Host Plant Reaction to Rice Yellow Mottle Virus and Allelic Diversity of RYMV1 Gene in Rice Cultivars in Uganda

Rice Yellow Mottle Virus (RYMV) disease is endemic to Africa where it affects rice production. Host plant resistance would form a cost effective and sustainable option for managing the disease. However, there is still lack of knowledge on the reaction of rice germplasm and the genetic basis of their resistance/susceptibility to RYMV coupled with lack of molecular markers to facilitate the development of RYMV resistant varieties. We screened 56 rice accessions drawn from breeding lines and varieties commercially cultivated in Uganda for their resistance/susceptibility to RYMV. We also sought to develop and validate allele specific markers for RYMV1 alleles. The rice accessions showed variation in their reaction to RYMV; 14, 12, 17 and 13 accessions were categorized as resistant, moderately resistant, moderately susceptible and susceptible respectively. Among the resistant accessions, five possessed a single SNP (G/A) corresponding to the rymv1-2 allele. The new accessions can be deployed as resistant cultivars and/or used to introgress rymv1-2 allele into susceptible adapted cultivars throughout Africa. We developed two functional allele specific markers, which co-segregated with the rymv1-2 resistance allele in an F2 population and clearly differentiated between the susceptible and resistant individuals in the F2 population. The functional allele specific marker developed in this study can be used in MAS programs for introgression of rymv1-2 resistance allele.