Genetic Diversity and Population Structure of the Rice False Smut Pathogen Ustilaginoidea virens in the Sichuan-Chongqing Region

Rice false smut caused by Ustilaginoidea virens is one of the most devastating fungal diseases of rice panicles worldwide. In this study, two novel molecular markers derived from single nucleotide polymorphism-rich genomic DNA fragments and a previously reported molecular marker were used for analyzing the genetic diversity and population structure of 167 U. virens isolates collected from nine areas in the Sichuan-Chongqing region, China. A total of 62 haplotypes were identified, and a few haplotypes with high frequency were found and distributed in two to three areas, suggesting gene flow among different geographical populations. All isolates were divided into six genetic groups. Groups I and VI were the largest, with 61 and 48 isolates, respectively. The pairwise F-ST values showed significant genetic differentiation among all compared geographical populations. Analysis of molecular variance showed that intergroup genetic variation accounted for 40.17% of the total genetic variation, while 59.83% of genetic variation came from intragroup genetic variation. The unweighted pair-group method with arithmetic means dendrogram and population structure revealed that the genetic composition of isolates collected from Santai, Nanchong, Yongchuan, and Wansheng dominated by the same genetic subgroup was different from those collected from other areas. In addition, genetic recombination was found in a few isolates. These findings will help to improve the strategies for rice false smut management and resistance breeding, such as evaluating breeding lines with different isolates or haplotypes at different elevations and landforms.

Automated summary

This study analyzed the genetic diversity and population structure of Ustilaginoidea virens isolates from the Sichuan-Chongqing region in China using novel molecular markers and a previously reported marker. The findings revealed gene flow among different populations and identified six genetic groups. Significant genetic differentiation was observed among different geographical populations. The study also found differences in genetic composition between isolates collected from different areas and identified genetic recombination in some isolates. These findings have important implications for the management of rice false smut and resistance breeding.