| Wheat stripe rust,caused by Puccinia striiformis f.sp.tritici(Pst),is a serious disease of wheat in the world.The obligate biotrophic fungal pathogen changes its virulence rapidly,which can circumvent resistance in wheat cultivars and thus cause severe epidemics.Because Pst races have been identified in the United States using different wheat genotypes in different time periods,it is difficult to make direct comparison of the current population with historical populations.The objective of this study was to characterize historical populations with 18 Yr single-gene lines that are currently used to differentiate Pst races in order to understanding virulence and race dynamics of the pathogen.From 908 Pst isolates collected from 1968 to 2009 in the United States,171 races were identified.Virulences to the 18 Yr genes,except Yr5 and Yr15,were detected but in different periods,and most virulences increased in frequency over time.Some virulences such as those to Yr17,Yr27,Yr32,Yr43,Yr44,YrTrl,and YrExp2 appeared much earlier than previously thought.Positive and negative associations were detected between virulences.The 171 races were clustered into two major virulence clusters(VCs)and further grouped into eight virulence groups(VGs).The eight VGs differ in the mean number of virulences,common virulences,and common avirulences.Three VGs(VG1,VG2,and VG5)in VC1 were detected in all periods from 1968 to 2009;VG4 in VC1 was detected in the periods from 1978 to 2009;VG3 in VC1 and VG6 in VC2 were detected only after the year 2000;and VG7 and VG8 in VG2 were detected after 1998 and 1993,respectively.About 127(74%)of the races were presumably evolved from previously existing races through a single-or double-step mutations,whereas the remaining 44(26%)races might appear through introduction and/or somatic recombination.The continual information on virulences and races in the Pst populations in the United States from 1968 to 2009 are useful for understanding the evolution of the pathogen and for breeding wheat cultivars with effective resistance to stripe rust.In population genetic studies,neutral genetic markers have been the most common tools because they are easily obtained and can provide unbiased estimates of divergence time and the amount of genetic drift.However,growing awareness has been raised on the non-neutral or adaptive markers which can provide more and better estimates of evolutionary differentiation caused by different selections among populations.In the present study,there are developed over three hundred single nucleotide polymorphism markers from genes predicted to encode secreted protein secreted protein(SP-SNP)and more than 100 pairs SSR markers in Puccinia striiformis,the causal agent of stripe rust which is one of the most severe diseases in world-wide wheat production areas including the United States.A total of 1084 isolates collected over all stripe rust epidemiological regions in the US from 1968 to 2009 were genotyped at 92 SNP loci and 14 SSR loci to study the population diversity and differentiation.A moderate,but significant correlation between the molecular data and virulence data suggested that when used together,the markers were suitable for studying population genetics of the pathogen.Clustering of all 711 multi-locus genotypes of SNP and 568 multi-locus genotypes of SSR were consistent by Bayesian clustering algorithm,neighbor-joining method,and principal component analysis.Analysis of molecular variance also detected significant differences among 9 times of US populations.A level of heterozygosity had an increase trend from 1968 to 2009.The year 2000 became a very important turning point.Population differentiation among different periods was analyzed.In general,isolates after 2000 were more diverse than those before 2000.At the same time,SNP and SSR were compared in order to find best method to use in identifying genomic regions or genes that are under different selection in both crop and pathogen populations.The population diversity and differentiation information would be useful for wheat breeding programs and stripe rust management. |
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