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Magnaporthe oryzae, a devastating pathogen of finger millet (Eleusine coracana), secretes effector molecules during infection to manipulate host immunity. This study determined the presence of avirulence effector genes PWL1 and PWL2 in 221 Eleusine blast isolates from eastern Africa. Most Ethiopian isolates carried both PWL1 and PWL2. Kenyan and Ugandan isolates largely lacked both genes, and Tanzanian isolates carried either PWL1 or lacked both. The roles of PWL1 and PWL2 towards pathogenicity on alternative Chloridoid hosts, including weeping lovegrass (Eragrostis curvula), were also investigated. PWL1 and PWL2 were cloned from Ethiopian isolate E22 and transformed separately into Ugandan isolate U34, which lacked both genes. Resulting transformants harboring either gene gained varying degrees of avirulence on E. curvula but remained virulent on finger millet. Strains carrying PWL1 and/or PWL2 infected the Chloridoid species Sporobolus phyllotrichus and Eleusine tristachya, indicating the absence of cognate resistance (R) genes for PWL1 and PWL2 in these species. Other Chloridoid grasses, however, were fully resistant, regardless of the presence of PWL1 and/or PWL2, suggesting the presence of effective R genes against PWL and/or other effectors. Partial resistance in some E. curvula accessions to some blast isolates lacking PWL1 and PWL2 also indicated the presence of other AVR-R interactions. Related Chloridoid species thus harbour resistance genes that could be useful to improve finger millet for blast resistance. Conversely, loss of AVR genes in the fungus could expand its host range, as demonstrated by E. curvula’s susceptibility to finger millet blast isolates that had lost PWL1 and PWL2.

Coral reefs face increased environmental threats from anthropomorphic climate change and pollution, from agriculture, industries and tourism. They are economically vital for many people worldwide, and harbour a fantastically diverse ecosystem, being the home for many species of fish and algae. Surprisingly little is known about the microbial communities living in and in the surrounding of coral reefs. Here we employ high throughput sequencing for investigating the bacteria living in the water column and upper sediment layer in close proximity to coral reefs on the Kenyan coast of the West Indian Ocean. We show that while the read-level taxonomic distribution of bacteria is similar with ones obtained from 16S metabarcoding, whole metagenome sequencing provides valuable functional insights not available with 16S metabarcoding. We find evidence of pollution, marked by the presence of Vibrio and more importantly the presence of antibiotic resistance notably to vancomycin, that we attribute to the use of avoparcin in agriculture. Additionally, 175 bacterial genomes not previously sequenced were discovered.Our study is the first whole-metagenome study from the West Indian Ocean, provides a much-needed baseline to study microbes surrounding coral reefs under different conditions as well as the microbiome of coral reefs.

Insect damage on trees can severely affect the quality of timber, reduce the fecundity of the host and render it susceptible to fungal infestation and disease. Such pathology weakens or eventually kills the host. Infestation by two insect woodborer species (a moth and a beetle) is causing mortality of Sonneratia alba, a wide-ranging pioneer mangrove species of the Indo-Pacific. Establishing the infestation mechanism of the two insect woodborer species is an initial and essential step towards understanding their ecological role in the mangroves and in determining sustainable management priorities and options. Our main objectives were to investigate the infestation mechanism employed by the two insect woodborers which infest S. alba trees, to establish the occurrence of secondary infestation by endophytic fungi in the infested S. alba branches, and to explore a control management option to the woodborer infestation. We conducted an external inspection of infested branches in two large embayments in Kenya, Gazi Bay and Mida Creek, and by splitting infested branches we determined the respective internal infestation mechanisms. Infested wood samples from Gazi Bay and Mida Creek were incubated at 28±1°C for 3.5 days to establish the presence of fungi. A survey was conducted in both Gazi Bay and Mida Creek to ascertain the presence of ants on S. alba. The infestation characteristics of the two insect woodborer species were different. It took 6.8 months for the beetle to kill a branch of 150 cm.200 cm long. For the moth to kill a branch, it depended upon several factors including the contribution by multiple species, other than the moth infestation alone. A total of 15 endophytic fungal species were identified. Two ant species Oecophylla longipoda and a Pheidole sp. inhabited 62% and 69% respectively of sampled S. alba trees in Gazi Bay whereas only Pheidole sp. inhabited 17% of the sampled S. alba trees in Mida Creek. In summary, we have documented the time it takes each woodborer species to kill a branch, the infestation mechanism of the two insect woodborers, and we hypothesized on the role of two ant species. The presence of several different fungal species was ascertained, and we discussed their possible role in the infested wood. Our results cannot unambiguously associate the woodborers and identified fungi. We recommend further studies to investigate the presence or absence, and if present, the nature of fungi in the gut of the woodborers., SCOPUS: ar.j, info:eu-repo/semantics/published

