A novel SCAR marker closely linked to the avirulence gene AVR-Pik~m in rice blast fungus Magnaporthe grisea

Avirulence genes are functional genes in pathogens that determine expression of the race-specific resistance in hosts. By using the technique of random amplified polymorphic DNAs(RAPD), this study identified a new DNA marker OPEl21400 that was closely linked to the avirulence gene, AVR-Pikm, in rice blast pathogen Magnaporthe grisea. Based on the nucleotide sequence of OPE121400 a pair of 17 nt primers was designed and used for PCR detection of DNA polymorphism in a mapping population, which was generated by crossing an avirulent strain S1522 with a virulent strain S159. A single DNA band with similar length to the RAPD marker OPE121400 was generated by the PCR in all the avirulent progenies but not in the virulent ones except for two recombinants. The genetic distance from the marker to AVR-Pikm was calculated as 1. 89 cM, which was 2. 86 cM closer to the gene than OPO121000, a RAPD marker previously identified by our group. Although lied in the same side with OPO121000, OPE121400 will be useful for locating the position of AVR-Pikm in the chromosome and orientating contigs for further screening of linked SSR markers that lie in the opposite side.