Phenotypic variation in plants can be evaluated by morphological characterization using visual attributes. Fruits have been the major descriptors for identification of different varieties of fruit crops. However, even in their absence, farmers, breeders and interested stakeholders require to distinguish between different mango varieties. This study aimed at determining diversity in mango germplasm from the Upper Athi River (UAR) and providing useful alternative descriptors for the identification of different mango varieties in the absence of fruits. A total of 20 International Plant Genetic Resources Institute (IPGRI) descriptors for mango were selected for use in the visual assessment of 98 mango accessions from 15 sites of the UAR region of eastern Kenya. Purposive sampling was used to identify farmers growing diverse varieties of mangoes. Evaluation of the descriptors was performed on-site and the data collected were then subjected to multivariate analysis including Principal Component Analysis (PCA) and Cluster analysis, one-way analysis of variance (ANOVA) and Chi square tests. Results classified the accessions into two major groups corresponding to indigenous and exotic varieties. The PCA showed the first six principal components accounting for 75.12% of the total variance. A strong and highly significant correlation was observed between the color of fully grown leaves, leaf blade width, leaf blade length and petiole length and also between the leaf attitude, color of young leaf, stem circumference, tree height, leaf margin, growth habit and fragrance. Useful descriptors for morphological evaluation were 14 out of the selected 20; however, ANOVA and Chi square test revealed that diversity in the accessions was majorly as a result of variations in color of young leaves, leaf attitude, leaf texture, growth habit, leaf blade length, leaf blade width and petiole length traits. These results reveal that mango germplasm in the UAR has significant diversity and that other morphological traits apart from fruits can be useful in morphological characterization of mango.

Papaya is an important fruit crop, produced in Kenya for local consumption and export. Despite a history of varietal introductions, no attempts concerned on developing varieties suited to Kenyan conditions have been documented. The objective of this study was to provide information on the diversity of germplasm available in Kenya, as a precursor to systematic plant breeding program. Forty two papaya accessions were collected from farmers' fields located in Coast, Rift Valley, Western, Nyanza, Central and Eastern provinces. Genetic diversity was determined using seven simple sequence repeat (SSR) markers, computing allelic richness and frequency, expected heterozygosity and cluster analysis. Results indicated that the markers were highly polymorphic among the accessions, with polymorphic information content (PIC) varying from 0.75 to 0.852 with an average of 0.81. The genetic similarity among the 42 papaya accessions ranged from 0.764 to 0.932 with an average of 0.844 showing that most papaya accessions used in this study were closely related. About 96.9% of the pair-wise comparisons among papaya accessions exhibited genetic similarity greater than 0.802, while less than 4% (3.1%) showed genetic similarity lower than 0.802. The phylogenetic analysis grouped the 42 accessions into two main clusters A and B. Cluster A had four sub-clusters while cluster B had one cluster. Accessions from Coast, and some from Rift Valley Provinces, presented the highest variation, being scattered throughout the tree, with little or no differentiation from most accessions, whereas some accessions from Coast regrouped in clusters A (iv) and B. The genetic differences among the accessions revealed by the formation of distinct clusters suggest significant genetic variability emanation from varying sources of the papaya germplasm in Kenya. Although the level of genetic diversity revealed by SSR markers in this study is sufficient to distinguish between breeding lines for varietal protection, the rather narrow genetic diversity demonstrated indicates the need to introduce new germplasm or use other techniques such as mutation and genetic engineering to provide breeding materials for the future improvement of papaya in Kenya.

Rolling circle amplification is a simple approach of enriching populations of single-stranded DNA plant begomovirus genomes (genus, Begomovirus; family, Geminiviridae). This is an innovative approach that utilizes the robustness of the bacteriophage phi29 DNA polymerase used in circle amplification, together with deep sequencing using Illumina Miseq and bioinformatics to assess population diversity of begomoviruses in naturally infected cassava. The approach is suitable for detecting rare members in a population in begomoviral populations in situation where mixtures of isolates, strains, and multiple species occur. The main objectives were to increase the sensitivity of detection of next generation sequencing by enriching it using rolling circle amplification then determination of the diversity of the cassava mosaic geminivirus. This was done by total nucleic acids isolated from symptomatic, field cassava infected plants, then using rolling circle amplification to multiply the less abundant viral sequences. Enriched and non-enriched virus-libraries were subjected to deep sequencing using Illumina Miseq. Using bioinformatic CLC Genomics 5.5.1 software programs the quality assessment of reads and contig assembly of viral sequences. This was done through de novo and reference-guided assembly. The identity and diversities of the begomoviral sequences were compared with sequences in Sanger sequencing of viral components deposited in the NCBI Gene Bank. In this study we have demonstrated that RCA increases the chances of detecting the virus by approximately 10 to 1000 fold and wide genome diversity of cassava mosaic geminivirus in various cassava growing zones in Kenya were detected. In conclusion, this approach described herein is simple and will enhance the exploration of begomovirus diversities from cassava infected plants, irrespective of their viral abundance. This will make it possible for routine screening of field samples as the cost of deep sequencing NGS is decreasing and the advances of bioinformatic software development become enhanced. This is the first report of the RCA-Illumina-NGS approach to explore cassava infected with begomoviruses under field conditions and their diversities.

Yam (Dioscorea spp.), a traditional crop in Kenya has not undergone improvement and little has been done to understand its genetic background. The taxonomy and phylogeny of the local landraces has not been fully studied. The main cultivated species is Dioscorea minutiflora Engl. Others found with low distribution are Dioscorea alata L., Dioscorea bulbifera L. and Dioscorea odoratissima Pax. Flow cytometry was used to estimate the ploidy level of 155 accessions of Kenyan yam including two checks, TDr.18544 a tetraploid and TDc 98/136 an octoploid from International Institute of Tropical Agriculture (IITA), Nigeria. Also included in the study were Dioscorea dumetorum Pax, Dioscorea asteriscus Burkill and Dioscorea schimperiana Kunth which are yam wild relatives. Leaf samples were harvested from the field genebank and nuclei extracted using an extraction buffer (Partec GmbH, Munster Germany). Plant nuclei were isolated and stained with propidium iodide then analyzed in a flow cytometer. Seven ploidy levels of 3x (11.4%), 4x(37.5%), 5x(29.2%), 6x(14.6), 7x(3.1%); 8x(3.1%) and 10x(0.6%) were observed. Tetraploids (4x) formed the highest proportion followed by pentaploids (5x). The highest ploidy, decaploid, (10x), was found in D. odoratissima Pax, a conspecific form of Dioscorea preahensilis found under cultivation in two farms in Western Kenya. No diploids were observed in the study. Ploidy level was not associated with geographical habitat of the landraces while farmer-named varieties were not associated with ploidy levels. The findings generated new knowledge and form a basis for future yam research and improvement in the country. Further work is required to establish the phylogeny of Kenyan yam landraces.

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