MARPLE, a point-of-care, strain-level disease diagnostics and surveillance tool for complex fungal pathogens.

BACKGROUND: Effective disease management depends on timely and accurate diagnosis to guide control measures. The capacity to distinguish between individuals in a pathogen population with specific properties such as fungicide resistance, toxin production and virulence profiles is often essential to inform disease management approaches. The genomics revolution has led to technologies that can rapidly produce high-resolution genotypic information to define individual variants of a pathogen species. However, their application to complex fungal pathogens has remained limited due to the frequent inability to culture these pathogens in the absence of their host and their large genome sizes. RESULTS: Here, we describe the development of Mobile And Real-time PLant disEase (MARPLE) diagnostics, a portable, genomics-based, point-of-care approach specifically tailored to identify individual strains of complex fungal plant pathogens. We used targeted sequencing to overcome limitations associated with the size of fungal genomes and their often obligately biotrophic nature. Focusing on the wheat yellow rust pathogen, Puccinia striiformis f.sp. tritici (Pst), we demonstrate that our approach can be used to rapidly define individual strains, assign strains to distinct genetic lineages that have been shown to correlate tightly with their virulence profiles and monitor genes of importance. CONCLUSIONS: MARPLE diagnostics enables rapid identification of individual pathogen strains and has the potential to monitor those with specific properties such as fungicide resistance directly from field-collected infected plant tissue in situ. Generating results within 48 h of field sampling, this new strategy has far-reaching implications for tracking plant health threats.

A single chromosome addition from Thinopyrum elongatum confers a polycarpic, perennial habit to annual wheat.

Annual wheat displays monocarpic senescence, but amphiploids between wheat and its wild perennial relatives in the genus Thinopyrum generally display a polycarpic, perennial growth habit. In order to determine the chromosomal basis of this phenomenon, life-history characteristics were examined using Chinese Spring wheat and a complete Thinopyrum elongatum (2n=2x=14) chromosome addition series in a Chinese Spring background. Both monosomic and disomic additions and substitutions of Th. elongatum chromosome 4E conferred a polycarpic life history to annual Chinese Spring wheat. Disomic addition lines were found to be perennial under field conditions. This is the first report of a single alien chromosome conferring a polycarpic growth habit to a monocarpic species. Chromosome 4E altered the timing of tiller initiation, such that two growth phases could be clearly identified, the first phase being indistinguishable from the growth of euploid Chinese Spring, followed by a second phase of tiller initiation after the sexual cycle of the first phase tillers was complete (post-sexual cycle regrowth).