensory characteristics. A total of 430 genotypes of the Andean Diversity Panel representing twenty seed types were grown in three locations, and cooked seeds were evaluated by a trained sensory panel for flavor and texture attribute intensities, including total flavor, beany, vegetative, earthy, starchy, sweet, bitter, seed-coat perception, and cotyledon texture. Extensive variation in sensory attributes was found across and within seed types. A set of genotypes was identified that exhibit extreme attribute intensities generally stable across all three environments. seed-coat perception and total flavor intensity had the highest broad-sense heritability (0.39 and 0.38, respectively), while earthy and vegetative intensities exhibited the lowest (0.14 and 0.15, respectively). Starchy and sweet flavors were positively correlated and highest in white bean genotypes according to principal component analysis. SNPs associated with total flavor intensity (six SNPs across three chromosomes), beany (five SNPs across four chromosomes), earthy (three SNPs across two chromosomes), starchy (one SNP), bitter (one SNP), seed-coat perception (three SNPs across two chromosomes), and cotyledon texture (two SNPs across two chromosomes) were detected. These findings lay a foundation for incorporating flavor and texture in breeding programs for the development of new varieties that entice growers, consumers, and product developers alike

Trait associations in diversity panels of the two common bean (Phaseolus vulgaris L.) gene pools grown under well-watered and water-stress conditions

Open Access Journal; Published online: 09 May 2017Common beans are a warm-season, food legume cultivated in areas prone to water limitation throughout their growing season. This study assessed the magnitude and pattern of trait associations for a total of 202 common bean genotypes divided into panels of 81 Andean and 121 Mesoamerican gene pool accessions grown under contrasting treatments of well-watered, non-stress, and water-limited, terminal drought-stress conditions. Linear correlation, complex path coefficient, and genetic divergence analyses were used to dissect the relationship dynamics between traits and the relative contribution of adaptive traits to differentiation among gene pools and genotypes based on drought stress. Drought severity level for the trial was high and created the ideal condition to reveal genotypic differences, as seen by the differential response of the genotypes for the various traits measured. The value for phenotypic coefficients of variation for all traits was higher than the corresponding genotypic values. Seed yield had positive and strong genotypic and phenotypic correlation with pods per plant across gene pools and stress levels. The overall amount of genetic correlation was greater than the corresponding phenotypic correlation matrix for all the traits within the gene pool and across stress levels. Moreover, the results depicted the phenotypic correlation as equal or better than its genotypic counterpart in estimating drought tolerance in common bean plants. Clustering analysis with Mahanalobis's coefficient of generalized distance grouped genotypes with a differential level of drought adaptation into different classes within each panel. This indicates drought tolerance involves different mechanisms of plant response and is present separately in each gene pool panel. Pods per plant, seed weight, pod partitioning index, and harvest index are useful selection objectives to improve drought adaptation in common bean, but must be differentially weighted in each gene pool. The analysis of genetic variation and association between adaptive traits on the two panels provided useful insights on which traits could be used to improve common bean adaptation to low water availability during the growth season

Sources of Resistance to Common Bacterial Blight and Charcoal Rot Disease for the Production of Mesoamerican Common Beans in the Southern United States

