The groundnut improvement network for Africa (GINA) germplasm collection: a unique genetic resource for breeding and gene discovery.

Cultivated peanut or groundnut (Arachis hypogaea L.) is a grain legume grown in many developing countries by smallholder farmers for food, feed, and/or income. The speciation of the cultivated species, that involved polyploidization followed by domestication, greatly reduced its variability at the DNA level. Mobilizing peanut diversity is a prerequisite for any breeding program for overcoming the main constraints that plague production and for increasing yield in farmer fields. In this study, the Groundnut Improvement Network for Africa assembled a collection of 1,049 peanut breeding lines, varieties, and landraces from 9 countries in Africa. The collection was genotyped with the Axiom_Arachis2 48K SNP array and 8,229 polymorphic single nucleotide polymorphism (SNP) markers were used to analyze the genetic structure of this collection and quantify the level of genetic diversity in each breeding program. A supervised model was developed using dapc to unambiguously assign 542, 35, and 172 genotypes to the Spanish, Valencia, and Virginia market types, respectively. Distance-based clustering of the collection showed a clear grouping structure according to subspecies and market types, with 73% of the genotypes classified as fastigiata and 27% as hypogaea subspecies. Using STRUCTURE, the global structuration was confirmed and showed that, at a minimum membership of 0.8, 76% of the varieties that were not assigned by dapc were actually admixed. This was particularly the case of most of the genotype of the Valencia subgroup that exhibited admixed genetic heritage. The results also showed that the geographic origin (i.e. East, Southern, and West Africa) did not strongly explain the genetic structure. The gene diversity managed by each breeding program, measured by the expected heterozygosity, ranged from 0.25 to 0.39, with the Niger breeding program having the lowest diversity mainly because only lines that belong to the fastigiata subspecies are used in this program. Finally, we developed a core collection composed of 300 accessions based on breeding traits and genetic diversity. This collection, which is composed of 205 genotypes of fastigiata subspecies (158 Spanish and 47 Valencia) and 95 genotypes of hypogaea subspecies (all Virginia), improves the genetic diversity of each individual breeding program and is, therefore, a unique resource for allele mining and breeding.

Impact of anticoagulation and antiplatelet therapy on dialysis catheter fibrin sheath formation.

PURPOSE Fibrin sheaths are a significant cause of dialysis catheter dysfunction. This study aimed to determine the role of anticoagulation, antiplatelet medications, and other factors in delaying fibrin sheath formation. METHODS An institutional review board-approved retrospective review of all patients treated for tunneled dialysis catheter fibrin sheaths from January 2014 to January 2020 was undertaken. All catheters were symmetric tipped, 14.5 F in diameter, and placed via the internal jugular vein. Seventy patients with venographically confirmed fibrin sheaths that developed after de novo catheter placement were identified. Recurrent fibrin sheaths were excluded. The impact of anticoagulation and antiplatelet therapy, as well as statin therapy, catheter side (right or left), hematocrit, platelet count, prothrombin time (PT), and international normalized ratio (INR), on the time to fibrin sheath formation was determined. RESULTS Patients on anticoagulation had a longer median catheter implantation time of 109.2 days (interquartile range (IQR): 29.3-178.5 days) compared to 80.7 days (IQR: 28.0-168.6 days) among patients not on anticoagulation. Catheter dwell time among patients taking antiplatelet therapy was 86.0 days (IQR: 31.5-160.7 days) versus 74.4 days (IQR: 27.5-202.4 days) for patients not on antiplatelet medication. Patients taking statins versus those not taking statins had median catheter dwell times of 97.5 days (IQR: 27.5-138.5 days) and 62.4 days (IQR: 29.9-259.6 days), respectively. Time to fibrin sheath formation was not significantly associated with hematocrit (P =.16), platelet count (0.12), PT (P =.51), or INR (P =.74). CONCLUSION Anticoagulation has no significant benefit in delaying sheath formation in patients with tunneled dialysis catheters. Hematologic and coagulation parameters at the time of catheter placement were also not associated with catheter dwell time.

