Serological and molecular detection of rice yellow mottle virus in western Kenya

Rice production remains very low with yields ranging from 1.5-3.5 ton ha-1.The low yields are due abiotic and biotic constraints with pests and diseases being the most important. Rice yellow mottle disease (RYMD), caused by the Rice yellow mottle virus, RYMV, is the greatest challenge causing crop loss of up to 100%. Studies have reported RYMV strain S4-S6 being found in East Africa, however, strains diversity and distribution remain unknown in Kenya. Two diagnostic surveys for RYMD in major rice growing schemes and farms in Western Kenya were conducted in July 2015 and June 2016. Leaf samples were collected from symptomatic and asymptomatic plants for laboratory analysis. Serological analysis was performed by DAS-ELISA. Selected samples (7 in 2015 isolates and 12 in 2016 isolates) representative of location of collection were subjected to molecular analysis. Extraction of total RNA was done using GeneJET Plant RNA Purification Mini Kit followed by RT-PCR detection using RYMV specific primers. Sequencing and sequence analysis of the coat protein gene was done. DAS-ELISA results showed that Western Kenya isolates were serologically similar with very narrow variability in the absorbance readings. Molecular analysis using RT-PCR confirmed the ELISA results. Sequences of the coat protein gene with a length of 720 bp were obtained from sequence analysis which identified RYMV strain S4. The strain of RYMV that exists in Western Kenya is strain S4. The presence of RYMV in samples collected was successful detected by DAS-ELISA and PCR. RYMD is widespread in rice growing areas of Western Kenya. Findings of this study may be useful in integrated management of RYMD in Western Kenya and will assist plant breeders develop resistant rice varieties to RYMV, thereby improve food security, increase smallholder farmers’ income, contribute to employment creation in rural areas and reduce the rice import bill.