Genetic diversity of Kenyan Prosopis populations based on random amplified polymorphic DNA markers

Several Prosopis species and provenances were introduced in Kenya, either as a single event or repeatedly. To date, naturally established Prosopis populations are described as pure species depending on site, despite the aforementioned introduction of several species within some sites. To determine whether naturally established stands consist of a single or mixture of species, six populations from Bamburi, Bura, Isiolo, Marigat, Taveta and Turkwel were compared for relatedness with reference to Prosopis chilensis, Prosopis juliflora and Prosopis pallida using random amplified polymorphic DNA markers. Cluster analysis based on Nei’s genetic distance clustered Kenyan populations as follows: Marigat, Bura and Isiolo with P. juliflora, Bamburi with P. pallida and Taveta with P. chilensis, whereas the Turkwel population is likely to be a hybrid between P. chileneis and P. juliflora. Four populations had private markers, revealing germplasm uniqueness. Expected heterozygosity tended to be larger for Kenyan populations (ranging from 0.091 to 0.191) than in the three reference (ranging from 0.065 to 0.144). For the six Kenyan populations and two P. juliflora provenances from the Middle East, molecular variation was larger within populations than between population. Higher molecular variance among populations is attributed to their geographical separation and the low variation within populations is due to gene flow between individuals within a population. Overall, this study shows that (1) the Kenyan Prosopis populations are genetically isolated, (2) multiple introductions enhanced genetic diversity within sites and (3) P. juliflora and its hybrid are the most aggressive invaders.Key words: Prosopis chilensis, Prosopis juliflora, Prosopis pallida, multiple introductions, genetic diversity

First report of Teratosphaeria gauchensis causing stem canker of Eucalyptus in Kenya

Teratosphaeria stem canker is an important disease of Eucalyptus species in many parts of the world where these trees are intensively propagated in plantations. Symptoms similar to those of Teratosphaeria stem canker were observed on Eucalyptus grandis and a E. grandis x E. camaldulensis hybrid clone in the Central Highlands of Kenya. Symptomatic bark samples were collected from two sites and the associated fungus isolated and identified using DNA sequence analyses of multiple gene regions. The pathogen was identified as Teratosphaeria gauchensis. This represents the first report of the disease and the pathogen in Kenya.Tree Protection Co-operative Program (TPCP), the THRIP initiative of the Department of Trade and Industry, the DST/NRF Centre of Excellence in Tree Health Biotechnology (CTHB) of the Forestry and Agricultural Biotechnology Institute (FABI), University of Pretoria, South Africa and the Kenya Forestry Research Institute (KEFRI).http://onlinelibrary.wiley.com/journal/10.1111/(ISSN)1439-03292017-04-30hb2016Forestry and Agricultural Biotechnology Institute (FABI)Microbiology and Plant PathologyPlant Production and Soil SciencePlant Scienc

tropiTree:an NGS-based EST-SSR resource for 24 tropical tree species

The development of genetic tools for non-model organisms has been hampered by cost, but advances in next-generation sequencing (NGS) have created new opportunities. In ecological research, this raises the prospect for developing molecular markers to simultaneously study important genetic processes such as gene flow in multiple non-model plant species within complex natural and anthropogenic landscapes. Here, we report the use of bar-coded multiplexed paired-end Illumina NGS for the de novo development of expressed sequence tag-derived simple sequence repeat (EST-SSR) markers at low cost for a range of 24 tree species. Each chosen tree species is important in complex tropical agroforestry systems where little is currently known about many genetic processes. An average of more than 5,000 EST-SSRs was identified for each of the 24 sequenced species, whereas prior to analysis 20 of the species had fewer than 100 nucleotide sequence citations. To make results available to potential users in a suitable format, we have developed an open-access, interactive online database, tropiTree (http://bioinf.hutton.ac.uk/tropiTree), which has a range of visualisation and search facilities, and which is a model for the efficient presentation and application of NGS data

Data from: Evidence of high genetic diversity and significant population structuring in Vachellia tortilis (Forsk.) Galasso & Bonfi population in Kenya

Context: Vachellia tortilis is an important dryland tree species valued for fuelwood and fodder production, however, no strategy has been put in place for sustainable management of the species genetic resources. Furthermore, there is inadequate information on the species population genetics to facilitate development of such strategies. Aim: We evaluated the amount and structure of neutral genetic diversity of V. tortilis population in Kenya and provided recommendations necessary for improvement and conservation of the species genetic resources. We hypothesised that the current genetic diversity of V. tortilis is high because of it is demographic history and that no population structuring was expected to occur due to the presumed long distance and effective gene flow within the species. Methods: Leaf tissues were collected from fifteen putative natural populations of V. tortilis covering the whole distribution range in Kenya. DNA was isolated from the leaf tissues and analysed using microsatellite markers. In total, 450 trees were genotyped using 10 polymorphic nuclear microsatellite loci, and genetic diversity and population structure parameters determined Results: We found high levels of genetic diversity within the populations with a mean gene diversity at 0.85. However, significant population differentiation was evident (FST = 0.026, P = 0.007; RST = 0.032, P = 0.004) despite large number of migrants per generation (Nm = 5.3). Population structure detected suggests presence of two clusters, although, some populations showed mixed ancestry. The groups reflect the influence of geographic patterns and historical population gene flow. Conclusion: There exist high genetic diversity in V. tortilis in Kenya with significant population structuring into two clusters. We recommend consideration of the two distinct groups in the development of the species improvement, breeding and conservation programmes. Such programmes should ensure maintenance of the majority of the extant genetic diversity