RGB-image method enables indirect selection for leaf spot resistance and yield estimation in a groundnut breeding program in Western Africa.

Early Leaf Spot (ELS) caused by the fungus Passalora arachidicola and Late Leaf Spot (LLS) also caused by the fungus Nothopassalora personata, are the two major groundnut (Arachis hypogaea L.) destructive diseases in Ghana. Accurate phenotyping and genotyping to develop groundnut genotypes resistant to Leaf Spot Diseases (LSD) and to increase groundnut production is critically important in Western Africa. Two experiments were conducted at the Council for Scientific and Industrial Research-Savanna Agricultural Research Institute located in Nyankpala, Ghana to explore the effectiveness of using RGB-image method as a high-throughput phenotyping tool to assess groundnut LSD and to estimate yield components. Replicated plots arranged in a rectangular alpha lattice design were conducted during the 2020 growing season using a set of 60 genotypes as the training population and 192 genotypes for validation. Indirect selection models were developed using Red-Green-Blue (RGB) color space indices. Data was collected on conventional LSD ratings, RGB imaging, pod weight per plant and number of pods per plant. Data was analyzed using a mixed linear model with R statistical software version 4.0.2. The results showed differences among the genotypes for the traits evaluated. The RGB-image method traits exhibited comparable or better broad sense heritability to the conventionally measured traits. Significant correlation existed between the RGB-image method traits and the conventionally measured traits. Genotypes 73-33, Gha-GAF 1723, Zam-ICGV-SM 07599, and Oug-ICGV 90099 were among the most resistant genotypes to ELS and LLS, and they represent suitable sources of resistance to LSD for the groundnut breeding programs in Western Africa.

Multi-locus genome-wide association studies reveal genomic regions and putative candidate genes associated with leaf spot diseases in African groundnut (Arachis hypogaea L.) germplasm.

Early leaf spot (ELS) and late leaf spot (LLS) diseases are the two most destructive groundnut diseases in Ghana resulting in ≤ 70% yield losses which is controlled largely by chemical method. To develop leaf spot resistant varieties, the present study was undertaken to identify single nucleotide polymorphism (SNP) markers and putative candidate genes underlying both ELS and LLS. In this study, six multi-locus models of genome-wide association study were conducted with the best linear unbiased predictor obtained from 294 African groundnut germplasm screened for ELS and LLS as well as image-based indices of leaf spot diseases severity in 2020 and 2021 and 8,772 high-quality SNPs from a 48 K SNP array Axiom platform. Ninety-seven SNPs associated with ELS, LLS and five image-based indices across the chromosomes in the 2 two sub-genomes. From these, twenty-nine unique SNPs were detected by at least two models for one or more traits across 16 chromosomes with explained phenotypic variation ranging from 0.01 - 62.76%, with exception of chromosome (Chr) 08 (Chr08), Chr10, Chr11, and Chr19. Seventeen potential candidate genes were predicted at ± 300 kbp of the stable/prominent SNP positions (12 and 5, down- and upstream, respectively). The results from this study provide a basis for understanding the genetic architecture of ELS and LLS diseases in African groundnut germplasm, and the associated SNPs and predicted candidate genes would be valuable for breeding leaf spot diseases resistant varieties upon further validation.

Long-term renal function outcomes after renal cryoablation complicated by major hemorrhage requiring selective transarterial embolization.