Sweet sorghum is an excellent feedstock for ethanol production and is also used for food and livestock feed. Germplasm collection and characterization in sweet sorghum is a crucial step towards breeding and development of superior genotypes for various end-uses. In the present study, 13 Simple Sequence Repeat (SSR) markers were used for genotyping 175 Ethiopian sweet sorghum genotypes alongside 27 improved accessions from eastern and southern Africa. All the tested markers detected 159 alleles and a high degree of polymorphism information content (PIC) averaging 0.69. A comparison between Ethiopian and improved accessions revealed higher allele numbers (124) in Ethiopian than improved accessions (92 alleles). More than half (65 out of 124) of the alleles observed in the Ethiopian accessions were rare (

Background. Metagenomics studies have reported on the complexity of microbiomes associated with seagrass and can provide critical insights into the sustainable use and conservation of seagrasses. Recent conservation activities in Kenya focused mainly on coral reefs and mangrove forests with little direct action taken to conserve seagrass meadows. Pollution, over-exploitation of marine resources and minimal efforts towards enforcement of conservation laws of marine environments, have caused degradation and defoliation of seagrass habitats. Little is known about the microbes associated with seagrass species in Kenya and this study aimed to characterize the genetic diversity of the microbiomes of two prominent seagrass species, Enhalus acoroides and Thallasodendron ciliatum, which are the most commonly occurring species. Methods. Replicate microbiome samples were collected from leaves, roots, sediment and water columns associated with the two seagrass species from two sites on the Kenyan coast. The microbial communities of the samples were characterized and compared using 16S ribosomal RNA gene PCR and sequencing. Microbiome features including diversity and taxonomic composition were used to compare within and between sample types and sites. Results. Leaf samples from both E. acoroides and T. ciliatum had significantly different microbial communities comparted to root and sediment samples, revealing a diversity gradient with lowest diversity in water samples and highest in sediment. There were no significant variation in seagrass microbial composition associated with leaf and rhizosphere microbiomes of either E. acoroides or T. ciliatum. However, we did see a difference between water samples associated with each seagrass species. Discussion. This study of the microbiomes associated with the sediments, roots, leaves and surrounding water of E. acoroides and T. ciliatum, included a limited number of samples from a small geographic area, providing a valuable first assessment of the microbial diversity of seagrass beds on the Kenyan coast. We found no significant differences between the plant-associated bacterial communities of the two-seagrass species investigated. Significant differences however, were observed amongst leaf-, root-, sediment- and water-associated bacterial communities. This work will contribute to understanding the dynamic environment of seagrass beds and will contribute to helping conserving and re-establishing seagrass beds degraded by due to anthropogenic activities.

