Early blight (EB) and leaf blight are two destructive diseases of tomato in North Carolina (NC), caused by Alternaria linariae and A. alternata, respectively. During the last decade, EB caused by A. solani has increased in potato-producing areas in Wisconsin (WI). We collected 152 isolates of three Alternaria spp. associated with tomato and potato in NC and WI and used the gene genealogical approach to compare the genetic relationships among them. Two nuclear genes: the glyceraldehyde-3-phosphate dehydrogenase (GPDH), RNA polymerase second largest subunit (RPB2), and the rDNA internal transcribed spacer (ITS) region of these isolates were sequenced. Besides, sequences of the GPDH locus from international isolates described in previous studies were included for comparison purposes. A set of single nucleotide polymorphisms was assembled to identify locus-specific and species-specific haplotypes. Nucleotide diversity varied among gene sequences and species analyzed. For example, the estimates of nucleotide diversity and Watterson’s theta were higher in A. alternata than in A. linariae and A. solani. There was little or no polymorphisms in the ITS sequences and thus restricted haplotype placement. The RPB2 sequences were less informative to detect haplotype diversity in A. linariae and A. solani, yet six haplotypes were detected in A. alternata. The GPDH sequences enabled strongly supported phylogenetic inferences with the highest haplotype diversity and belonged to five haplotypes (AaH1 to AaH5), which consisted of only A. alternata from NC. However, 13 haplotypes were identified within and among A. linariae and A. solani sequences. Among them, six (AsAlH1 to AsAlH6) were identical to previously reported haplotypes in global samples and the remaining were new haplotypes. The most divergent haplotypes were AaH1, AsAlH2/AsAlH3, and AsAlH4 and consisted exclusively of A. alternata, A. linariae, and A. solani, respectively. Neutrality tests suggested an excess of mutations and population expansion, and selection may play an important role in nucleotide diversity of Alternaria spp.

Tomatoes (Solanum lycopersicum L.) are a valuable horticultural crop that are grown and consumed worldwide. Optimal production is hindered by several factors, among which Verticillium dahliae, the cause of Verticillium wilt, is considered a major biological constraint in temperate production regions. V. dahliae is difficult to mitigate because it is a vascular pathogen, has a broad host range and worldwide distribution, and can persist in soil for years. Understanding pathogen virulence and genetic diversity, host resistance, and plant-pathogen interactions could ultimately inform the development of integrated strategies to manage the disease. In recent years, considerable research has focused on providing new insights into these processes, as well as the development and integration of environment-friendly management approaches. Here, we discuss the current knowledge on the race and population structure of V. dahliae, including pathogenicity factors, host genes, proteins, enzymes involved in defense, and the emergent management strategies and future research directions for managing Verticillium wilt in tomatoes.

Host resistance is one of the few strategies available to combat the soil borne pathogenic fungus Verticillium dahliae. Understanding pathogen diversity in populations is key to successfully deploying host resistance. In this study the genomes of 18 V. dahliae isolates of races 1 (n = 2), 2 (n = 4), and 3 (n = 12) from Japan, California, and North Carolina were sequenced and mapped to the reference genome of JR2 (from tomato). The genomes were analyzed for phylogenetic and pathogen specific signatures to classify specific strains or genes for future research. Four highly clonal lineages/groups were discovered, including a lineage unique to North Carolina isolates, which had the rare MAT1-1 mating type. No evidence for recombination between isolates of different mating types was observed, even in isolates of different mating types discovered in the same field. By mapping these 18 isolates genomes to the JR2 reference genome, 193 unique candidate effectors were found using SignalP and EffectorP. Within these effectors, 144 highly conserved effectors, 42 mutable effectors (truncated or present in some isolates but absent in others), and 7 effectors present in highly variable regions of the chromosomes were discovered. Of the 144 core effectors, 21 were highly conserved in V. alfalfae and V. longisporum, 7 of which have no known function. Within the non-core effectors 30 contained large numbers of non-synonymous mutations, while 15 of them contained indels, frameshift mutations, or were present on highly variable regions of the chromosome. Two of these highly variable region effectors (HVREs) were only present in race 2 isolates, but not in race 3 isolates. The race 1 effector Ave1 was also present in a highly variable region. These data may suggest that these highly variable regions are enriched in race determinant genes, consistent with the two-speed genome hypothesis.