The gene pool of Mesoamerican common beans (Phaseolus vulgaris L.) includes genotypes in the small-to-medium-size seeded dry beans, as well as some snap beans from hotter environments adapted to the Southeastern United States. However, the warm and humid climate of the Southeastern United States is conducive to diseases such as Common Bacterial Blight (CBB) and Charcoal Rot (CR). The pathogens for these two diseases can survive long periods in infested soil or on seeds and are difficult to control through pesticides. Hence, field-level resistance would be the best management strategy for these diseases. The goals of this study were (1) to evaluate field-level resistance from the various commercial classes and subgroups represented in the Mesoamerican gene pool as sources for breeding beans for the region and (2) to evaluate genome-wide marker × trait associations (GWAS) using genetic markers for the genotypes. A total of 300 genotypes from the Mesoamerican Diversity Panel (MDP) were evaluated for CBB and CR in field experiments for three years. CBB resistance was also tested with a field isolate in controlled greenhouse conditions. The analysis of variance revealed the presence of variability in the MDP for the evaluated traits. We also identified adapted common bean genotypes that could be used directly in Southeastern production or that could be good parents in breeding programs for CBB and CR resistance. The GWAS detected 14 significant Single-Nucleotide Polymorphism (SNP) markers associated with CBB resistance distributed on five chromosomes, namely Pv02, Pv04, Pv08, Pv10, and Pv11, but no loci for resistance to CR. A total of 89 candidate genes were identified in close vicinity (±100 kb) to the significant CBB markers, some of which could be directly or indirectly involved in plant defense to diseases. These results provide a basis to further understand the complex inheritance of CBB resistance in Mesoamerican common beans and show that this biotic stress is unrelated to CR resistance, which was evident during a drought period. Genotypes with good yield potential for the Southeastern U.S. growing conditions were found with resistant to infection by the two diseases, as well as adaptation to the hot and humid conditions punctuated by droughts found in this region

Morphological and Agronomic Variability among Cultivars, Landraces, and Genebank Accessions of Purple Passion Fruit, Passiflora edulis f. edulis

Global demand for juice of the purple passion fruit, Passiflora edulis f. edulis, is growing, making it a promising species for farmers to grow in the highland tropics, to which it is adapted. However, research centers and private companies have done little to produce new high-yielding varieties. The objective of the present study, therefore, was to evaluate the agronomic and morphological characteristics of 50 passion fruit genotypes across two different elevations and agro-ecological sites as a base for germplasm enhancement. Three groups of genotypes were commercial cultivars (8 genotypes), genebank accessions (8), and landraces (34) collected from throughout the highlands of Colombia. The locations were at 1800 m above sea level (masl) (Pasca), in a place where cultivation of passion fruits is common; and at 2500 masl (Susacón), at a higher elevation site compared with most commercial plantings equal to a new agroecology for cultivation of the crop. Results indicated that the mid-elevation site produced higher yields (kg fruit/plant) than the high elevation site, although some landraces were highly productive there. Commercial cultivar and genebank accessions clustered together in a principal component analysis (PCA); while landraces showed high levels of variation in the trait descriptors with five different clusters. Therefore, landraces of purple passion fruit contained greater genetic diversity than commercial cultivars or the genebank, and breeding programs for the crop should use landraces to increase diversity of varieties available to producers and to further expand the crop to new regions, at higher elevations, or with different agro-ecologies

Chronic Kidney Disease and Associated Risk Factors Assessment among Diabetes Mellitus Patients at A Tertiary Hospital, Northwest Ethiopia

BACKGROUND: The prevalence of chronic kidney disease, particularly in diabetic patients, is increasing rapidly throughout the world. Nowadays, many individuals in developing nations are suffering from diabetes which is one of the primary risk factors of chronic kidney disease.METHODS: Institution based cross-sectional study was conducted at the University of Gondar Hospital from February to April 2016. A total of 229 study participants were selected using systematic random sampling technique. Urine sample was collected for albumin determination by dipstick. The Simplified Modification of Diet in Renal Disease study equation was used to estimate glomerular filtration rate. Binary logistic regression model was used to identify risk factors.RESULTS: Of the total 229 study participants, 50.2% were females and the mean age was 47±15.7 years. Among study participants, the prevalence of chronic kidney disease (CKD) was found to be 21.8% (95% CI: 16% - 27%). Of all study participants, 9(3.9%) had renal impairment (eGFR < 60 ml/min/ 1.73 m2) and 46 (20.1%) had albuminuria. Older age (AOR: 5.239, 95% CI: 2.255-12.175), systolic blood pressure ≥140mmHg (AOR: 3.633, 95% CI: 1.597-8.265), type 2 diabetes mellitus (AOR: 3.751, 95% CI: 1.507-9.336) and longer duration of diabetes (AOR: 3.380, 95% CI: 1.393-8.197) were independent risk factors of CKD.CONCLUSIONS: The study identified high prevalence (21.8%) of CKD among diabetic adults. CKD was significantly associated with older age, systolic blood pressure, type 2 DM and longer duration of DM. Thus, DM patients should be diagnosed for chronic kidney disease and then managed accordingly.