The parasitic weed Striga hermonthica hampers the production of sorghum, the most important cereal crop in Eritrea. This weed has a complex mode of infestation that adapts to many hosts and environments, complicating conventional breeding for resistance, which is the only form of crop improvement available to Eritrean breeders, but has failed. This study aimed at improving resistance against this parasite by transferring 5 Striga resistant Quantitative Trait Loci (QTLs) from resistance donor N13 to Striga susceptible Farmer-Preferred Sorghum Variety (FPSV) Hugurtay from Eritrea. The method involved backcrossing using marker-assisted selection (MAS) and evaluation of the best introgressed lines for Striga resistance in artificially infested fields. Foreground selection was performed with up to 11 polymorphic simple sequence repeat (SSR) markers linked to Striga resistance QTLs, while background selection was conducted in the BC 3 F 2 generation with 27 polymorphic unlinked SSR markers to identify the best recovery of the recurrent parent (RP) genetic background. Out of 84 BC 3 F 3 lines, L2P3-B, L1P5-A and L2P5P35 performed best with respect to both grain yield and reduced Striga infestation. These lines were more resistant to Striga than Hugurtay, but less resistant than N13. The three lines yielded twice as much as N13, with Area Under Striga Number Progression Curve (AUSNPC) values on average 18% higher than that of N13 and 38% lower than that of Hugurtay. This suggests that the introgressed QTLs conferred significant Striga resistance and yield advantage to these BC 3 F 3 backcross progenies under Striga pressure. These lines have good potential for future release and demonstrate that when MAS is available to conventional breeders, even in countries with no genotyping facilities, it is a useful tool for enhancement, expediency and precision in crop improvement.

Background: Pigeonpea ( Cajanus cajan (L.) Millsp.) is a drought tolerant legume of the Fabaceae family and the only cultivated species in the genus Cajanus . It is mainly cultivated in the semi-arid tropics of Asia and Oceania, Africa and America. In Malawi, it is grown as a source of food and income and for soil improvement in intercropping systems. However, varietal contamination due to natural outcrossing causes significant quality reduction and yield losses. In this study, 48 polymorphic SSR markers were used to assess the diversity amongst all pigeonpea varieties cultivated in Malawi to determine if a genetic fingerprint could be identified to distinguish the popular varieties. Results: A total of 212 alleles were observed with an average of 5.58 alleles per marker and a maximum of 14 alleles produced by CCttc019 (Marker 40). Polymorphic information content (PIC), ranged from 0.03 to 0.89 with an average of 0.30. A neighbor-joining tree produced 4 clusters. The most commonly cultivated varieties, which include released varieties and cultivated land races, were well-spread across all the clusters observed, indicating that they generally represented the genetic diversity available in Malawi, although substantial variation was evident that can still be exploited through further breeding. Conclusion: Screening of the allelic data associated with the five most popular cultivated varieties, revealed 6 markers - CCB1, CCB7, Ccac035, CCttc003, Ccac026 and CCttc019 - which displayed unique allelic profiles for each of the five varieties. This genetic fingerprint can potentially be applied for seed certification to confirm the genetic purity of seeds that are delivered to Malawi farmers.

Crop wild relatives are important components of agroecosystems and have over the years been exploited in breeding programs as sources of genes for novel traits. Information on the extent and patterns of variability is important in formulating effective conservation and utilization strategies for existing crop wild relative populations. We conducted surveys and collections of wild and weedy accessions of Sorghum bicolor (L.) Moench in Lambwe Valley in western Kenya in order to investigate occurrence, distribution, and morphological variability in the wild-weedy complex of S. bicolor under local agroecological conditions. We also attempted to understand the role, if any, of crop-to-wild gene flow in structuring variability within and among populations. The morphological data presented here showed wide variability within wild-weedy sorghum populations with respect to habitats and morphotypes. True wild sorghum populations in national parks and the sugarcane belt were clearly distinguishable from the putative...

Gene flow between cultivated and their wild relatives is one of the main ecological concerns associated with the introduction genetically modified (GM) cultivars. GM sorghum cultivar has been developed and its commercial production may be possible in the near future. The rate of gene flow depends on the fitness of wild × cultivated sorghum hybrids. The study aimed at estimating adaptive values of wild × cultivated sorghum hybrids in generations F1, F2, and F3 compared to their parents. Artificial crosses of four wild sorghums, five cultivated sorghums, and two male sterile lines were made to produce the F1 generation, which were advanced to F2 and F3. Each hybrid generation and their respective parents were evaluated for their adaptive value at two sites in a randomised complete block design with seven replicates. The resulting progenies did not show serious fitness penalties. Some hybrids were as fit as their respective wild parents and no consistent differences exist between the three generations studied. Thus, the resultant wild × cultivated hybrids may act as avenue for introgression.

