Analysis of genetic difference within and between of wild relatives of sorghum in Sudan, using SSRs

Sorghum (Sorghum bicolor (L.) Moench) originated in East Africa specifically Sudan and Ethiopia where wild relatives of sorghum are widely distributed. The wild relatives harbored important genes. However they are often ignored and orphaned. This study aimed to explore genetic diversity among the accessions, and the results will enhance the utilization of wild sorghum in Sudan. 59 wild and cultivated sorghum accessions, representing three sorghum growing regions in Sudan: Gezira state (central), North Kordofan (Western), and the Gadareff area (Eastern). The materials were assessed for genetic diversity and population structure using a panel of 32 SSR markers. A total of 255 allelic variations were detected with a mean of 0.6721. The Polymorphic Information Content (PIC) value averaged 0.6301 showing the polymorphic and discriminatory nature of the selected markers. The populations showed little external gene-flow. Variations calculated with AMOVA are lower among populations (4%), moderate within individuals (23%), and higher among individuals within population (73%). A rooted neighbor-joining tree of four sorghum cultivars and 55 wild relatives revealed three distinct groups independent on their geographical origins. The results will be useful for future collection and utilization in genetics and breeding program

Genetic diversity of provitamin a cassava in Uganda

Global efforts are being made towards developing provitamin A cassava (Manihot esculenta Cranz) varieties for sustainably addressing vitamin A malnutrition commonly noted in communities where cassava is a major staple. To elucidate the diversity in Uganda’s core collection of yellow root cassava germplasm, genetic variability was assessed for 64 yellow and white root cassava accessions including Ugandan landraces, and accessions introduced from the International Center for Tropical Agriculture (CIAT) and the International Institute of Tropical Agriculture (IITA). Phenotypic characterization was based on 12 morphological descriptors, total carotenoid content (TCC) and dry matter content (DMC). Variation of twenty six simple sequence repeat (SSR) markers was assessed and compared with morphological data. Total carotenoid content varied from 1.2 to 14.2 ?g/100 g and correlated negatively (R2 = -0.46) with dry matter content which ranged from 27.2 to 39.8 %. Genetic diversity was high in all accession groups with an average heterozygosity of 0.5583 ± 0.0182. Phenetic analyses using Unweighted Pair Group Method with Arithmetic Mean (UPGMA) and Principle Coordinate Analysis (PCoA) clustered the CIAT accessions into a distinct group, discriminating them from the landraces and IITA accessions. Based on the clustering pattern, it suffices to suggest limited gene flow between CIAT accessions and the landraces/IITA accessions which is an opportunity for broadening the genetic base through hybridization by exploiting the heterotic pool in the germplasm

Simple sequence repeat (SSR) diversity of cassava in South, East and Central Africa in relation to resistance to cassava brown streak disease

This study was conducted to: (1) determine the amount and structure of the genetic diversity of cassava in southern, eastern and central (SEC) Africa using simple sequence repeat (SSR) markers, (2) determine the frequency and distribution of alleles putatively associated with resistance to cassava brown streak disease (CBSD) derived from the variety ‘Namikonga’, and (3) examine the genetic relationships among some CBSD resistant genotypes. The major findings from this study were: (1) little genetic differentiation was confirmed among countries (7%) with the majority of variation distributed among individuals (93%), (2) the frequency of alleles putatively associated with resistance to CBSD was found to be generally low (0.2 to 0.5) but widely dispersed in the cassava germplasm of the SEC Africa region implying that if validated the markers will be useful for marker-assisted breeding on a broad scale, (3) several distinct putative sources of resistance to CBSD seem to be present in the cassava germplasm of SEC Africa offering the potential to pyramid genes for more effective and durable resistance and (4) it may be more informative to assess cassava diversity in the SEC Africa region based on pedigree (if known) or genetic relatedness, rather than geographical origin

Multi-locus genotyping reveals absence of genetic structure in field populations of the brown ear tick (Rhipicephalus appendiculatus) in Kenya

Rhipicephalus appendiculatus is an important tick vector of several pathogens and parasitizes domestic and wild animals across eastern and southern Africa. However, its inherent genetic variation and population structure is poorly understood. To investigate whether mammalian host species, geographic separation and resulting reproductive isolation, or a combination of these, define the genetic structure of R. appendiculatus, we analyzed multi-locus genotype data from 392 individuals from 10 geographic locations in Kenya generated in an earlier study. These ticks were associated with three types of mammalian host situations; (1) cattle grazing systems, (2) cattle and wildlife co-grazing systems (3) wildlife grazing systems without livestock. We also analyzed data from 460 individuals from 10 populations maintained as closed laboratory stocks and 117 individuals from five other species in the genus Rhipicephalus. The pattern of genotypes observed indicated low levels of genetic differentiation between the ten field populations (FST = 0.014 ± 0.002) and a lack of genetic divergence corresponding to the degree of separation of the geographic sampling locations. There was also no clear association of particular tick genotypes with specific host species. This is consistent with tick dispersal over large geographic ranges and lack of host specificity. In contrast, the 10 laboratory populations (FST = 0.248 ± 0.015) and the five other species of Rhipicephalus (FST = 0.368 ± 0.032) were strongly differentiated into distinct genetic groups. Some laboratory bred populations diverged markedly from their field counterparts in spite of originally being sampled from the same geographic locations. Our results demonstrate a lack of defined population genetic differentiation in field populations of the generalist R. appendiculatus in Kenya, which may be a result of the frequent anthropogenic movement of livestock and mobility of its several wildlife hosts between different locations

