Genome-wide association studies reveal novel loci for resistance to groundnut rosette disease in the African core groundnut collection.

KEY MESSAGE: We identified markers associated with GRD resistance after screening an Africa-wide core collection across three seasons in Uganda Groundnut is cultivated in several African countries where it is a major source of food, feed and income. One of the major constraints to groundnut production in Africa is groundnut rosette disease (GRD), which is caused by a complex of three agents: groundnut rosette assistor luteovirus, groundnut rosette umbravirus and its satellite RNA. Despite several years of breeding for GRD resistance, the genetics of the disease is not fully understood. The objective of the current study was to use the African core collection to establish the level of genetic variation in their response to GRD, and to map genomic regions responsible for the observed resistance. The African groundnut core genotypes were screened across two GRD hotspot locations in Uganda (Nakabango and Serere) for 3 seasons. The Area Under Disease Progress Curve combined with 7523 high quality SNPs were analyzed to establish marker-trait associations (MTAs). Genome-Wide Association Studies based on Enriched Compressed Mixed Linear Model detected 32 MTAs at Nakabango: 21 on chromosome A04, 10 on B04 and 1 on B08. Two of the significant markers were localised on the exons of a putative TIR-NBS-LRR disease resistance gene on chromosome A04. Our results suggest the likely involvement of major genes in the resistance to GRD but will need to be further validated with more comprehensive phenotypic and genotypic datasets. The markers identified in the current study will be developed into routine assays and validated for future genomics-assisted selection for GRD resistance in groundnut.

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.

Physical activity interventions for glycaemic control in African adults - A systematic review and meta-analysis.

BACKGROUND AND AIM: Growing evidence indicates that increasing physical activity may aid in regulating altered glycaemic control, thereby mitigating the risk of diabetes. However, the evidence summarising the efficacy of physical activity on glycaemic control among African adults remains unconsolidated. Our objective was to provide an amalgamated summary of the empirical evidence that explored the effectiveness of physical activity interventions on glycaemic control among African adults. METHODS: A systematic search of six journal databases for the studies exploring the efficacy of physical activity on glycaemic control among African adults until March 21, 2022, was administered. Two independent reviewers screened the citations based on a priori set eligibility criteria. Data were analysed using inverse variance method and a summary of findings was synthesised using the Grading of Recommendations, Assessment, Development and Evaluations approach. RESULTS: Of the 14,624 citations retrieved, 26 articles with 1474 participants were included for final analysis. Most of the included trials had a high risk of bias (N = 20; 76.92%). Our review found a significant reduction in fasting blood glucose (FBG, -2.18 [ 95% CI -3.18, -1.18] mmol/L), insulin (-0.99 [-2.71, 0.74] µU/L), Glycosylated haemoglobin (HbA1C) (-0.53% [-0.88, -0.19]), Homeostatic Model Assessment for Insulin Resistance (HOMA-IR) (-0.74% [-1.10, -0.38]) and insulin sensitivity (-0.90 µU/l/min [-1.75, -0.06]) following physical activity interventions. The review reports low certainty of evidence across all outcome measures. DISCUSSION AND CONCLUSION: Physical activity interventions were found to improve glycaemic control among African adults. However, the optimal physical activity dose for demonstrating meaningful benefits on glucose tolerance still remains unclear due to the limited number of primary studies available.

Exploration of Alternative Approaches to Phenotyping of Late Leaf Spot and Groundnut Rosette Virus Disease for Groundnut Breeding.

