Genetic structure and diversity of wild sorghum populations (Sorghum spp.) from different eco-geographical regions of Kenya

Wild sorghums are extremely diverse phenotypically, genetically and geographically. However, there is an apparent lack of knowledge on the genetic structure and diversity of wild sorghum populations within and between various eco-geographical regions. This is a major obstacle to both their effective conservation and potential use in breeding programs. The objective of this study was to assess the genetic diversity and structure of wild sorghum populations across a range of eco-geographical conditions in Kenya. Sixty-two wild sorghum populations collected from the 4 main sorghum growing regions in Kenya were genotyped using 18 simple sequence repeat markers. The study showed that wild sorghum is highly variable with the Coast region displaying the highest diversity. Analysis of molecular variance showed a significant variance component within and among wild sorghum populations within regions. The genetic structure of wild sorghum populations indicated that gene flow is not restricted to populations within the same geographic region. A weak regional differentiation was found among populations, reflecting human intervention in shaping wild sorghum genetic structure through seed-mediated gene flow. The sympatric occurrence of wild and cultivated sorghums coupled with extensive seed-mediated gene flow, suggests a potential crop-to-wild gene flow and vice versa across the regions. Wild sorghum displayed a mixed mating system. The wide range of estimated outcrossing rates indicate that some environmental conditions may exist where self-fertilisation is favoured while others cross-pollination is more advantageous

Geographical patterns of phenotypic diversity and structure of Kenyan wild sorghum populations (Sorghum spp.) as an aid to germplasm collection and conservation strategy

Kenya lies within sorghum centre of diversity. However, information on the relative extent of diversity patterns within and among genetically defined groups of distinct ecosystems is lacking. The objective was to assess the structure and phenotypic diversity of wild sorghum populations across a range of geographical and ecological conditions in the country. Sixty-two wild sorghum populations (30 individuals per population) sampled from four distinct sorghum growing regions of Kenya and covering different agroecologies were characterized for ten qualitative traits. Plant height, number of tillers, panicle sizes and flag leaf dimensions were also recorded. Frequencies of the phenotypic classes of each character were calculated. The Shannon diversity index (H') was used to estimate the magnitude of diversity. Principal component analysis was used to differentiate populations within and between regions. Wild sorghum is widely distributed in Kenya, occurring in sympatric ranges with cultivated sorghum, and both have overlapping flowering windows. All characters considered displayed great phenotypic diversity. Pooled over characters within regions, the mean H' ranged between 0.60 and 0.93 in Western and Coast regions, respectively. Wild sorghum was found to show a weak regional differentiation, probably reflecting the importance of seed-mediated gene flow in shaping the wild sorghum population structure. Trait distribution was variable among regions, but there was no conspicuous distribution of the traits studied in any given region. Spontaneous hybridization and introgression of genes from cultivated to wild sorghum seems to be likely, and may already have occurred for a long time, although undocumented. Implications for in situ and ex situ genetic resources conservation are discussed

Local scale patterns of gene flow and genetic diversity in a crop–wild–weedy complex of sorghum (Sorghum bicolor (L.) Moench) under traditional agricultural field conditions in Kenya

Little information is available on the extent and patterns of gene flow and genetic diversity between cultivated sorghum and its wild related taxa under local agricultural conditions in Africa. As well as expanding knowledge on the evolutionary and domestication processes for sorghum, such information also has importance in biosafety, conservation and breeding programmes. Here, we examined the magnitude and dynamics of crop–wild gene flow and genetic variability in a crop–wild–weedy complex of sorghum under traditional farming in Meru South district, Kenya. We genotyped 110 cultivated sorghum, and 373 wild sorghum individuals using a panel of ten polymorphic microsatellite loci. We combined traditional measures of genetic diversity and differentiation with admixture analysis, population assignment, and analyses of spatial genetic structure to assess the extent and patterns of gene flow and diversity between cultivated and wild sorghum. Our results indicate that gene flow is asymmetric with higher rates from crop to wild forms than vice versa. Surprisingly, our data suggests that the two congeners have retained substantial genetic distinctness in the face of gene flow. Nevertheless, we found no significant differences in genetic diversity measures between them. Our study also did not find evidence of isolation by distance in cultivated or wild sorghum, which suggests that gene dispersal in the two conspecifics is not limited by geographic distance. Overall our study highlights likely escape and dispersal of transgenes within the sorghum crop–wild–weedy complex if genetically engineered varieties were to be introduced in Africa’s traditional farming system