Combining morphological and molecular data to identify genetic variation and marker–trait association is one of the most important prerequisites for genomics-assisted selection in crop improvement. To this end, a total of 138 finger millet (Eleusine coracana subsp. coracana) accessions including five improved varieties were evaluated to assess the genetic variation and population structure and undertake association mapping. These accessions were basically collected from Ethiopia (96), Eritrea (8), Kenya (7), Zambia (9) and Zimbabwe (13). Finger millet accessions were evaluated in the field for 10 important agronomic traits and also characterised using a set of 20 microsatellite markers. Mean polymorphism information content of 0.61 was observed from a total of 222 alleles with an average of 11.1 alleles per microsatellite locus. About 61% of alleles detected were rare (

The potential gene flow between a crop and its wild relatives is largely determined by the overlaps in their ecological and geographical distributions. Ecogeographical databases are therefore indispensable tools for the sustainable management of genetic resources. In order to expand our knowledge of Sorghum bicolor distribution in Kenya, we conducted in situ collections of wild, weedy and cultivated sorghum. Qualitative and quantitative morphological traits were measured for each sampled wild sorghum plant. Farmers' knowledge relating to the management of sorghum varieties and autecology of wild sorghum was also obtained. Cluster analysis supports the existence of several wild sorghum morphotypes that might correspond to at least three of the five ecotypes recognized in Africa. Intermediate forms between wild and cultivated sorghum belonging to the S. bicolor ssp. drummondii are frequently found in predominantly sorghum growing areas. Crop-wild gene flow in sorghum is likely to occur in many agroecosystems of Kenya.

article i nfo Background: Genetic diversity of finger millet (Eleusine coracana), a nutritious neglected staple cereal in Africa and South Asia is largely uncharacterized. This study analysed 82 published SSR markers for finger millet across 10 diverse accessions to compile an informative set for genetic characterisation. Extensive optimization compared single samples with bulked leaf or bulked DNA samples for capturing within accession genetic diversity. The markers were evaluated to determine (1) how effi ciently they amplified target loci during high-throughput genotyping with a generic PCR protocol, (2) ease of scoring PCR products and (3) polymorphism and ability to discern genetic diversity within the tested finger millet germplasm. Results: Across 88 samples, the 52 markers that worked well amplified 274 alleles, ranging from 2 to 14 per locus with a mean of 4.89. Major allele frequency ranged from 0.18 to 0.93 with a mean of 0.57. Polymorphic Information Content (PIC) ranged from 0.13 to 0.88 with a mean of 0.5 and availability varied between 64 and 100% with a mean of 92.8%. Heterozygosity ranged from 0 to 1.0, with a mean of 0.26. Discussion: Five individual samples from an accession captured the largest number of alleles per locus compared to the four different bulked sampling strategies but this difference was not significant. The identified set comprised 20 markers: UGEP24, UGEP53, UGEP84, UGEP27, UGEP98, UGEP95, UGEP64, UGEP33, UGEP67, UGEP106, UGEP110, UGEP57, UGEP96, UGEP66, UGEP46, UGEP79, UGEP20, UGEP12, UGEP73 and UGEP5 and was since used to assess East African finger millet genetic diversity in two separate studies.