Late leaf spot (LLS), caused by Nothopassalora personata (Berk. & M.A Curt.), and groundnut rosette disease (GRD), [caused by groundnut rosette virus (GRV)], represent the most important biotic constraints to groundnut production in Uganda. Application of visual scores in selection for disease resistance presents a challenge especially when breeding experiments are large because it is resource-intensive, subjective, and error-prone. High-throughput phenotyping (HTP) can alleviate these constraints. The objective of this study is to determine if HTP derived indices can replace visual scores in a groundnut breeding program in Uganda. Fifty genotypes were planted under rain-fed conditions at two locations, Nakabango (GRD hotspot) and NaSARRI (LLS hotspot). Three handheld sensors (RGB camera, GreenSeeker, and Thermal camera) were used to collect HTP data on the dates visual scores were taken. Pearson correlation was made between the indices and visual scores, and logistic models for predicting visual scores were developed. Normalized difference vegetation index (NDVI) (r = -0.89) and red-green-blue (RGB) color space indices CSI (r = 0.76), v* (r = -0.80), and b* (r = -0.75) were highly correlated with LLS visual scores. NDVI (r = -0.72), v* (r = -0.71), b* (r = -0.64), and GA (r = -0.67) were best related to the GRD visual symptoms. Heritability estimates indicated NDVI, green area (GA), greener area (GGA), a*, and hue angle having the highest heritability (H 2 > 0.75). Logistic models developed using these indices were 68% accurate for LLS and 45% accurate for GRD. The accuracy of the models improved to 91 and 84% when the nearest score method was used for LLS and GRD, respectively. Results presented in this study indicated that use of handheld remote sensing tools can improve screening for GRD and LLS resistance, and the best associated indices can be used for indirect selection for resistance and improve genetic gain in groundnut breeding.

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.

Bridging the gap: decomposing sources of gender yield gaps in Uganda groundnut production.

Female plot managers in Sub-Saharan Africa often realize significantly lower crop yields than their male counterparts. Even for legumes, which are often referred to as 'women's crops', yields are significantly lower. This study investigated the underlying causes of this gender yield gap in groundnut production. The analysis is based on survey data from 228 farm households from two groundnut growing regions in Uganda. We used the Blinder-Oaxaca model to decompose factors that contribute to this yield gap. Results show 63% and 44% gender yield gaps for improved and local varieties, respectively, with female plot managers realizing less than their male counterparts. Improved groundnut seeds increase female plot manager's yields but not the yields of male plot managers. Male advantage and female disadvantage combined account for more than 70% of the yield gap in both improved and local groundnut variety production and exceed pure productivity differences. Labor use differences between female and male plot managers and variety types explain the observed yield gap. Interventions and policies that increase women's access to productive inputs including improved seed will significantly contribute to closing the yield gap, and thereby increase crop production, food security, as well as women's incomes.

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.

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.

Building Health System Capacity Through Implementation Research: Experience of INSPIRE-A Multi-country PMTCT Implementation Research Project.

BACKGROUND: The INSPIRE-Integrating and Scaling Up PMTCT through Implementation REsearch-initiative was established as a model partnership of national prevention of mother-to-child transmission of HIV (PMTCT) implementation research in 3 high HIV burden countries-Malawi, Nigeria, and Zimbabwe. INSPIRE aimed to link local research groups with Ministries of Health (MOH), build local research capacity, and demonstrate that implementation research may contribute to improving health care delivery and respond to program challenges. METHODOLOGY: We used a mixed methods approach to review capacity building activities, as experienced by health care workers, researchers, and trainers conducted in the 6 INSPIRE projects before and during study implementation. RESULTS: Between 2011 and 2016, over 3400 health care workers, research team members, and community members participated in INSPIRE activities. This included research prioritization exercises, proposal development, good clinical practice and research ethics training, data management and analysis workshops, and manuscript development. Health care workers in clinics and district health offices acknowledged the value of hosting implementation research projects and how the quality of services improved. Research teams acknowledged the opportunities that projects provided for personal development and the value of participating in a multicountry research network. DISCUSSION: INSPIRE provided an opportunity for African-led research in which researchers worked closely with national MOH to identify priority research questions and implement studies. Close partnerships between research teams and local implementers facilitated project responsiveness to local program issues. Consequently, processes and training needed for study implementation also improved local program management and service delivery. Additional benefits included improved data management, publications, and career development.

Effect of agro-ecological zone and grazing system on incidence of East Coast Fever in calves in Mbale and Sironko Districts of Eastern Uganda.

