Occurrence and genetic diversity of groundnut rosette assistor virus in western Kenya

Abstract Groundnut (Arachis hypogaea) is an important legume in western Kenya, but yields are low and declining. Pests and diseases are ranked high among the yield reducing factors. Groundnut rosette disease (GRD) is the main disease and can cause up to 100% yield loss. Groundnut rosette disease is transmitted by the groundnut aphid, Aphis craccivora Koch and caused by two synergistic viruses; groundnut rosette assistor virus (GRAV) and groundnut rosette virus (GRV) associated with a satellite-ribonucleic acid (sat-RNA). Inadequate information was available on the occurrence and molecular diversity of GRAV in western Kenya, which is a limiting factor on proper diagnosis and management. This study determined the occurrence and molecular diversity of GRAV on groundnuts in western Kenya. A survey of GRD was conducted in 144 farms in Bungoma and Kakamega counties during the short and long rains of 2016–2017. A total of 301 symptomatic leaf samples were collected and preserved until use. Incidence and severity data was collected and subjected to pairwise comparison of means using the standardized disease diagnostic score sheet at P ≤ 0.05. Screening for resistance/tolerance to GRD was done on five popular legume varieties (Arachis hypogaea, Phaseolus vulgaris, Vigna unquiculata, Glycine max and Vigna radiata) and one solanaceous Physalis peruviana. The plants were monitored for GRD symptoms development in the screenhouse for 8 weeks. Total RNA was extracted from the leaf samples using RNeasy Mini Kit (Qiagen) according to the manufacturers’ protocol. DNA libraries were prepared and sequenced on the MiSeq platform (Illumina). Phylogenetic analyses and comparisons were performed using the MEGA X software. From the sequences obtained, primers were designed for use in RT-PCR. Groundnut rosette disease was prevalent in all the surveyed areas with chlorotic rosette symptoms being dominant followed by green rosette and mosaic rosette. Groundnut rosette disease incidence ranged between 31 and 67%, but was higher in Bungoma (67%) than Kakamega (61%) county, while the short rains had higher incidence than the long rains season. All screened indicator plants developed typical GRD viral symptoms and tested positive for GRAV. Nucleotide sequences of GRAV coat protein (CP) gene revealed 97–99% identity among the western Kenya isolates and those from Ghana, Malawi and Nigeria respectively. The fact that GRD occurs wherever groundnuts are grown in western Kenya, is of great concern and may be the reason for the observed low yields. Incorporation of GRD resistance genes in the local cultivars/varieties may be the only practical solution.