Coding SNPs analysis highlights genetic relationships and evolution pattern in eggplant complexes

[EN] Brinjal (Solanum melongena), scarlet (S. aethiopicum) and gboma (S. macrocarpon) eggplants are three Old World domesticates. The genomic DNA of a collection of accessions belonging to the three cultivated species, along with a representation of various wild relatives, was characterized for the presence of single nucleotide polymorphisms (SNPs) using a genotype-by-sequencing approach. A total of 210 million useful reads were produced and were successfully aligned to the reference eggplant genome sequence. Out of the 75,399 polymorphic sites identified among the 76 entries in study, 12,859 were associated with coding sequence. A genetic relationships analysis, supported by the output of the FastSTRUCTURE software, identified four major sub-groups as present in the germplasm panel. The first of these clustered S. aethiopicum with its wild ancestor S. anguivi; the second, S. melongena, its wild progenitor S. insanum, and its relatives S. incanum, S. lichtensteinii and S. linneanum; the third, S. macrocarpon and its wild ancestor S. dasyphyllum; and the fourth, the New World species S. sisymbriifolium, S. torvum and S. elaeagnifolium. By applying a hierarchical FastSTRUCTURE analysis on partitioned data, it was also possible to resolve the ambiguous membership of the accessions of S. campylacanthum, S. violaceum, S. lidii, S. vespertilio and S. tomentsum, as well as to genetically differentiate the three species of New World Origin. A principal coordinates analysis performed both on the entire germplasm panel and also separately on the entries belonging to sub-groups revealed a clear separation among species, although not between each of the domesticates and their respective wild ancestors. There was no clear differentiation between either distinct cultivar groups or different geographical provenance. Adopting various approaches to analyze SNP variation provided support for interpretation of results. The genotyping-by-sequencing approach showed to be highly efficient for both quantifying genetic diversity and establishing genetic relationships among and within cultivated eggplants and their wild relatives. The relevance of these results to the evolution of eggplants, as well as to their genetic improvement, is discussed.This work has been funded in part by European Unions Horizon 2020 Research and Innovation Programme under grant agreement No 677379 (G2P-SOL project: Linking genetic resources, genomes and phenotypes of Solanaceous crops) and by Spanish Ministerio de Economia, Industria y Competitividad and Fondo Europeo de Desarrollo Regional (grant AGL2015-64755-R from MINECO/FEDER). Funding has also been received from the initiative "Adapting Agriculture to Climate Change: Collecting, Protecting and Preparing Crop Wild Relatives", which is supported by the Government of Norway. This last project is managed by the Global Crop Diversity Trust with the Millennium Seed Bank of the Royal Botanic Gardens, Kew and implemented in partnership with national and international gene banks and plant breeding institutes around the world. For further information see the project website:http://www.cwrdiversity.org/. Pietro Gramazio is grateful to Universitat Politecnica de Valencia for a pre-doctoral (Programa FPI de la UPV-Subprograma 1/2013 call) contract. Mariola Plazas is grateful to Spanish Ministerio de Economia, Industria y Competitividad for a post-doctoral grant within the Santiago Grisolia Programme (FCJI-2015-24835). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.Acquadro, A.; Barchi, L.; Gramazio, P.; Portis, E.; Vilanova Navarro, S.; Comino, C.; Plazas Ávila, MDLO.... (2017). Coding SNPs analysis highlights genetic relationships and evolution pattern in eggplant complexes. PLoS ONE. 12(7). https://doi.org/10.1371/journal.pone.0180774Se018077412

