Abstract：Head smut is a common and serious disease of corn. To clarify the genetic relationship of Sporisorium reilianum f. sp. zeae of different regions and different years in Shanxi Province, inter simple sequence repeats (ISSR) marker was used to analyse their genetic diversity, furthermore, Popgene Version 1.31, PowerMarker V 3.25, Mega 5.0 and Ntsys 2.10 softwares were used to estimate genetic diversity parameters, analyse genetic differentiation, and construct cluster maps. The results indicated that a total of 92 bands were detected using the 9 polymorphic primers screened, 90 (97.83%) among which were polymorphic, with an average of 10.0 polymorphic bands per primer. The average index of effective alleles (Ne), Nei's gene diversity (H), Shannon information (I) and polymorphism information content (PIC) were 1.360 0, 0.231 3, 0.370 7 and 0.443 7, respectively. All the tested strains were clustered into 9 ISSR groups at genetic similarity of 0.718. Strains from the same geographic origin were distributed into different IG groups, and strains from the same host variety in the same region were not preferentially clustered together. Comparing the population genetic diversity and variation of S. reilianum f. sp. zeae in 2015 and 2020, it was found that the genetic diversity parameters (PPB, Ne, H and I) showed a decreasing trend, and the genetic variation among geographic populations rose from 16.40% to 59.41%, while that within populations decreased from 83.60% to 40.59%. The gene flow changed from 2.549 1 to 0.341 6. All the results showed that rich genetic diversity existed among the tested S. reilianum f. sp. zeae strains. The ISSR groups of the strains had no correlation with the origin and host variety the population structure of S. reilianum f. sp. zeae changed significantly in 2020 comparing that in 2015. There are potential genetic differentiation factors among geographical populations and the stability of the populations has decreased significantly. The results provide an important theoretical basis for rational distribution of maize varieties and integrated control of head smut in Shanxi Province.
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