Genetic diversity of cassava (Manihot esculenta Crantz) landraces and cultivars from southern, eastern and central Africa

Studies to quantify genetic variation in cassava germplasm, available within the national breeding programmes in Africa, have been limited. Here, we report on the nature and extent of genetic variation that exists within 1401 cassava varieties from seven countries: Tanzania (270 genotypes); Uganda (268); Kenya (234); Rwanda (184); Democratic Republic of Congo (DRC; 177); Madagascar (186); Mozambique (82). The vast majority of these genotypes do not exist within a formal germplasm conservation initiative and were derived from farmers' fields and National Agricultural Research Systems breeding programmes. Genotypes were assayed using 26 simple sequence repeat markers. Moderate genetic variation was observed with evidence of a genetic bottleneck in the region. Some differentiation was observed among countries in both cultivars and landraces. Euclidean distance revealed the pivotal position of Tanzanian landraces in the region, and STRUCTURE analysis revealed subtle and fairly complex relationships among cultivars and among landraces and cultivars analysed together. This is likely to reflect original germplasm introductions, gene flow including farmer exchanges, disease pandemics, past breeding programmes and the introduction of cultivars from the International Institute of Tropical Agriculture – Nigeria. Information generated from this study will be useful to justify and guide a regional cassava genetic resource conservation strategy, to identify gaps in cassava diversity in the region and to guide breeding strategies

Diversity of genetic types of local chickens and introgression with commercial exotic strains in Cameroon

Local chicken in Cameroon has a great diversity that is not yet fully explored. The objective of this study was to evaluate the diversity in genetic types of local chickens in Cameroon and level of introgression with exotic strains on the basis of 25 microsatellite markers. The number of alleles per locus varied from 2 (MCW0103) to 22 (LEI0192), with an average of 9.04. The average Ne was 3.78, while the heterozygosity between loci ranged from 0.31 to 0.75 (Ho), 0.33 to 0.86 (He), 0.40 to 0.81 (UHe) and 0.37 to 0.77 (Ht) with means of 0.60; 0.69; 0.65 and 0.63 respectively for the observed, expected, unbiased and total heterozygosity. The inbreeding coefficients FIS, FIT and FST were 0.03, 0.12 and 0.09 respectively. Only an average 4/25 loci significantly deviates from the Hardy-Weinberg equilibrium. Among the local chicken types, the highest Ho was that of naked necks (0.66 ± 0.17). Feathered tarsus and naked necks have the highest diversity across loci (0.67 ± 0.33 and 0.67 ± 0.34). The commercial strains Hybro and Lohman Brown showed excessive inbreeding. Only 4% of the total molecular variance is attributable to phenotypic differences. The number of migrants was high (6.302) showing admixture among populations. The maximum Nei genetic distances are found between exotic broilers and layers strains. Genetic distances between commercial broilers strains and feathered tarsus and with the normal feathered chicken are moderately high but comparable. Genetic distances among types of local chicken are very low, and the genetic identities very high. The dendrograms reveals that genetic types of local chicken are at intermediate position between commercial broilers and layers. Within the cluster of Cameroon local chickens, it is noticed that the Frizzle local chicken is a much more distant sub-group from other four genetic types, while the feathered tarsus and normal feathered chicken are closer. Broilers and layers chicken are clearly divergent, unlike the genetic types of local chickens. Local chicken types have variable levels of introgression with the various exotic broilers and layers strains. The local normal feathered chicken, although differing from exotic strains presents various introgression levels ranging from low (Lohman Brown) to medium (Arbor Acres and Hybro) and high (Rhode Island Red). In general only 35% of the chicken genomes found in Cameroon could be considered as pure or fully belonging to their respective strains.Key words: chicken, diversity, genetic types, introgressio

Clinical profile and containment of the Ebola virus disease outbreak in two large West African cities, Nigeria, July–September 2014

Introduction: The Ebola virus disease (EVD) outbreak in Nigeria began when an infected diplomat from Liberia arrived in Lagos, the most populous city in Africa, with subsequent transmission to another large city. Methods: First-, second-, and third-generation contacts were traced, monitored, and classified. Symptomatic contacts were managed at Ebola treatment centers as suspected, probable, and confirmed EVD cases using standard operating procedures adapted from the World Health Organization EVD guidelines. Reverse transcription PCR tests confirmed EVD. Socio-demographic, clinical, hospitalization, and outcome data of the July–September 2014 Nigeria EVD cohort were analyzed. Results: The median age of the 20 EVD cases was 33 years (interquartile range 26–62 years). More females (55%), health workers (65%), and persons <40 years old (60%) were infected than males, non-health workers, and persons aged ≥40 years. No EVD case management worker contracted the disease. Presenting symptoms were fever (85%), fatigue (70%), and diarrhea (65%). Clinical syndromes were gastroenteritis (45%), hemorrhage (30%), and encephalopathy (15%). The case-fatality rate was 40% and there was one mental health complication. The average duration from symptom onset to presentation was 3 ± 2 days among survivors and 5 ± 2 days for non-survivors. The mean duration from symptom onset to discharge was 15 ± 5 days for survivors and 11 ± 2 days for non-survivors. Mortality was higher in the older age group, males, and those presenting late. Conclusion: The EVD outbreak in Nigeria was characterized by the severe febrile gastroenteritis syndrome typical of the West African outbreak, better outcomes, rapid containment, and no infection among EVD care-providers. Early case detection, an effective incident management system, and prompt case management with on-site mobilization and training of local professionals were key to the outcome