A genotyping by target sequencing chip for population genetic analysis
of the wheat stripe rust pathogen (Puccinia striiformis)
Abstract
Puccinia striiformis f. sp. tritici (Pst), the causative agent of wheat
stripe rust, poses a significant threat to wheat production due to its
rapid long-distance migration and epidemic properties. Understanding the
genetic structure and dynamics of the Pst population is crucial for
early prediction and establishment of effective control strategies. The
types of molecular marker analyses used in previous population genetic
studies are often costly, time-consuming, and labor-intensive. We
developed a genotyping by target sequencing (GBTS) chip for Pst designed
with candidate secretion proteins and highly polymorphic single
nucleotide polymorphism (SNP) sites identified from genome resequencing.
The chip can be used directly with diseased leaves, saving time and
avoiding cross-contamination between samples. The feasibility and
efficiency of the chip was tested using 225 infected leaf samples
collected from the northwest oversummering region of China. This test
yielded 1,293,150 high-quality SNPs with a maximum gap of 99,512 bp.
Strict quality controls produced 19,139 SNPs, comprising the final Pst
20K GBTS chip. Population genetic analysis revealed frequent gene flow
and similar genetic diversity of Pst between epidemic regions,
consistent with wind field analysis, trajectory tracking, and field
monitoring. The results demonstrated that the GBTS chip is more
efficient, convenient, and lower in cost than previous methods. This
study provides new insights into stripe rust population dynamics.
Furthermore, the newly established chip offers a valuable method for
enriching epidemiological recognition, guiding future research into
inter-regional or continental transmission of an important plant
pathogen.