article i nfo Background:Thisstudyaimedtoidentifyand select informative SimpleSequenceRepeat (SSR) markers that may be linked to resistance to important groundnut diseases such as Early Leaf Spot, Groundnut Rosette Disease, rust and aflatoxin contamination. To this end, 799 markers were screened across 16 farmer preferred and other cultivated African groundnut varieties that are routinely used in groundnut improvement, some with known resistance traits. Results: The SSR markers amplified 817 loci and were graded on a scale of 1 to 4 according to successful amplification and ease of scoring of amplified alleles. Of these, 376 markers exhibited Polymorphic Information Content (PIC) values ranging from 0.06 to 0.86, with 1476 alleles detected at an average of 3.7 alleles per locus. The remaining 423 markers were either monomorphic or did not work well. The best performing polymorphic markers were subsequently used to construct a dissimilarity matrix that indicated the relatedness of the varieties in order to aid selection of appropriately diverse parents for groundnut improvement. The closest related varieties were MGV5 and ICGV-SM 90704 and most distant were Chalimbana and 47-10. The mean dissimilarity value was 0.51, ranging from 0.34 to 0.66. Discussion: Of the 376 informative markers identified in this study, 139 (37%) have previously been mapped to the Arachis genome and can now be employed in Quantitative Trait Loci (QTL) mapping and the additional 237 markers identifi ed can be used to improve the efficiency of introgression of resistance to multiple important biotic constraints into farmer-preferred varieties of Sub-Saharan Africa.

The Association for Strengthening Agricultural Research in Eastern and Central Africa (ASARECA) through its Agrobiodiversity and Biotechnology Programme is enhancing the utilization of biotechnology research and development innovations in Eastern and Central Africa (ECA). We present successes in the application of biotechnology to enhance the productivity of cassava, sweet potato, banana, maize and sorghum in ECA. These products—drought tolerant maize, sorghum resistant to striga, as well as the technology for producing and distributing disease free planting materials of cassava, sweet potato and banana to farmers—are central for the agro-ecological intensification of farming systems in the central African highlands.

Ornithogalum (chincherinchee) is a genus in the Hyacinthaceae. It is popular as a cut flower or pot plant. However, susceptibility to disease, especially ornithogalum mosaic virus, prevents commercial exploitation of micropropagated hybrids. Provided that it is possible to transform Ornithogalum, this problem might be alleviated by the transfer of genes that code for resistance to the virus. The purpose of this study was to develop a transformation protocol using the pat gene as a selectable marker. Callus, induced on leaf segments of an Ornithogalum thyrsoides x O. dubium hybrid cultured in vitro, was bombarded with a particle gun 4-6 weeks after initiation. We first used β-glucuronidase transient expression to optimise the bombardment parameters and then for stable transformation used both a conventional microprojectile-mediated method as well as a modification that entailed complexing single-stranded p35SAC DNA, containing the pat gene, with histone H1 prior to bombardment. Transgenic plants were regenerated from the bombarded tissues and cultured on a medium containing 15 μM phosphinothricin as selective agent. Rooted plants were tested for the presence of the pat gene by polymerase chain reaction. Integration of the gene into the genomic DNA was verified by Southern blotting. Northern blots, enzyme-linked immunosorbent assay, and leaf paint assays with the herbicide Ignite® (glufosinate ammonium) confirmed expression of phosphinothricin acetyl transferase, the enzyme that detoxifies the herbicide.

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.

Knowledge of mating systems is required in order to understand the genetic composition and evolutionary potential of plant populations. Outcrossing in a population may co-vary with the ecological and historical factors influencing it. However, literature on the outcrossing rate is limited in terms of wild sorghum species coverage and eco-geographic reference. This study investigated the outcrossing rates in wild sorghum populations from different ecological conditions of Kenya. Twelve wild sorghum populations were collected in four sorghum growing regions. Twenty-four individuals per population were genotyped using six polymorphic simple sequence repeat (SSR) markers to compute their indirect equilibrium estimates of outcrossing rate as well as population structure. In addition, the 12 populations were planted in a field in a randomised block design with five replications. Their progeny (250 individuals per population) were genotyped with the six SSR markers to estimate multi-locus outcrossing rates. Equilibrium estimates of outcrossing rates ranged from 7.0 to 75.0%, while multi-locus outcrossing rates (t (m)) ranged from 8.9 to 70.0% with a mean of 49.7%, indicating that wild sorghum exhibits a mixed mating system. The wide range of estimated outcrossing rates in wild sorghum populations indicate that environmental conditions may exist under which fitness is favoured by outcrossing and others under which selfing is more advantageous. The genetic structure of the populations studied is concordant with that expected for a species displaying mixed mating system.