PURPOSE: To determine long-term renal function outcomes after renal cryoablation complicated by major hemorrhage requiring transarterial embolization compared to patients who underwent uncomplicated renal cryoablation without major hemorrhage. METHODS: Utilizing a matched cohort study design, retrospective review identified 23 patients who underwent percutaneous image-guided renal cryoablation complicated by major hemorrhage requiring ipsilateral transarterial embolization (TAE group) and a control group of 23 patients who underwent uncomplicated renal cryoablation matched 1:1 by age, gender and RENAL Nephrometry score at a single institution from 1/1/2005 to 12/31/2019. Primary outcome parameters included change in creatinine (mg/dl) and estimated glomerular filtration rate (ml/min/1.73 m2; eGFR) from baseline and were compared between TAE and control group using a paired t-test. RESULTS: There was a significantly higher proportion of patients on pre-ablation anticoagulation in the TAE v. control group (30% v. 4%; p = 0.047), but all patients were off anticoagulation and with normal coagulation parameters at the time of cryoablation. Otherwise there were no significant differences in clinical, renal tumor, Charlson co-morbidity index, baseline renal function or cryoablation parameters between the TAE and control group. In the post-ablation period, there was trend toward greater increase in creatinine from baseline to worst post-ablation creatinine in the TAE v. the control group (+ 0.5 ± 0.7 mg/dl v. 0.2 ± 0.1 mg/dl; p = 0.056). However, at a mean follow-up of 42.7 ± 35.7 months, there was no significant difference between the TAE and control group in creatinine (p = 0.68), eGFR (p = 0.60) or change from baseline in creatinine (p = 0.28), eGFR (p = 0.80) or CKD stage (p = 0.74). No patient required initiation of hemodialysis. CONCLUSION: Selective transarterial embolization for post-renal cryoablation hemorrhage does not significantly affect long-term renal function compared to cryoablation alone. Pre-ablation anticoagulation despite normal coagulation at time of ablation may be a risk factor for post-ablation hemorrhage, and warrants further evaluation when considering pre-ablation embolization.

Characterization of Groundnut (Arachis hypogaea L.) Test Locations Using Representative Testing Environments With Farmer-Preferred Traits.

In this study, the differential rankings of 36 groundnut genotypes under varying environmental conditions were studied at various levels of phenotype. Locations that are generally accepted by the crop- and soil-based research community to represent the entire Guinea and Sudan Savanna agro-ecological zones in Ghana were characterized, this time using a crop. The characterization was done based on four farmer-preferred traits (early and late leaf spot disease ratings, and haulm and pod yields) using three models (i.e., AMMI, GGE, and Finlay-Wilkinson regression). These models were used to capture specific levels of phenotype, namely, genotype-by-environment interaction (GE), genotype main effect plus GE (G+GE), and environment and genotype main effects plus GE (E+G+GE), respectively. The effect of three major environmental covariables was also determined using factorial regression. Location main effect was found to be highly significant (p < 0.001), confirming its importance in cultivar placement. However, unlike genotypes where the best is usually adjudged through statistical ranking, locations are judged against a benchmark, particularly when phenotyping for disease severity. It was also found that the locations represent one complex mega-environment, justifying the need to test new technologies, including genotypes in all of them before they can be approved for adoption nationally. Again, depending on the phenotypic level considered, genotypic rankings may change, causing environmental groupings to change. For instance, all locations clustered to form one group in 2017 for early and late leaf spot diseases and pod yield when GE was considered, but the groupings changed when G+GE was considered for the same traits in the same year. As a result, assessing genotypic performance at the various levels to arrive at a consensus decision is suggested. Genotypes ICGV-IS 141120 and ICGV-IS 13937 were found to be the best performing.

Genetic diversity and population structure of groundnut (Arachis hypogaea L.) accessions using phenotypic traits and SSR markers: implications for rust resistance breeding.

