Rapid development of durable bacterial blight resistance in African rice through marker-assisted pyramiding of four resistance genes

Abstract Bacterial blight of rice causes substantial crop losses in Asia and Africa. The recent introduction of Asian strains into African countries has led to two independent outbreaks detected in 2019, causing severe damage in Madagascar and Tanzania. The strains are highly virulent on local rice varieties and rapidly spread from Tanzania to neighboring countries. Multiplex genome editing of effector-binding elements in the promoter of rice SWEET has successfully generated elite rice lines with broad-spectrum resistance against bacterial blight. While genome-edited crops can be released in countries with genome editing regulations, their use in countries that have yet to establish regulations, e.g., Tanzania and Madagascar, is hindered. To circumvent this, marker-assisted breeding (MAB) of the African elite varieties Komboka P , FARO-44, and NERICA-4 was adopted to introgress resistance genes to confer resistance to Xoo strains identified in Tanzania (iTz) and Madagascar (iMg). We hypothesized that xa13 and Xa21 can confer resistance to the introduced strains, and that a combination of R genes would enhance durability. Resistance gene pyramiding, namely the endogenous Xa1 , Xa4 with xa13 , and Xa21 genes in the elite rice varieties Komboka P , FARO-44 and NERICA-4 conferred resistance to the introduced iTz and iMg strains as well as select Asian and West African Xoo strains. Our study presents one potential solution by providing rice breeders in East Africa with robust bacterial blight resistance in three local rice varieties for field trials, line registration, and deployment.