Population genomic analyses reveal extensive genomic regions within selective sweeps associated with adaptation and demographic history of a wheat fungal pathogen
Authors: Xing Yun , Xia Chongjing , Huang Liang , Zhao Na , Li Hongfu , Zhang Xingzong , Qiu AGe , Tang Wanqiang , Wang Meinan , Chen Xianming , Liu Bo , Zhang Hao , Gao Li , Chen Wanquan , Liu Taiguo 
Published: August 2023

Plant pathogens can quickly evolve in response to the changing host and environment, resulting in destructive epidemics. The fungusPuccinia striiformisf. sp.tritici(Pst), causing wheat stripe rust disease worldwide, is one such pathogen. In the arms race between pathogens and hosts, changes in host populations exerted continuous selective forces on the dynamics of pathogens. However, the footprints of these selection forces and the demography ofPstremain poorly explored, limited our understanding the evolutionary processes that shape the spread and evolution of pathogens. In this study, we revealed several features of worldwidePstpopulations through population genomic analyses. There might be limited gene flow betweenPstpopulations from China and other countries. A slower rate of linkage disequilibrium decay was detected comparing to rust fungi with known sexual reproduction. Furthermore, we detected extensive hard and soft sweeps associated withPstadaptation. Genes within the selective sweeps were enriched in secreted proteins and effectors and showed functions related to pathogenicity or virulence, temperature tolerance, and fungicide resistance implying that ChinesePstpopulations suffered positive selection pressures from host and abiotic factors. Moreover, demographic history indicatedPstpopulations experienced strong bottlenecks at the beginning of the wheat domestication around 10,000 years ago and during modern agriculture around 100 years ago, suggesting that the crop domestication and breeding programs could continuously contribute to the decline of pathogen effective population sizes. Our results provided insights into the evolution of thePstgenome and highlighted the role of modern agriculture on pathogen demography.

Author Summary

Wheat stripe rust, as a pathogen of wheat, is capable of inducing significant yield reduction on a global scale. Traditional epidemiological investigations have elucidated the causative agent behind this disease, the wheat stripe rust pathogen, as an organism exhibiting swift adaptive evolution in response to its environment.

However, the precise mechanisms underpinning its adaptive strategies and the ensuing alterations in population dynamics remain relatively unexplored.

In our research, we have undertaken an analysis encompassing wheat stripe rust samples throughout the world. Employing population genomics methods, we have sought to discern the genomic footprints corresponding to the adaptive process within the pathogen. These genomic footprints have illuminated the operation of positive selection pressures caused by both the host plant and the ecological context.

Concurrently, it have provided insights into the population size that the wheat stripe rust pathogen has undergone over millennia. Notably, its change in population size revealed the demographic history associated with wheat domestication.