Groundnut (Arachis hypogaea L.) is a multi-purpose legume serving millions of farmers and their value chain actors globally. Use of old poor-performing cultivars contributes to low yields (< 1 t/ha) of groundnut in sub-Saharan Africa including Tanzania. The objectives of this study were to determine the extent of genetic variation among diverse groundnut collections using phenotypic traits and simple sequence repeat (SSR) markers to select distinct and complementary genotypes for breeding. One hundred and nineteen genotypes were evaluated under field conditions for agronomic traits and susceptibility to rust and leaf spot diseases. The study was conducted in two locations across two seasons. In addition, the 119 accessions were profiled with 13 selected SSR markers. Genotype and genotype by environment interaction effects were significant (p < 0.05) for days to flowering (DTF), late leaf spot score at 85 and 100 days after planting, pod yield (PDY), kernel yield (KY), hundred seed weight (HSW) and shelling percentage (SP). Principal components analysis revealed that plant stand, KY, SP, NPP (number of pods per plant), late leaf spot and rust disease scores accounted for the largest proportion of the total variation (71.9%) among the tested genotypes. Genotypes ICGV-SM 08587 and ICGV-SM 16579 had the most stable yields across the test environments. Moderate genetic variation was recorded with mean polymorphic information content of 0.34 and gene diversity of 0.63 using the SSR markers. The majority (74%) of genotypes showed high membership coefficients to their respective sub-populations, while 26% were admixtures after structure analysis. Much of the variation (69%) was found within populations due to genotypic differences. The present study identified genotypes ICGV-SM 06737, ICGV-SM 16575, ICG 12725 and ICGV-SM 16608 to be used for development of mapping population, which will be useful for groundnut improvement. This study provided a baseline information on characterization and selection of a large sample of groundnut genotypes in Tanzania for effective breeding and systematic conservation.

Rapid vertical flow immunoassay on AuNP plasmonic paper for SERS-based point of need diagnostics.

SERS based immunoassays for point-of-care diagnostics are a promising tool to facilitate biomarker detection for early disease diagnosis and disease control. The technique is based on a sandwiched system in which antigen is first captured by a selective plasmonic paper substrate and then labeled by an extrinsic Raman label (ERL), consisting of a 60 nm gold nanoparticle (AuNP) functionalized with a mixed monolayer of detection antibody and 4-nitrobenezenethiol (NBT) as a Raman reporter molecule. Here, we report on the use of AuNP modified filter paper as a novel capture membrane in a vertical flow format. This vertical flow configuration affords reproducible flow of sample and label through the capture substrate to overcome diffusion limited kinetics and significantly reduced assay time. The filter paper was selected due to its affordability and availability, while the embedded AuNPs maximized plasmonic coupling with the ERLs and SERS enhancement. Additionally, the embedded AuNP served as a scaffold to immobilize capture antibody to specifically bind antigen. In this work, a SERS-based rapid vertical flow (SERS-RVF) immunoassay for detection of mouse IgG was developed to establish proof-of-principle. Optimization of assay conditions led to a limit of detection of 3 ng/mL, which is comparable to more traditional formats carried out in multi-well plates, and significantly reduced assay time to less than 2 min. Additionally, IgG was accurately quantified in normal mouse serum to validate the SERS-RVF assay for application to the analysis of biological samples. These results highlight the potential advantages of the SERS-RVF platform for point-of-need testing.

Genomics, genetics and breeding of tropical legumes for better livelihoods of smallholder farmers.

Legumes are important components of sustainable agricultural production, food, nutrition and income systems of developing countries. In spite of their importance, legume crop production is challenged by a number of biotic (diseases and pests) and abiotic stresses (heat, frost, drought and salinity), edaphic factors (associated with soil nutrient deficits) and policy issues (where less emphasis is put on legumes compared to priority starchy staples). Significant research and development work have been done in the past decade on important grain legumes through collaborative bilateral and multilateral projects as well as the CGIAR Research Program on Grain Legumes (CRP-GL). Through these initiatives, genomic resources and genomic tools such as draft genome sequence, resequencing data, large-scale genomewide markers, dense genetic maps, quantitative trait loci (QTLs) and diagnostic markers have been developed for further use in multiple genetic and breeding applications. Also, these mega-initiatives facilitated release of a number of new varieties and also dissemination of on-the-shelf varieties to the farmers. More efforts are needed to enhance genetic gains by reducing the time required in cultivar development through integration of genomics-assisted breeding approaches and rapid generation advancement.

Multienvironment Testing for Trait Stability and G × E Interaction on N2 Fixation, Plant Development, and Water-Use Efficiency of 21 Elite Groundnut (Arachis hypogaea L.) Genotypes in the Guinea Savanna.

