In order to analyze the population structure of Puccinia striiformis f.sp.tritici(Pst),SNPs primers of Pst were developed from DNA sequences of nine house-keeping genes Chs,Act,Mapk1,Tub,Cdc2,Rd,Sm,Ls and Ef-1α obtained from GenBank.Eight of which were from Pst and one from P.graminis f.sp.tritici(Pgt).Thirteen pairs of primers were designed and screened based on at least 30 isolates of Pst obtained from diverse locations.Three of them were polymorphic namely Mapl351S/Mapl683 A,Cd28S/Cd352 A and Efl37S/Ef531 A.Polymorphic loci analysis based on 149 Pst isolates from 5 provinces indicated that the three primers had good polymorphism.Cd28S/Cd352 A had 8 polymorphic loci,three of them were phylogenetically informative.Efl37S/Ef531 A had 6 polymorphic loci and 4 of them were informative.Mapl351S/Mapl683 A had 8 polymorphic loci and 4 were informative.The 3 primers were used for analyzing Pst population and revealed the ancestral origin,phylogeny relation of haplotypes,genetic differentiation of the population,gene flow,and the evolution and migration relation between Pst populations thereby.The findings indicate that the 3genes SNP primers can be used for Pst population genetic structure analysis.