In self-compatible plant species stigmata receive a mixture of self and outcrossed pollen and competition between them is expected to play a major role in determining the pollen-mediated gene flow. The use of male sterile bait plants in field trials to demonstrate the rate of gene flow is questionable due to lack of pollination competition. However, little direct evidence has been published. A field experiment of male sterile and male fertile sorghum pollen recipient bait plants was conducted to evaluate pollen competition between wild and cultivated sorghums and the effects of pollen competition on gene flow assessment. Pollen competition between wild and cultivated sorghums was estimated from two-component pollen mixtures of wild and cultivated sorghum (1:1 ratio) applied to wild, cultivated and male-sterile maternal bait plants. Paternity was determined in the progeny using two diagnostic Simple Sequence Repeat markers. The study found that self pollen has higher seed-siring success. Maternal genotype influences the siring ability of the pollen donor components which significantly deviated from the 1:1 pollen loads. The study showed that published estimates of gene flow derived from studies using male-sterile bait plants seriously overestimate gene flow and that pollen competition may be a significant factor influencing outcrossing rates. The results suggest that the predominant direction of gene flow is from cultivated to wild sorghum, potentially leading to introgression of crop genes into wild sorghum. Pollen competition should be taken into account in gene flow estimation, since presence of self-pollen can account for over half of seed produced irrespective of maternal genotype.

Magnaporthe oryzae, a fungal pathogen that attacks more than 50 gramineous species, causes severe yield losses particularly on rice and finger millet. A study was conducted at Bako Agricultural Research Center in Ethiopia during the 2012 cropping season to evaluate the pathogenicity of four different finger millet blast isolates on 12 cultivated finger millet accessions and 4 of its wild relatives (Eleusine coracana subsp. africana). A split plot design, replicated three times, was used. Test accessions showed significant difference (Pd”0.01) but the isolates and genotype by isolate interaction showed no significant differences for grain yield. Pathogenicity tests revealed that isolates Pg. 11 and Pg. 22, isolated from neck and head of finger millet, respectively, were most virulent in infecting all plant tissues. The isolate from neck of the wild type (Pg. 41), infected both the cultivated and its wild types, confirming that wild types or weeds can act as hosts or reservoirs of the pathogen and source of inoculum. The mean grain yield per plant was lower for isolate Pg.22 (2.8g) and Pg.11 (2.9g) but relatively better for Pg.41 (3.6g) and Pg.26 (3.1g), indicating the inverse correlation between infection severity and grain yield. Finger millet accessions such as Acc. 214995 and PW-001-022 recorded lower blast infection consistently during 2011 and 2012 and are thus potential candidates for further evaluation in variety development activities. Among the wild accessions, AAU-ELU-15 showed the least blast infection. Mean yield loss assessment results from 2011 and 2012 field experiments calculated using Relative Area Under Progress Curve (RAUDPC) and multiple point models, respectively, revealed an average of 42% grain yield lost due to blast disease.

Sorghum is the world’s fifth most important cereal, in terms of both production and area planted. Striga hermonthica is one of the major constraints of sorghum production globally and particularly so in Eastern Africa. This study aimed at transferring five Striga resistances Quantitative Trait Loci (QTL) located on linkage groups SBI-01, SBI-02, SBI-05 and SBI-06 from a genetically mapped donor source line N13 into a locally adapted farmer preferred variety, IS8193 using Simple Sequence Repeats (SSRs). Nine polymorphic SSR markers were used to identify F1 generations and the subsequent BC1F1 progenies carrying Striga resistance QTL. Sixteen F1 progenies and twelve BC1F1 were found to have incorporated one to three Striga resistances QTL. The twelve BC1F1 lines with Striga resistance QTL were subsequently backcrossed to IS8193 to produce BC2F1 generation for further fore-ground and back-ground selection in the future. This work was conducted during March 2010 to August 2011 at University of Nairobi and at Biosciences eastern and central Africa (BecA)-Nairobi Kenya.