Serological and Molecular Characterization Detects Unique Rice Yellow Mottle Virus Strains in Kenya

Abstract

Rice (<i>Oryza sativa</i> L.) is an economically important food crop in western Kenya but its production remains very low due to abiotic and biotic constraints. Rice yellow mottle disease (RYMD) caused by <i>Rice yellow mottle virus</i> (RYMV, genus: <i>Sobemovirus</i>) can cause up to 100% yield loss. This study characterized and determined the genetic diversity of RYMV strains in the ten isolates collected in February 2020 from both symptomatic and asymptomatic plants in western Kenya. The samples from the two rice fields A and B had two major common rice varieties of IR; field A (IR 2793) and field B (IR 2793-8-1). Total RNA was extracted using GeneJET Plant RNA Purification Mini Kit followed by RT-PCR using RYMV CP specific primers. The PCR products were sequenced by Sanger sequencing technology. Phylogenetic analysis was done by MEGA X. RYMV presence was confirmed serologically by DAS-ELISA. Isolates Ke_A1, KeB3 and KeB4 are novel sequences. KeB3 and KeB4 isolates clustered uniquely from the other Kenyan sequences depicting new evolutionary diversity. KeB3 and KeB4 shared 99% sequence identity with Ke105 and Ke101, while isolate Ke_A1 shared 98% identity with Ke101 and 99% with Ke105. Phylogenetic analysis of the CP gene sequences revealed that the isolates from Uganda (Ug), Kenya (Ke) and Tanzania (Tz) clustered together by country, implying that there was a possibility of single introduction of the RYMV CP gene in the three East African (EA) countries once, before further local viral diversity occurred in each country with new recombinations for further research.