A rapid genotyping method for an obligate fungal pathogen, Puccinia striiformis f.sp. tritici, based on DNA extraction from infected leaf and Multiplex PCR genotyping

Abstract

Background: Puccinia striiformis f.sp. tritici (PST), an obligate fungal pathogen causing wheat yellow/stripe rust, a serious disease, has been used to understand the evolution of crop pathogen using molecular markers. However, numerous questions regarding its evolutionary history and recent migration routes still remains to be addressed, which need the genotyping of a large number of isolates, a process that is limited by both DNA extraction and genotyping methods. To address the two issues, we developed here a method for direct DNA extraction from infected leaves combined with optimized SSR multiplexing.

Findings: We report here an efficient protocol for direct fungal DNA extraction from infected leaves, avoiding the costly and time consuming step of spore multiplication. The genotyping strategy we propose, amplified a total of 20 SSRs in three Multiplex PCR reactions, which were highly polymorphic and were able to differentiate different PST populations with high efficiency and accuracy.

Conclusion: These two developments enabled a genotyping strategy that could contribute to the development of molecular epidemiology of yellow rust disease, both at a regional or worldwide scale.

Figure 1

Gel run for the amplification of three multiplexes for DNA extracted directly from spores and from leaves infected with PST. A: J1023M2 spore extracted, B: DNA extracted from plant infected with J1023M2, C: Non-infected cv. Michigan Amber seedling leaf DNA, D: Non-infected cv. Sogood adult plant DNA.

Figure 2

Chromatogram of Multiplex-2 with seven SSR loci labelled with blue (2 SSRs), green (2SSRs) and black (3 SSRs) fluorescent dyes, while the red dye represents the length markers. The RJO-24 locus with a low strength peak could be read after zooming (top left).