Distribution of groundnut rosette disease and sequence diversity of groundnut rosette virus associated satellite RNA (Sat-RNA) in Western Kenya

Abstract

Production of groundnuts (Arachis hypogaea L.) in Western Kenya is mainly constrained by groundnut rosette disease (GRD) which cause up to 100% yield loss. This disease expresses different symptoms as a result of variations in the groundnut rosette virus (GRV) associated satellite-ribonucleic acid (GRV Sat-RNA). Over the past 20 years, no work had been done to document the status of the disease in Kenya. Additionally, no sequences of any of the GRD associated viruses were available in the GeneBank from Kenya. This study determined the distribution of GRD and the genetic diversity of GRV Sat-RNA. Sampling was done in main groundnut growing areas of Western Kenya during the long and short rain seasons in 2016/2017. Total RNA was extracted from the leafy samples collected using RNeasy Mini Kit (Qiagen) according to the manufacturers’ protocol and used for double stranded cDNA synthesis using the SuperScript II kit. DNA libraries were sequenced on the Illumina MiSeq platform (Illumina). Reads were used for de novo assembly and contigs aligned to the viral genomes database using CLC Genomics Workbench 10.1.2. The assembled contigs were subjected to a BLASTn search against the GenBank database. Average GRD incidence was 53 and 41% in the short and long rain seasons, respectively. Chlorotic rosette was the dominant symptom followed by green rosette and mosaic. Nucleotide sequences of Sat-RNA revealed identities of 88 to 100% between the Kenyan isolates and those from Malawi, Nigeria and Ghana. All Kenya isolates clustered closest with green rosette variants of Malawi except one which clustered with chlorotic/yellow blotch variants. Rosette is widely distributed in Western Kenya and occurs wherever groundnuts are grown. The variations of GRD symptoms in Western Kenya could be due to the existence of different variants of Sat-RNA or other agents. Key words: Groundnuts, satellite-ribonucleic acid (Sat-RNA), diversity, Western Kenya.