Genome-wide association analysis identifies resistance loci for bacterial blight in diverse East African rice germplasm

Abstract

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 the rapid evolution of Xoo, several resistances have broken down. The continuous challenge of ever-evolving Xoo and the breakdown of resistance in cultivated rice varieties make 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 with BB resistance and new genetic donors for the breeding program. To identify candidate sources of resistance for advancing breeding, four virulent strains of Xoo (PXO99, MAI1, BAI3, and Xoo3-1) were used to screen 78 East African accessions by genome-wide association studies. The diverse accessions' core genetic base exhibited high 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). Novel loci were identified that gives a useful basis for more investigation and a wide core genetic pool of high resistance for broad-spectrum resistance for genetic improvement.