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Background  Rice blast disease is one of the most destructive fungal disease of rice worldwide. The avirulence ( AVR ) genes of  Magnaporthe oryzae  are recognized by the cognate resistance ( R ) genes of rice and trigger race-specific resistance. The variation in  AVR  is one of the major drivers of new races. Detecting the variation in the  AVR  gene in isolates from a population of  Magnaporthe oryzae  collected from rice production fields will aid in evaluating the effectiveness of  R  genes in rice production areas. The  Pik  gene contains 5  R  alleles ( Pik ,  Pikh ,  Pikp ,  Pikm  and  Piks ) corresponding to the  AVR  alleles ( AVR-Pik/kh/kp/km/ks ) of  M. oryzae . The  Pik  gene specifically recognizes and prevents infections by isolates of  M. oryzae  that contain  AVR-Pik . The molecular variation in  AVR - Pik  alleles of  M. oryzae  and  Pik  alleles of rice remains unclear.    Results  We studied the possible evolutionary pathways of  AVR-Pik  alleles by analyzing their DNA sequence variation and assaying their avirulence to the cognate  Pik  alleles of resistance genes under field conditions in China. The results of PCR products from genomic DNA showed that 278 of the 366 isolates of  M. oryzae  collected from Yunnan Province, China, carried  AVR-Pik  alleles. Among the isolates from six regions of Yunnan, 66.7–90.3% carried  AVR-Pik  alleles. Moreover, 10  AVR-Pik  haplotypes encoding five novel  AVR-Pik  variants were identified among 201 isolates. The  AVR-Pik  alleles evolved to virulent from avirulent forms via stepwise base substitution. These findings demonstrate that  AVR-Pik  alleles are under positive selection and that mutations are responsible for defeating race-specific resistant  Pik  alleles in nature.    Conclusions  We demonstrated the polymorphism and distribution of  AVR - Pik  alleles in Yunnan Province, China. By pathogenicity assays used to detect the function of the different haplotypes of  AVR - Pik , for the first time, we showed the avoidance and stepwise evolution of  AVR - Pik  alleles in rice production areas of Yunnan. The functional  AVR-Pik  possesses diversified sequence structures and is under positive selection in nature.    Electronic supplementary material  The online version of this article (10.1186/s12870-019-1817-8) contains supplementary material, which is available to authorized users.

Novel haplotypes and networks of AVR-Pik alleles in Magnaporthe oryzae