Alternaria spp. form a heterogeneous group of saprophytic and plant-pathogenic fungi widespread in temperate and tropical regions. However, the relationship between evolutionary processes and genetic diversity with epidemics is unknown for several plant-pathogenic Alternaria spp. The interaction of Alternaria solani populations with potato and tomato plants is an interesting case study for addressing questions related to molecular evolution of an asexual fungus. Gene genealogies based on the coalescent process were used to infer evolutionary processes that shape the A. solani population. Sequences of the rDNA internal transcribed spacer (ITS) region and the genes which encode the allergenic protein alt a 1 (Alt a 1) and glyceraldehyde-3-phosphate dehydrogenase (Gpd) were used to estimate haplotype and nucleotide diversity as well as for the coalescent analyses. The highest number of parsimony informative sites (n = 14), nucleotide diversity (0.007), and the average number of nucleotide differences (3.20) were obtained for Alt a 1. Although the highest number of haplotypes (n = 7) was generated for ITS, haplotype diversity was the lowest (0.148) for this region. Recombination was not detected. Subdivision was inferred from populations associated with hosts but there was no evidence of geographic subdivision, and gene flow is occurring among subpopulations. In the analysis of the Alt a 1, balancing selection and population expansion or purifying selection could have occurred in A. solani subpopulations associated with potato and tomato plants, respectively. There is strong evidence that the subpopulation of A. solani that causes early blight in potato is genetically distinct from the subpopulation that causes early blight in tomato. The population of A. solani is clonal, and gene flow and mutation are the main evolutionary processes shaping its genetic structure.

Understanding the genetic structure of the population of Alternaria solani (AS) is an important component of epidemiological studies of early blight, a severe disease that affects potato (Po) and tomato (To) worldwide. Up to 150 isolates obtained from both hosts were analysed with RAPD and AFLP markers to estimate the amount and distribution of genetic variability of AS in Brazil. Using RAPD, gene diversity (h = 0.20) and scaled indices of diversity of Shannon (H¢ = 0.66) and Stoddart and TaylorÕs (G = 0.31) for the Po population were higher than those of the To (h = 0.07, H¢ = 0.34, G = 0.17). For AFLP, the statistics for the Po (h = 0.17, H¢ = 0.86, G = 0.49) and To (h = 0.17, H¢ = 0.85, G = 0.36) populations were similar. For each RAPD and AFLP locus, the allele frequency for the overall population ranged from 0.006 to 0.988, and 0.007 to 0.993, respectively. Genetic differentiation was high (G ST = 0.41 and h = 0.59) and moderately high (G ST = 0.23 and h = 0.37) when estimated with RAPD and AFLP, respectively. Based on cluster analyses, there was strong evidence of association of pathogen haplotypes with host species. The null hypothesis of random association of alleles was rejected in the analysis of both RAPD (I A = 13.1, P < 0.001) and AFLP (I A = 2.2, P < 0.001) markers. The average number of migrants was estimated to be around one and two individuals per generation, using RAPD and AFLP, respectively. There was no correlation between genetic distance and geographical origin of AS haplotypes for RAPD (r = )0.07, P = 0.84) and AFLP (r = )0.03, P = 0.70). The AS population is clonal with high genetic variability, and there is genetic differentiation between the populations that affect To and Po.

Stromatinia cepivora (= Sclerotium cepivorum), causal agent of the white rot, is a major soilborne pathogen that attacks garlic (Allium sativum L.), onion (Allium cepa L.), and other plants of the Alliacea family. The pathogen is difficult to control because it survives as sclerotia for decades in soil. White rot can cause total crop losses when sclerotia levels are high in soil and environmental conditions favorable for disease development. Aspects of the biology and epidemiology of S. cepivora have been investigated extensively worldwide. These studies have provided essential information to develop different control strategies. Currently, white rot management is based primarily on the application of fungicides and biocontrol agents to protect the crop against infection, and the use of natural and synthetic germination stimulants of sclerotia, soil fumigation and solarization to reduce sclerotia density in soils. In Brazil, few studies have been conducted to understand white rot epidemiology and effectiveness of control measures currently available, despite the disease being an economically important in garlic and onion production regions for many years. This review provides updated information on the biology of S. cepivora, and epidemiology and control of white rot to identify important knowledge gaps and future research directions for white rot in Brazil.