Development and validation of SNP-based functional codominant markers for two major disease resistance genes in rice (O. sativa L.)

Blast and bacterial leaf blight are major diseases of rice that limit grain yield significantly. These two devastating biotic stresses have to be controlled to meet the demand for 23 % more rice production by 2035 to feed the increasing number of rice consumers. Incorporating appropriate disease resistance genes into elite varieties is considered as the best method to enhance crop resistance. Molecular markers play an important role in multiple gene pyramiding programs to select desirable genotypes with targeted genes. Two major resistance genes, Pita and xa5, for blast and bacterial leaf blight races, respectively, have been used in many gene pyramiding programs. However, simple PCR-based functional codominant markers have not been reported for these genes. Hence, in the present study, time- and cost-effective codominant markers for Pita and xa5 have been developed and validated in segregating populations. High-throughput screening has been demonstrated using parallel capillary electrophoresis to replace laborious gel-based electrophoresis. Additionally, the presence of Pita and xa5 alleles was evaluated with 260 diverse rice varieties that were collected from different parts of the world. Of the 260 cultivars tested, 55 were identified with the Pita resistance allele while all the tested cultivars had the susceptible Xa5 allele. The identified Pita allele-derived cultivars can be used as an alternative resistance source for blast disease. The newly developed Pita and xa5 functional markers will help toward tracking the two target genes for blast and bacterial leaf blight resistance in breeding programs.