Fungicide Application on Alternate Host Barberry Has Significant Roles in Declining Population Genetic Diversity and the Risk of Emerging New Races of <i>Puccinia striiformis</i> f. sp. <i>tritici</i>

<i>Puccinia</i> <i>striiformis</i> f. sp. <i>tritici</i> (<i>Pst</i>) is a destructive pathogen renowned for its dual reproductive modes, an asexual stage on wheat and a sexual stage on barberry (<i>Berberis</i>), which makes wheat cultivars vulnerable to newly emerging races. However, little has been known about the impact of treatment on barberry plants on declining population genetic diversity and race composition. In this study, we selected six barberry-wheat coexisting sites in which <i>Pst</i> occurs sexually as treatment and control groups for experimental purposes. The treatment group was treated with triadimefon fungicides on barberry at the early pycnial stage to suppress sexual reproduction. Conversely, the control group represented sexual reproduction without fungicide application. <i>Pst</i> populations from wheat fields close to barberry with and without fungicide treatment were phenotyped on Chinese differentials and genotyped using a DNA microarray. The results showed the treatment population displayed a lower heterozygosity level (<i>F</i>_<i>hom</i> = -0.36945, Tajima's <i>D</i> = 0.285033) and a lower genetic diversity (<i>π</i> = 0.000156053) compared with the control population (<i>F</i>_<i>hom</i> = -0.41745, Tajima's <i>D</i> = 0.955451, <i>π</i> = 0.000184483), and a significant difference was observed between both populations (<i>P <</i> 0.001; <i>P <</i> 0.05). The treatment population identified 17 new races and 3 known races, and the control population identified 46 new races and 8 known races. The treatment population (<i>α</i> = 4.644) showed a lower diversity of the standard races than that of the control population (<i>α</i> = 5.194) based on a set of 25 <i>Yr</i>-single gene lines. Our results showed the significant impact of fungicide application on barberry to minimize the emergence of new races and the level of genetic diversity. This study provides guidance to growers, emphasizing the importance of timely fungicide application on barberry to ensure the long-term resistance durability of wheat cultivars against stripe rust.