Groundnut production constitutes an integral part of the livelihoods of the people in the Guinea savanna of West Africa. This region accounts for over 70% of the total groundnut production in Ghana, 90% in Nigeria, and 100% in Mali and Burkina Faso. However, harsh environmental conditions often result in drastic yield reductions. In this study, we identified groundnut genotypes with superior symbiotic efficiency, greater pod yield, and plant water-use efficiency from 21 advanced groundnut breeding lines from ICRISAT after testing them at three locations in the Guinea savanna of Ghana over two consecutive years. Average N contribution by the groundnut genotypes ranged from 48 to 108 kg N ha-1, and mean pod yield from 580 to 2,100 kg ha-1. Genotype 17 (ICGV-IS 08837) produced about 2.5-fold more pods than genotype 1 (Chinese), which was the most widely cultivated variety by farmers. Of the 21 genotypes studied, genotype 16 (ICGV 99247) recorded the highest shoot δ13C value and was superior in water-use efficiency, which was consistent with stability estimates and mean performance. We also measured the effects of G × E on pod yield, N2 fixation, shoot δ13C, and mega-environments for testing groundnut in the Guinea savanna, and these were all significant, although the effect was minimal on shoot δ13C values. Of the locations studied, Nyankpala and Damongo were more discriminating, and each constituted a mega-environment for conducting future groundnut trials in the Guinea savanna. Genotype 3 (ICG 6222) emerged as the best cultivar for the Damongo mega-environment, while genotype 17 was the best genotype for the Nyankpala mega-environment. The genotypes exhibiting the highest sensitivity of N2 fixation in the environment included genotype 3 (ICG 6222), genotype 4 (ICGV 00068), and genotype 10 (ICGV 03315) (bi > 1.3), while Pi estimates ranked genotypes 3, 10, and 17 as the best groundnut cultivars in terms of symbiotic N contribution. Based on the results of this study, genotype 17 (ICGV-IS 08837), genotype 3 (ICG 6222), genotype 10 (ICGV 03315), and genotype 4 (ICGV 00068), which were the most outstanding in terms of the overall pod yield, shoot biomass production, and amount of N-fixed, were the most suitable candidates to recommend for use in developing new varieties for the Guinea savanna of Ghana. Genotype 17 (ICGV-IS 08837) has already been released as a commercial variety for the Guinea savanna of Ghana since October 2018.

Genetics, genomics and breeding of groundnut (Arachis hypogaea L.).

Groundnut is an important food and oil crop in the semiarid tropics, contributing to household food consumption and cash income. In Asia and Africa, yields are low attributed to various production constraints. This review paper highlights advances in genetics, genomics and breeding to improve the productivity of groundnut. Genetic studies concerning inheritance, genetic variability and heritability, combining ability and trait correlations have provided a better understanding of the crop's genetics to develop appropriate breeding strategies for target traits. Several improved lines and sources of variability have been identified or developed for various economically important traits through conventional breeding. Significant advances have also been made in groundnut genomics including genome sequencing, marker development and genetic and trait mapping. These advances have led to a better understanding of the groundnut genome, discovery of genes/variants for traits of interest and integration of marker-assisted breeding for selected traits. The integration of genomic tools into the breeding process accompanied with increased precision of yield trialing and phenotyping will increase the efficiency and enhance the genetic gain for release of improved groundnut varieties.

Sandwiching analytes with structurally diverse plasmonic nanoparticles on paper substrates for surface enhanced Raman spectroscopy.

