Genome-Wide Association Analysis Identifies Resistance Loci for Bacterial Blight in Diverse East African Rice Germplasm

Abstract

Abstract Background Xanthomonas oryzae pv. Oryzae (Xoo), the causal agent of rice bacterial blight disease has been extensively characterized and loci against different races identified. Many rice cultivars have been developed and utilized to combat the disease, however due to rapid evolution of Xoo, a number of resistances have broken-down. The continuous challenge of ever evolving Xoo and breakdown of resistance in cultivated rice varieties makes it even more important to discover new loci to enable sustainable durable deployment of broad-spectrum resistance genes in elite breeding lines. African germplasm can be exploited as reservoirs of useful genetic variation for bacterial blight (BB) resistance. This study was conducted to identify loci associated to BB resistance and new genetic donors for breeding program. Results To identify candidate sources of resistance for advancing breeding, we used highly four virulent strains of Xoo (PXO99, MAI1, BAI3 and Xoo3-1) to screen 78 East African accessions by genome-wide association studies. The core genetic base of the diverse accessions exhibited high degree of resistance to the Xoo strains. 50.63% of the accessions were highly resistant to the Philippines strain PX099, while 20.25% were highly susceptible to the virulent West African strain MAI1. Two novel resistant loci significantly associated hotspots were identified using 1901 SNPs. The two hits were located on chromosome 12 (Xa25) and Chr. 6 (Xa7, Xa27, Xa33). Conclusions Our finding have identified novel loci that gives a useful basis for more investigation and a wide core genetic pool of high resistance for broad-spectrum resistance genetic improvement.