Identifying a source of a bacterial blight resistance gene xa5 in rice variety ‘IR62266’ and development of a functional marker ‘PAxa5’, the easy agarose based detection

Abstract

Bacterial blight (BB) caused by Xanthomonas oryzae pv. oryzae (Xoo) is one of the most important diseases in rice worldwide causing tremendous damage to rice yield in many countries. The use of resistant rice varieties is the most economical and effective method to manage and control this disease. IR62266, a rice variety developed by IRRI , was identified as a good genetic resource for broad spectrum BB resistance in Thailand. The genetic factor determining BB resistance was studied in the F 2:3 population developed from a cross between IR62266 and KDML105 using three Thai Xoo isolates , TXO1 , TXO2 , and TXO5. A total of 190 F 2:3 individuals were challenged with TXO1 , TXO2 , and TXO5 and lesion lengths were measured. The resistant reactions of the F 2:3 population showed the ratio of 3 susceptible : 1 resistant, thereby indicating a single recessive gene controlled BB resistance in IR62266. Genetic analysis indicated that RM122 was located on the short arm of chromosome 5 and was the tightly linked to the resistance gene accounting for 66.03% of phenotypic variance . The RM122 was located very close to the cloned xa5 gene, a broad spectrum BB resistance gene . . Therefore, the PAxa5 was developed as a new functional SNP marker and tested in the F 2:3 individuals. PAxa5 clearly differentiated the resistant and susceptible reactions in the population. PAxa5 was then validated in a wide range of germplasms and was found to clearly identify xa5 . PAxa5 is currently implemented in the marker-assisted breeding program to facilitate the selection for the xa5 gene