Phenotypic and molecular assessment of bacterial blight resistance genes in elite rice germplasm of Pakistan

Abstract Bacterial blight (BB) caused by Xanthomonas oryzae pv. oryzae (Xoo) is a major constraint to rice production, necessitating the identification of resistant germplasm. This study aimed to isolate and confirm Xoo from infected rice fields and to evaluate rice genotypes for BB resistance genes and phenotypic response. Xoo was successfully isolated on Wakimoto’s medium and confirmed by multiplex PCR through species- and pathovar-specific amplicons. Thirty rice genotypes were screened for dominant and recessive Xa/xa resistance genes using gene-specific markers and evaluated for disease reaction. Considerable genetic variation was observed among fine, coarse, and hybrid rice lines. The recessive gene xa13, detected in a single fine rice line, conferred a resistant phenotype, while Xa4, although widely distributed, was ineffective alone. Improved responses were observed when Xa4 was combined with Xa21. Overall, gene combinations rather than single genes were associated with enhanced resistance, highlighting the importance of gene pyramiding for durable BB management in rice.