Genetic Variability in the Potato Pathogen Colletotrichum coccodes as Determined by Amplified Fragment Length Polymorphism and Vegetative Compatibility Group Analyses

ABSTRACT Amplified fragment length polymorphism (AFLP) using three primer sets was used to characterize 211 Colletotrichum coccodes isolates from North America, 112 of which were assigned to six vegetative compatibility groups (VCGs) using nitrate nonutilizing (nit) mutants. These isolates clustered into five corresponding groups by unweighted pairgroup method with arithmetic means-based cluster analysis of AFLP banding patterns. Isolates of C. coccodes belonging to NA-VCG1 and NA-VCG3 were closely related, as were isolates belonging to NA-VCG2 and NA-VCG5. Based on bootstrap analysis of AFLP data, the two isolates originally assigned to NA-VCG4 clustered with isolates belonging to NA-VCG2 and NA-VCG5. C. coccodes isolates that clustered with two isolates belonging to NA-VCG6 were the most diverged from other groups, including seven isolates collected from hosts other than potato. As opposed to the bootstrap analysis, a quadratic discriminant analysis (QDA) of AFLP data correctly categorized the two isolates of NA-VCG4. Furthermore, in isolates where VCG determinations had been made, this model correctly classified isolates of all VCGs. QDA classifications were identical to those made by the bootstrap analysis, with the exception of VCG4. Overall, classifications made by the QDA model were strongly correlated (r = 0.970, P < 0.001) to the VCGs assigned by traditional methods. All 99 C. coccodes isolates evaluated only by AFLP also were subjected to QDA, leading to the assignment of a presumptive VCG for each isolate. No isolates of VCG4 or VCG6 were identified by QDA within this population. Symptoms of black dot developed in plants inoculated with isolates collected from both potato and non-potato hosts. However, total yield was not significantly reduced by infection with non-potato isolates. The lack of any additional groups identified by AFLP analysis may be an indicator of a limited level of genetic variation among North American C. coccodes isolates. AFLP is a much more efficient technique for subspecific characterization in C. coccodes than VCG analysis utilizing nit mutants and will provide an effective means by which the population biology of this pathogen can be further investigated worldwide.     

Untangling the positive and negative effects of shrubs on herbaceous vegetation in drylands

Woody vegetation, as an ecosystem engineer, can modulate the landscape such that the levels of resources in its vicinity undergo positive and negative changes as far as the herbaceous vegetation is concerned. To better understand how these processes play out in a semi-arid ecosystem, we examined resource modulation by woody vegetation, and the response of herbaceous vegetation to that modulation, at a fine spatial scale. Experimental manipulations were employed to separate the positive and negative effects of water, light and seed dispersal in determining herbaceous species density and biomass in three patch types within and adjacent to the shrub (core, periphery and open). We synthesized our results into a multilayered landscape diversity (MLLD) model. Woody vegetation creates distinct multilayered resource patches at its core and periphery which do not correspond to the dichotomous structural pattern of shrub canopy versus intershrub background. The combined effect of these multilayered resource patches had higher herbaceous species density (8.2 vs. 4.0 species 400?cm^?2) and herbaceous biomass (5.4 vs. 1.0?g 400?cm^?2) in the periphery than in the core (3-yr averages). The periphery??s net positive effects are due to enhancement of soil properties (water infiltration depth of 11.1?cm at periphery vs. 8.1?cm at core), while the core??s net negative effects are due to modulation of seed (seed abundance per seed trap of 44.2 at periphery vs. 3.0 at core) and light availability (PAR transmittance of 41.9?% at periphery vs. 16.5?% at core) by the shrub canopy. Thus, when examined at this fine spatial resolution, woody vegetation has both net positive and net negative effects on herbaceous vegetation. Analysis of our results by means of the MLLD model emphasizes the importance of examining the landscape at the spatial scale of the modulated resources and of recognizing different patch types and their differing effects on herbaceous vegetation.