In recent years, greenhouse-grown tomato ( Solanum lycopersicum ) plants showing vascular wilt and yellowing symptoms have been observed between 2015 and 2018 in North Carolina (NC) and considered as an emerging threat to profitability. In total, 38 putative isolates were collected from symptomatic tomatoes in 12 grower greenhouses and characterized to infer pathogenic and genomic diversity, and mating-type ( MAT ) idiomorphs distribution. Morphology and polymerase chain reaction (PCR) markers confirmed that all isolates were Fusarium oxysporum f. sp. lycopersici (FOL) and most of them were race 3. Virulence analysis on four different tomato cultivars revealed that virulence among isolates, resistance in tomato cultivars, and the interaction between the isolates and cultivars differed significantly ( P < 0.001). Cultivar ‘Happy Root’ ( I-1, I-2 , and I-3 genes for resistance) was highly resistant to FOL isolates tested. We sequenced and examined for the presence of 15 pathogenicity genes from different classes ( Fmk1 , Fow1 , Ftf1 , Orx1 , Pda1 , PelA , PelD, Pep1 , Pep2 , eIF-3 , Rho1 , Scd1 , Snf1 , Ste12 , and Sge1 ), and 14 S ecreted I n X ylem ( SIX ) genes to use as genetic markers to identify and differentiate pathogenic isolates of FOL. Sequence data analysis showed that five pathogenicity genes, Fmk1, PelA , Rho1 , Sge1 , and Ste12 were present in all isolates while Fow1 , Ftf1 , Orx1 , Peda1 , Pep1 , eIF-3 , Scd1 , and Snf1 genes were dispersed among isolates. Two genes, Pep2 and PelD , were absent in all isolates. Of the 14 SIX genes assessed, SIX1, SIX3, SIX5, SIX6, SIX7, SIX8, SIX12 , and SIX14 were identified in most isolates while the remaining SIX genes varied among isolates. All isolates harbored one of the two mating-type ( MAT-1 or MAT-2 ) idiomorphs, but not both. The SIX4 gene was present only in race 1 isolates. Diversity assessments based on sequences of the effector SIX3 - and the translation elongati...

Grafting high yielding tomato cultivars (Solanum lycopersicum L.) onto vigorous rootstocks can increase marketable yields, but questions remain regarding optimal cultural and growing conditions such as pinching and plant spacing. This study addressed some of the dynamics between grafted plants and cultural practices. Two scions, ‘Tasti-Lee’ (TL) and ‘Mountain Fresh Plus’ (MFP) were grafted onto each of three rootstocks, ‘Beaufort’, ‘Arnold’, and ‘Shield’. Plants were pinched (removal of main shoot to induce both axillary shoots to grow) or non-pinched, and spaced at 56 or 61 cm. All 32 grafted treatments were compared to the grower standard: non-grafted TL and MFP spaced at 46 cm, which were non-pinched. Fruit quality traits including soluble solids content, pH, lycopene concentration, and titratable acidity were recorded for fruit harvested from tomatoes grafted onto ‘Arnold’, ‘Beaufort’, ‘Shield’ and non-grafted TL. The overall effect of grafting TL and MFP onto vigorous rootstocks ‘Arnold’, ‘Beaufort’, and ‘Fortamino’ increased marketable yields per hectare by 24-35% compared to non-grafted grower standards. The rootstock ‘Shield’ did not significantly increase yields with either scion. TL had a more positive response to grafting than MFP. ‘Arnold’, ‘Beaufort’, and ‘Fortamino’ significantly increased TL fruit size, but the fruit size results were not as significantly impacted by graft treatments for MFP. Plants spaced at 56 compared to 61 cm generated similar yields. Pinched plants significantly increased yields over non-pinched plants by 15% in 2018 but did not impact yield in 2017. No consistent difference was observed between pinched and non-pinched plants with regard to fruit size, only plants grafted with ‘Shield’ benefited significantly from being pinched. Soluble solids content, pH, total lycopene concentration, and titratable acidity differed slightly between grafted and non-grafted plants but was unlikely to positively or negatively affect overall perception of fruit quality in tomatoes. A partial budget analysis revealed that grafting with ‘Arnold’ or ‘Beaufort’ consistently increased profits in this low-disease field.