This report describes the systematic combination of structurally diverse plasmonic metal nanoparticles (AgNPs, AuNPs, Ag core-Au shell NPs, and anisotropic AuNPs) on flexible paper-based materials to induce signal-enhancing environments for surface enhanced Raman spectroscopy (SERS) applications. The anisotropic AuNP-modified paper exhibits the highest SERS response due to the surface area and the nature of the broad surface plasmon resonance (SPR) neighboring the Raman excitation wavelength. The subsequent addition of a second layer with these four NPs (e.g., sandwich arrangement) leads to the notable increase of the SERS signals by inducing a high probability of electromagnetic field environments associated with the interparticle SPR coupling and hot spots. After examining sixteen total combinations, the highest SERS response is obtained from the second layer with AgNPs on the anisotropic AuNP paper substrate, which allows for a higher calibration sensitivity and wider dynamic range than those of typical AuNP-AuNP arrangement. The variation of the SERS signals is also found to be below 20% based on multiple measurements (both intra-sample and inter-sample). Furthermore, the degree of SERS signal reductions for the sandwiched analytes is notably slow, indicating their increased long-term stability. The optimized combination is then employed in the detection of let-7f microRNA to demonstrate their practicability as SERS substrates. Precisely introducing interparticle coupling and hot spots with readily available plasmonic NPs still allows for the design of inexpensive and practical signal enhancing substrates that are capable of increasing the calibration sensitivity, extending the dynamic range, and lowering the detection limit of various organic and biological molecules.

Selecting elite groundnut (Arachis hypogaea L) genotypes for symbiotic N nutrition, water-use efficiency and pod yield at three field sites, using 15N and 13C natural abundance.

About 70% of the groundnut (Arachis hypogaea L.) produced in Ghana is from the Guinea savanna. However, low soil nutrients, especially N, together with erratic rainfall distribution have often resulted in poor grain yield. The aim of this study was to evaluate plant growth, N2-fixing efficiency, N contribution, water-use efficiency and pod yield of 21 elite groundnut genotypes in the Guinea savanna of Ghana, using the 15N natural abundance technique. The data revealed significant variations in plant growth, symbiotic N contribution, and pod yield among the 21 genotypes tested at each field site. Average N contribution by groundnut genotypes ranged from 48 to 108 kg N ha-1. Also, mean pod yield ranged from 0.58 to 2.1 t ha-1. Genotypes ICGV-IS 08837, ICG 6222, ICGV 03315 and NKATIESARI demonstrated superior plant growth, symbiotic N contribution and greater pod yield. In fact, ICGV-IS 08837 yielded almost 2.5 fold more than CHINESE which is the most widely cultivated variety in the region. Genotypes ICGV-IS 08837, ICG 6222, ICGV 03315 and ICGV 99247 are therefore recommended for development into varieties for the Guinea savanna of Ghana. Genotypes ICG (FDRS) 4, ICGV00362 and ICGV99247 exhibited increased water-use efficiency, but were low in N2 fixation and N contribution, and would therefore be good parental material in breeding programs aimed at enhancing water-use efficiency in high N2-fixing genotypes.

Sarcopenia in Children With End-Stage Liver Disease.

BACKGROUND: Sarcopenia, reflected by decreased psoas muscle surface area (PMSA), has been identified as a novel and independent predictor of wait-list mortality and outcomes in adult liver transplantation (LT). We hypothesized that children with end-stage liver disease (ESLD) would have smaller PMSA than healthy controls. METHODS: Computer tomography images of children (ages 0 to 18 years) listed for LT in 2015 and a control group comprised 2:1 age- and gender-matched healthy pediatric trauma victims were reviewed. PMSA was determined at 2 intervertebral disc (L3/4; L4/5) levels. A subset of images was reviewed by 2 radiologists to determine interrater correlation. RESULTS: A total of 23 children with ESLD were included, and the most prevalent diagnosis was biliary atresia (61%). On both lumbar levels, median PMSA was significantly smaller in ESLD subjects compared with the 46 healthy controls (L4/5; median total PMSA (tPMSA) 407 mm (interquartile range 339-537) versus controls 513 mm (interquartile range 437-672); P = 0.004), independent of participants' weight z scores (r = 0.01; P = 0.95). Excellent interrater correlation was seen (intraclass correlation 0.99). CONCLUSIONS: In this retrospective pilot study, PMSA was significantly lower in children with ESLD compared with healthy age- and gender-matched controls. Because this finding was independent of growth in ESLD subjects, PMSA may represent a novel objective nutritional biomarker in children with advanced liver disease.