Identification of a Pi9-Containing Rice Germplasm with a Newly Developed Robust Marker

The Pi9 gene in rice, originating from Oryza minuta, is an effective resistance gene for controlling rice blast disease. However, currently available linked DNA markers do not accurately identify the function of Pi9, thus hindering its efficient incorporation into new cultivars through marker-assisted selection (MAS). In addition, no known Pi9-containing rice germplasm is available to breeders. In the present study, DNA sequence variation of Pi9 alleles and their family members was analyzed in 40 diverse rice germplasm accessions from the AA genome to develop a robust Pi9 marker. In total, 29 DNA primers of 20 to 23 nucleotides were designed and each possible combination of primer pairs was used to detect Pi9. Only one combination of DNA primers, KS28/KS6, was identified to specifically detect Pi9 in the monogenic line IRBL9-W. The presence of Pi9 was verified with the predicted Pi9-specific blast reaction. Subsequently, 201 genetically diverse mini-core rice accessions from 114 countries were screened with KS28/KS6. One germplasm, IR 9660-48-1-1-2, was identified to carry Pi9 and the function of Pi9 was verified with pathogenicity assays. This robust Pi9 marker and a rice germplasm, IR9660-48-1-1-2 (GSOR310687), carrying Pi9 can be used to improve blast resistance with a MAS approach.