Between May 2002 and February 2003 a longitudinal survey was carried out in Mbale and Sironko Districts of Eastern Uganda to determine the influence of agro-ecological zones (AEZ) and grazing systems on tick infestation patterns and incidence of East Coast Fever (ECF) in bovine calves. The study area was stratified into AEZ (lowland, midland and upland) and grazing systems {zero grazing (ZG), restricted-outdoor grazing (ROG) and communal grazing (CG)}, whose strata had previously been shown to influence the prevalence of ECF, babesiosis and anaplasmosis. One hundred and eighty-five smallholder dairy farms with a total of 198 calves of both sexes, between the ages of 1 day and 6 weeks, were purposively selected from the AEZ-grazing system strata. Nine dynamic cohorts (11-51 calves in each) of these calves were examined and sampled monthly. Ticks infesting the calves were counted from one side of the animal body and categorized into the different species, sex and feeding status. Sera were collected at recruitment and monthly thereafter and antibodies against Theileria parva, T. mutans, Babesia bigemina, B. bovis and Anaplasma marginale were measured using ELISA. Tick challenge (total and specific) varied with AEZ and grazing system. The risk of infection with T. parva was higher in the lowland zone compared to the upland zone (hazard ratio (HR)=2.59; 95% CI: 1.00-6.34). The risk of infection with T. parva was higher in the CG system than the ZG system (HR=10.00; 95% CI: 3.61-27.92). The incidence risk for sero-conversion, over the 10 months study period, was 62, 16 and 9% in the lowland, midland and upland zones, respectively. Ninety-eight percent of the calves in lowland-CG stratum sero-converted by the age of 6 months, while 56 and 8% did so in the lowland-ROG and the lowland-ZG stratum, respectively. The results of this study show the need to consider farm circumstances and the variation in ECF risk, both spatially and temporally when designing control strategies for ECF.

Prioritizing the PMTCT implementation research agenda in 3 African countries: INtegrating and Scaling up PMTCT through Implementation REsearch (INSPIRE).

Countries with high HIV prevalence face the challenge of achieving high coverage of antiretroviral drug regimens interventions including for the prevention of mother-to-child transmission of HIV (PMTCT). In 2011, the World Health Organization and the Department of Foreign Affairs, Trade and Development, Canada, launched a joint implementation research (IR) initiative to increase access to effective PMTCT interventions. Here, we describe the process used for prioritizing PMTCT IR questions in Malawi, Nigeria, and Zimbabwe. Policy makers, district health workers, academics, implementing partners, and persons living with HIV were invited to 2-day workshops in each country. Between 42 and 70 representatives attended each workshop. Using the Child Health Nutrition Research Initiative process, stakeholder groups systematically identified programmatic barriers and formulated IR questions that addressed these challenges. IR questions were scored by individual participants according to 6 criteria: (1) answerable by research, (2) likely to reduce pediatric HIV infections, (3) addresses main barriers to scaling-up, (4) innovation and originality, (5) improves equity among underserved populations, and (6) likely value to policy makers. Highest scoring IR questions included health system approaches for integrating and decentralization services, ways of improving retention-in-care, bridging gaps between health facilities and communities, and increasing male partner involvement. The prioritized questions reflect the diversity of health care settings, competing health challenges and local and national context. The differing perspectives of policy makers, researchers, and implementers illustrate the value of inclusive research partnerships. The participatory Child Health Nutrition Research Initiative approach effectively set national PMTCT IR priorities, promoted country ownership, and strategically allocated research resources.

Efficient management of health centres human resources in Zambia.

This study uses Data Envelopment Analysis (DEA) to estimate the degree of technical, allocative and cost efficiency in individual public and private health centres in Zambia; and to identify the relative inefficiencies in the use of various inputs among individual health centers. About 83% of the 40 health centres were technically inefficient; and 88% of them were both allocatively and cost inefficient. The privately owned health centers were found to be more efficient than public facilities.