Novel sources of drought tolerance from landraces and wild sorghum relatives

Sorghum (Sorghum bicolor [L.] Moench) is the fifth most important cereal crop worldwide and second aftermaize (Zeamays L.) in Kenya. It is an important food security crop in arid and semi-arid lands, where its production potential is hampered by drought. Drought tolerance can be measured by a plant’s ability to resist premature senescence, often described as stay-green. This study was carried out with the objective of identifying novel stay-green trait among wild and landrace genotypes of sorghum. Forty-four sorghum genotypes that included 16 improved, nine landraces, and 17 wild relatives of sorghum alongside known stay-green sources, B35 and E36-1, were evaluated under well-watered and water-stressed conditions in an alpha-lattice design of three replications. Data was collected on plant height (PHT), flag leaf area (FLA), panicle weight (PWT), 100-seed weight (HSW), relative chlorophyll content (RCC), number of green leaves at maturity (GLAM), days to 50% flowering (DFL), and grain yield (YLD). Genetic diversity was determined using diversity arrays technology (DArT) sequencing and quality control (QC) markers were generated using a java script. Lodoka, a landrace, was the most drought-tolerant genotype, recorded the highest numbers of RCC and GLAM, and outperformed B35 and E36-1 in yield under water-stress and well-watered conditions. The RCC was highly correlated with GLAM (r = .71) and with yield-related traits, HSW (r = .85), PWT (r = .82), and YLD (r = .78). All traits revealed high heritability (broad-sense) ranging from 60.14 to 98.4% for RCC and DFL, respectively. These results confirm earlier reports that wild relatives and landraces are a good source of drought tolerance alleles

The effects of exposures to mycotoxins on immunity in children: a systematic review

The majority of childhood deaths occur in low-income countries, with vaccine-preventable infections contributing greatly. Of the many possible environmental factors that could hamper a child's immune response, mycotoxins rank among the least studied in spite of the high exposure in vulnerable populations. Aflatoxin crosses the placenta, is secreted in breast milk and is consumed widely in weaning diets by children with developing organ systems. This review describes the effects of mycotoxin exposure on immunity in children that may contribute to sub-optimal vaccine effectiveness. We searched electronic databases and references of identified articles for relevant studies on the effects of mycotoxins on the immune system in children. Geographical location, publication year, study design, sample selection, sample size, mean age, route of exposure were extracted on a standard template. Quality was assessed using Joanna Briggs Institute tool for appraisal of systematic reviews for prevalence studies. Our analyses and reporting were conducted in accordance with the preferred reporting items for systematic reviews and meta-analyses (PRISMA) guidelines. Out of 806 articles screened, 5 observational studies met criteria for inclusion for review. The definition of exposures to mycotoxins and outcomes varied across the studies. Exposure to mycotoxins was positively associated with low birth weight and concentration of antibodies to asexual malaria parasites and hepatitis B surface antigen, and negatively associated with death and sIgA, antibodies to pneumococcal antigen 23. Despite the far-reaching clinical and public health effects of mycotoxin exposure among children, studies on the effects of mycotoxin exposure on immunity in children were few, small and mostly of low quality. There is an urgent need for carefully designed prospective studies in this neglected field to inform policy interventions for child health in settings where exposure to mycotoxins is high

The effects of aflatoxin exposure on Hepatitis B-vaccine induced immunity in Kenyan children

Background: Globally, approximately three million children die each year from vaccine preventable infectious diseases mainly in developing countries. Despite the success of the expanded immunization program, not all infants and children around the world develop the same protective immune response to the same vaccine. A vaccine must induce a response over the basal immune response that may be driven by population-specific, environmental or socio-economic factors. Mycotoxins like aflatoxins are immune suppressants that are confirmed to interfere with both cell-mediated and acquired immunity. The mechanism of aflatoxin toxicity is through the binding of the bio-activated AFB1-8, 9-epoxide to cellular macromolecules. Methods: We studied Hepatitis B surface antibodies [anti-HBs] levels to explore the immune modulation effects of dietary exposure to aflatoxins in children aged between one and fourteen years in Kenya. Hepatitis B vaccine was introduced for routine administration for Kenyan infants in November 2001. To assess the effects of aflatoxin on immunogenicity of childhood vaccines Aflatoxin B1-lysine in blood serum samples were determined using High Performance Liquid Chromatography with Fluorescence detection while anti-HBs were measured using Bio-ELISA anti-HBs kit. Results: The mean ± SD of AFB1-lysine adducts in our study population was 45.38 ± 87.03 pg/mg of albumin while the geometric mean was 20.40 pg/mg. The distribution of AFB1-lysine adducts was skewed to the right. Only 98/205 (47.8%) of the study population tested positive for Hepatitis B surface antibodies. From regression analysis, we noted that for every unit rise in serum aflatoxin level, anti-HBs dropped by 0.91 mIU/ml (−0.9110038; 95% C.I −1.604948, −0.21706). Conclusion: Despite high coverage of routine immunization, less than half of the study population had developed immunity to HepB. Exposure to aflatoxin was high and weakly associated with low anti-HBs antibodies. These findings highlight a potentially significant role for environmental factors that may contribute to vaccine effectiveness warranting further research