Pathotype Diversity ofPhytophthora sojaein Eleven States in the United States

Race Ug99 of the fungus Puccinia graminis tritici that causes stem or black rust disease on wheat was first detected in Uganda in 1998. Seven races belonging to the Ug99 lineage are now known and have spread to various wheat-growing countries in the eastern African highlands, as well as Zimbabwe, South Africa, Sudan, Yemen, and Iran. Because of the susceptibility of 90% of the wheat varieties grown worldwide, the Ug99 group of races was recognized as a major threat to wheat production and food security. Its spread, either wind-mediated or human-aided, to other countries in Africa, Asia, and beyond is evident. Screening in Kenya and Ethiopia has identified a low frequency of resistant wheat varieties and breeding materials. Identification and transfer of new sources of race-specific resistance from various wheat relatives is underway to enhance the diversity of resistance. Although new Ug99-resistant varieties that yield more than current popular varieties are being released and promoted, major efforts are required to displace current Ug99 susceptible varieties with varieties that have diverse race-specific or durable resistance and mitigate the Ug99 threat. Copyright © 2011 by Annual Reviews. All rights reserved.

ABSTRACT Estimation of genotypic diversity is an important component of the analysis of the genetic structure of plant pathogen and microbial populations. Estimates of genotypic diversity are a function of both the number of genotypes observed in a sample (genotype richness) and the evenness of distribution of genotypes within the sample. Currently used measures of genotypic diversity have inherent problems that could lead to incorrect conclusions, particularly when diversity is low or sample sizes differ. The number of genotypes observed in a sample depends on the technique used to assay for genetic variation; each technique will affect the maximum number of genotypes that can be detected. We developed an approach to analysis of genotypic diversity in plant pathology that makes specific reference to the techniques used for identifying genotypes. Preferably, populations that are being compared should be very similar in sample size. In this case, the number of genotypes observed can be used directly for comparing richness. In most cases, sample sizes differ and use of the rarefaction method to calculate richness is more appropriate. In all cases, scaling either Stoddart and Taylor's G or Shannon and Wiener's H' by sample size should be avoided. Under those circumstances where it might be important to distinguish whether richness or evenness contribute more to diversity, a bootstrapping approach, where confidence intervals are calculated for indices of diversity and evenness, is recommended.