Seedling Blight of Rice in the Southern United States and Its Management

Seedling blight of rice is one of the most important diseases in dry-seeded rice system in the southern U. S. Surveys were conducted in five southern rice-producing states (Arkansas, Louisiana, Mississippi, Missouri, and Texas) during the 2018 and 2019 cropping seasons to determine the distribution and importance of fungal pathogens associated with seedling blight in rice. A total of 349 fungal isolates were collected and identified as Rhizoctonia solani, Fusarium spp., Sclerotium rolfsii, and Marasmius graminum. R. solani was the most prevalent fungus in this survey study. There were two anastomosis groups of R. solani associated with rice seedlings, with R. solani AG-11 (n= 245) being the most predominant pathogen and R. solani AG-4 (n=7) being the most aggressive pathogen. R. solani AG-4 and M. graminum were identified as new pathogens causing seedling blight of rice and were more aggressive than R. solani AG-11, Fusarium spp., and S. rolfsii. A total of 202 rice breeding lines and commercial inbreed and hybrid cultivars were evaluated for resistance to R. solani AG-11 and AG-4 under greenhouse and field conditions. There were no cultivars or breeding lines showing a high level of resistance to either R. solani pathogen. However, the hybrid cultivar RT7521 FP and inbred cultivar CLL15 showed less than 50% stand loss against R. solani AG-11. To understand genetic structure of the populations of R. solani AG-11, the major seedling blight pathogen, we used whole-genome sequencing of the R. solani AG-11 populations from Arkansas (n= 31), Mississippi (n= 4), Missouri (n= 21), and Texas (n= 24). Demographic analysis suggested the Texas population is separated from Arkansas, Mississippi, and Missouri populations. The results from the dendrogram and discriminate analysis of principal components grouped the Arkansas, Mississippi, and Missouri isolates in a single cluster, suggesting the possibility of genotype flow among these populations. The Texas population was further differentiated into two subpopulations with respect to geographical zone (east and northwest rice producing zones). This finding provides new insights into the evolution and structure of R. solani AG-11 populations in rice fields in the southern U.S. This research project provides the foundation for the future studies to develop effective management strategies for rice seedling blight, including proper diagnostics, cultivar resistance, and fungicide seed treatment