Undiagnosed diabetes mellitus and associated factors among psychiatric patients receiving antipsychotic drugs at the University of Gondar Hospital, northwest Ethiopia

Background: Undiagnosed diabetes mellitus cases are at higher risk for diabetic related complications. In low-income African countries, patients with undiagnosed diabetes mellitus account for 75% of diabetes cases. Psychiatric disorders have a greater impact on the global burden of diseases and disability associated with chronic diseases like diabetes mellitus and cardiovascular diseases.Methods: Institution based cross-sectional study was conducted at the University of Gondar Hospital from February to April 2016. A total of 205 psychiatric patients aged above 15 years that were taking antipsychotic were included by the simple random sampling method. Fasting blood glucose, triglycerides and cholesterol level were determined from venous blood samples to evaluate diabetes mellitus based on WHO criteria.Results: Among 205 psychiatric patients taking antipsychotics, 15(7.3%) had undiagnosed diabetes mellitus. Duration of antipsychotic treatment and sex had a statistically significant association with the prevalence of undiagnosed diabetes mellitus. As the duration of antipsychotic drug treatment increased by one year, the risk of having a diabetes mellitus increase by 1.47 times (AOR: 1.47 CI: 1.021-2.125).Conclusion: The prevalence of undiagnosed diabetes mellitus among psychiatry patients taking antipsychotics was higher than the estimated diabetes national prevalence of Ethiopia. Screening of diabetes mellitus in particular, patients having a longer duration of antipsychotic treatment is mandatory to bring more undiagnosed cases for medical attention.Keywords: Diabetes mellitus, Psychiatric disorder, Antipsychoti

Errors in the total testing process in the clinical chemistry laboratory at the University of Gondar Hospital, northwest Ethiopia

Background: Laboratory services have been described as the major processes contributing to safe patient care in the modern healthcare sector. However, occurrences of errors in the overall testing processes impair the clinical decision-making process. Such errors are supposed to be high in resource-poor countries, like Ethiopia. The objective of this study was to assess errors in the total testing process in the Clinical Chemistry laboratory of the University of Gondar Hospital, Northwest EthiopiaMethods: A cross-sectional study was conducted at the University of Gondar Hospital from February to March 2016. All the required data were collected using established quality indicators. Data were analyzed using SPSS version 20. Frequencies and cross-tabulations were used to summarize descriptive statistics.Results: A total of 3259 samples and corresponding laboratory request forms were received for analysis. The analysis of the overall distribution of errors revealed that 89.6% were preanalytical errors, 2.6% were analytical, and 7.7% were postanalytical errors. Of the pre-analytical errors, incomplete request form filling was the most frequent error observed, followed by sample rejection rate (3.8%). Analytical errors related to internal and external quality control exceeding the target range, (14.4%) and (51.4%) respectively, were reported. Excessive turnaround time and unreported critical value cases were the major defects in the post-analytical phase of quality assurance.Conclusion: The present finding showed relatively high frequency of errors, which alarms the importance of quality indicators to assess errors in the total testing process. The University of Gondar Hospital laboratory should improve the quality of healthcare services based on these findings using laboratory standards.Keywords: Analytical errors; clinical laboratory; postanalytical errors; pre-analytical errors; qualit

Genome sequence data from 17 accessions of Ensete ventricosum, a staple food crop for millions in Ethiopia.

Published online: 11 Mar 2018We present raw sequence reads and genome assemblies derived from 17 accessions of the Ethiopian orphan crop plant enset (Ensete ventricosum (Welw.) Cheesman) using the Illumina HiSeq and MiSeq platforms. Also presented is a catalogue of single-nucleotide polymorphisms inferred from the sequence data at an average density of approximately one per kilobase of genomic DNA