No abstract

Groundnut (Arachis hypogaea, L.) is grown in diverse environments throughout the semi-arid and sub-tropical regions of the world. Poor yields of 500-800kg/ha are attributed to poor agronomic practices, pests and diseases. The major disease reported in Kenya is Groundnut rosette disease (GRD). But recent observations in the field showed that the crop has varied and severe symptoms in addition to those caused by GRD. This required deeper analysis to establish the causal agents. Groundnut samples with virus-like symptoms were collected from western Kenya in 2016. Total RNA was extracted using All Prep RNA Mini Kit. Five mRNA libraries were prepared using the Illumina TrueSeq stranded mRNA library Prep Kit and pooled for multiplexed sequencing using an Illumina HiSeq 2500 to generate paired end reads (FastQ Sanger). The reads were analysed in the Galaxy project platform (customized). Quality reads were first mapped onto plant genome Refseq and unmapped reads isolated and mapped onto virus Refseq using Bowtie 2 (v2.2.3). Groundnut rosette virus satellite RNA, Groundnut rosette virus, Groundnut rosette assistor virus, Ethiopian tobacco bushy top virus, Cowpea polerovirus 2, Chickpea chlorotic stunt virus, Melon aphid-borne yellow virus, Phasey bean mild yellow virus, Beet mild yellowing virus, White clover mottle virus and Cotton leafroll dwarf virus were identified in four libraries. Other viruses (with less than 100 reads) including Bean common mosaic virus, Bean common mosaic necrosis virus, Cowpea chlorotic mottle virus RNA 3, Broad bean mottle virus RNA 3, Passion fruit woodiness virus among others were also mapped. Some of the viruses common in western Kenya were confirmed by PCR. The presence of at least three viruses in groundnuts in Western Kenya highlights the importance of starting a germplasm clean-up program of the plant material used as seed in this crop. Key words: Groundnuts, NGS, RefSeq, Viruses.

Tomato (Solanum lycopersicum) is one of the most important vegetable crop whose production involves the use of synthetic herbicides with detrimental impact on biodiversity. Allelopathy effectively controls horticultural crop weeds. Different plant parts (flowers, leaves, stems, bark, roots) have allelopathic activity that varies over a growing season when used as mulch.  Mulching is a horticultural technique that protects the roots of plants from heat and cold by use of mulch to cover the soil surface around plants. Tomato production in Kakamega County is below 2% and weeds are ranked high among the yield reducing factors. This study assessed the allelopathic effect of guava leaves mulch type (18.0 cm thick) as a management tool for weed control in tomato crops and no mulch as control treatment with three most popular determinate tomato varieties. The mulch treatments were arranged as factorial in a Randomized Complete Block Design (RCBD) to minimize non–experimental bias. Tomato variety sub-treatments were replicated three times in the experimental plots at Masinde Muliro University of Science and Technology (00171N, 340451E). The field project was conducted during the short rains and long rains season of 2016-2017. Data obtained was subjected to analysis of variance (ANOVA) using SAS software, version 9.3 at p<0.05 confidence level. Least Significance Difference (LSD) was used to separate the means. Weed density incidence was significantly highest in control plots up to 100% and lowest in mulched plots (13.41%). Allelopathic control of weeds sustains global food and nutrition security for future generations.

Tomato (Solanum lycopersicum) is the third most important vegetable crop after potato (Solanum tuberosum) and onion (Allium cepa). Its production heavily involves the use of synthetic pesticides with detrimental impact on humans, insect pollinators, water sources, soil fertility and environment. This study uses different mulch types to mitigate this problem. Mulching is an agricultural technique that protects the roots of plants from heat and cold by use of inorganic and organic mulch types to cover the soil surface around plants. Tomato production in Kakamega County is below 2%. Weeds are ranked high among the yield reducing factors. This study consists of four mulch treatments of white polyethylene (0.18mm thick), maize stalks (18.0cm thick), grass clippings (18.0cm thick), guava leaves (18.0cm thick) and no mulch as control with three popularly grown tomato varieties. The mulch treatments were arranged as factorial in a completely randomized block design replicated three times in the experimental plots, at Masinde Muliro University of Science and Technology (0°17 1 N, 34°45 1 E). Tomato variety sub-treatments were completely randomized in the plots to minimize non-experimental bias during sampling weeds incidence. The field project was conducted during the short rains and long rains season of 2016-2017. Data obtained was subjected to analysis of variance (ANOVA) using SAS software, version 9.3 (SAS Institute lnc.) at p<0.05 confidence level. Least Significance Difference (LSD) was used to separate the means. Mean weed density was significantly highest in control plots (94.51%) and least in mulched plots (11.41%). The tomato plant growth parameters (leaf length, leaf width, stem height and stem width) were significantly higher in mulched than control plots. Mulches provide clean field sanitation, inhibits weed seed germination, promotes plant growth with high crop yields and reduces synthetic pesticides and herbicides application.

Synergism among the groundnut rosette disease (GRD) pathogens of Groundnut rosette assistor virus (GRAV, Luteovirus) and Groundnut rosette virus (GRV, Umbravirus) associated with a satellite-ribonucleic acid (sat-RNA), have declined groundnut (Peanut, Arachis hypogaea L.) production in Kenya. The polyphagous groundnut aphid (Aphis craccivora Koch; Homoptera: Aphididae) efficiently transmits GRD in sub-Saharan Africa. Inadequate information available on the pathosystem, epiphytology and genomic characterization of GRAV, GRV and sat-RNA pathogens in Kenya, have hampered control and management technologies due to their intimate complex etiology, the bottleneck which this study unravels. A survey of GRD was conducted in western Kenya among the four counties of Bungoma, Busia, Kisumu and Kisii during the short rains season of 2019. A total of 10 symptomatic leaf samples were selected from the collected samples and preserved until use. Total RNA was extracted from the symptomatic leaf samples using GeneJET Plant RNA Purification Mini Kit according to the manufacturers' protocol. RT-PCR detection of GRD pathogens was done using specific primers of GRAV, GRV and sat-RNA. DNA libraries were prepared and sequenced using the Sanger sequencing platform. Phylogenetic analyses and comparisons were performed using MEGA X software. The sequence quality were checked based on the peak of the electrophoregram and trimmed using CLC main work bench v20. The sequences were assembled with final consensus exported as FASTA file format and BLAST searched against NCBI database using BLASTn. The BLAST hit with nucleotide identity of at least 97% identity were considered, downloaded, uploaded to MEGA X and multiple alignment done with Gap Opening Penalty of 15 and Gap Extension Penalty of 5.5. Phylogenetic trees were constructed with best DNA/Protein model based on automatic Neighbor Joining Tree and Maximum Likelihood method of nucleotides substitution by Kimura 2 Parameter with Invariant Plus Gamma. The two GRAV isolates from Kenya (Ken_G10 and Ken_G2) clustered together in group II while the rest clustered in group I. The Kenyan novel GRAV isolates are more similar to each other than with any other sequences implying common ancestry than with the other African isolates. The Kenyan sat-RNA isolates formed two distinct groups with sub-groups within the clusters. Isolates Ken_G11 and Ken_G6 clustered together in group II while Ken_G10 and Ken_G7 clustered together in group I. Ken_G6 clustered with other Kenyan sat-RNA isolates implying a possible identity by descent (IBD), suggesting a possible impact of a genetic bottleneck whose cause should be investigated further to infer any conclusions.