Highly transferable microsatellite markers for the genera Lasiodiplodia and Neofusicoccum

Population genetic studies play an integral role in understanding the ecology and management of fungal plant pathogens. Such studies for species of Botryosphaeriaceae are hampered by a lack of available markers. Genomic sequences are available for multiple species in this family and they provide excellent resources for the development of population genetic markers. Here we describe highly transferable microsatellite or simple sequence repeat (SSR) markers for species in Lasiodiplodia and Neofusicoccum; two important and globally distributed members of the Botryosphaeriaceae. These were developed by extracting SSR-containing sequences from available genomes. Seventy-seven markers were developed for Lasiodiplodia and 32 markers were developed for Neofusicoccum. Most of these markers were transferable between species within a genus. Twelve markers tested for fragment length polymorphism in 20 isolates of Lasiodiplodia mahajangana identified between two and nine alleles and gene diversities between 0.18 and 0.83. Eleven markers indicated between two and five alleles for 20 isolates of Neofusicoccum parvum and gene diversities between 0.26 and 0.57. The large number and high transferability of the developed markers will facilitate population studies of a wide range of Lasiodiplodia and Neofusicoccum species associated with tree diseases globally.The University of Pretoria, The Department of Science and Technology (DST) / National Research Foundation (NRF) Centre of Excellence in Tree Health Biotechnology and members of the Tree Protection Cooperative Program.http://www.elsevier.com/locate/funeco2021-04-01hj2020BiochemistryForestry and Agricultural Biotechnology Institute (FABI)GeneticsMicrobiology and Plant Patholog

Utilization of digital tools to enhance COVID-19 and tuberculosis testing and linkage to care: A cross-sectional evaluation study among Bodaboda motorbike riders in the Nairobi Metropolis, Kenya.

Kenya has registered over 300,000 cases of COVID-19 and is a high-burden tuberculosis country. Tuberculosis diagnosis was significantly disrupted by the pandemic. Access to timely diagnosis, which is key to effective management of tuberculosis and COVID-19, can be expanded and made more efficient through integrated screening. Decentralized testing at community level further increases access, especially for underserved populations, and requires robust systems for data and process management. This study delivered integrated COVID-19 and tuberculosis testing to commercial motorbike (Bodaboda) riders, a population at increased risk of both diseases with limited access to services, in four counties: Nairobi, Kiambu, Machakos and Kajiado. Testing sheds were established where riders congregate, with demand creation carried out by the Bodaboda association. Integrated symptom screening for tuberculosis and COVID-19 was conducted through a digital questionnaire which automatically flagged participants who should be tested for either, or both, diseases. Rapid antigen-detecting tests (Ag-RDTs) for COVID-19 were conducted onsite, while sputum samples were collected and transported to laboratories for tuberculosis diagnosis. End-to-end patient data were captured using digital tools. 5663 participants enrolled in the study, 4946 of whom were tested for COVID-19. Ag-RDT positivity rate was 1% but fluctuated widely across counties in line with broader regional trends. Among a subset tested by PCR, positivity was greater in individuals flagged as high risk by the digital tool (8% compared with 4% overall). Of 355 participants tested for tuberculosis, 7 were positive, with the resulting prevalence rate higher than the national average. Over 40% of riders had elevated blood pressure or abnormal sugar levels. The digital tool successfully captured complete end-to-end data for 95% of all participants. This study revealed high rates of undetected disease among Bodaboda riders and demonstrated that integrated diagnosis can be delivered effectively in communities, with the support of digital tools, to maximize access

Information on 24 tropical trees subjected to next-generation sequencing and screened for SSRs.

a<p>Based on the Agroforestree Database (<a href="http://www.worldagroforestry.org/resources/databases/agroforestree" target="_blank">www.worldagroforestry.org/resources/databases/agroforestree</a>), an open access resource of ICRAF that provides data on >650 trees.</p>b<p>The seed source of material for NGS varied and included natural stands, seed orchards and landraces. The numerical reference is the ICRAF accession number.</p>c<p>Current data from NGS; complete information is available at the tropiTree portal (<a href="http://bioinf.hutton.ac.uk/tropiTree" target="_blank">http://bioinf.hutton.ac.uk/tropiTree</a>). In () is the number of perfect SSRs identified. In [] is the percentage of the corresponding transcripts that have TAIR hits (for all SSRs).</p>d<p>Data from National Center for Biotechnology Information of the USA (NCBI) searches were included to illustrate previous sequencing work. Searches were undertaken on 14 April 2014 via the Entrez search system (<a href="http://www.ncbi.nlm.nih.gov/sites/gquery" target="_blank">www.ncbi.nlm.nih.gov/sites/gquery</a>). Species names for NCBI searches were checked as correct against current nomenclature using the Agroforestry Species Switchboard (<a href="http://www.worldagroforestry.org/products/switchboard/" target="_blank">www.worldagroforestry.org/products/switchboard/</a>), an open access resource of ICRAF that provides links to information on >20,000 plants. Current names were set as ‘organism’ in NCBI searches. In () is the number of ESTs listed in NCBI nucleotide citations (if any). In [] is the number of NGS studies cited in NCBI’s Sequence Read Archive (if any).</p>e<p>As well as being of importance to small-scale farmers, <i>Acacia mangium</i> and <i>Jatropha curcas</i> have wide commercial interests (see text), explaining the high NCBI citations.</p>f<p>Species were subject to primer validation (see text).</p

SSR repeats in 24 tree species subjected to next-generation sequencing.

<p>The proportion of di-, tri- and tetra-nucleotide repeats is shown. The species are ordered by the proportion of di-nucleotide repeats revealed.</p