Incidence of Groundnut Rosette Disease (GRD) and Genetic Diversity of Groundnut Rosette Assistor Virus (GRAV) in Western Kenya

Abstract

This study determined the incidence of groundnut rosette disease (GRD) and genetic diversity of groundnut rosette assistor virus (GRAV, genus Luteovirus) in western Kenya. The diseases is a major constraint of groundnuts in Sub-Saharan Africa (SSA) causing up to 100% yield losses in severe cases. Among the GRD associated viruses, GRAV plays a crucial role in vector transmission of the other viruses. Therefore understanding the genetics of GRAV across SSA could enhance development of resistance to the disease. In Kenya, groundnuts are mainly grown in western region, however, the yields are poor mainly due to GRD. Information on occurrence and distribution of GRD in western Kenya was not documented and little was known about the characteristics of associated viruses. Two diagnostic surveys were conducted in six counties; Bungoma, Busia, Homabay, Kakamega, Siaya and Vihiga. Symptomatic and asymptomatic groundnut were collected in RNAlater® solution for laboratory analysis. Total RNA was extracted from the leaf samples using RNeasy Mini Kit (Qiagen) according to the manufacturers' protocol and used for double stranded cDNA synthesis using the SuperScript II kit. The cDNA was column-purified with the DNA Clean & ConcentratorTM-5-DNA kit. The samples were then processed with the transposon-based chemistry library preparation kit (Nextera XT, Illumina) following manufacturer's instructions. The fragment sizes structure of the DNA libraries was assessed using the Agilent 2100 Bioanalyzer. The indexed denatured DNA libraries were sequenced (200-bp paired-end sequencing) on the Illumina MiSeq platform (Illumina). Reads quality check was done using FastQC. Trimmed 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. Phylogenetic analyses and comparisons were performed using the MEGA X. Average 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. The GRAV coat protein (GRAV-CP) gene sequences revealed 97-100% identity with GeneBank isolates showing very slight variations across SSA. The study concludes that GRD incidence is high in western Kenya and that GRAV is highly conserved across SSA. The study recommends an urgent need to curb GRD, possibly through the exploitation of pathogen derived resistance (PDR) with GRAV as the suitable candidate.