Philip B. Hamm

Whole genome characterization of Potato virus Y isolates collected in the western USA and their comparison to isolates from Europe and Canada

Summary.Potato virus Y (PVY) is a serious potato pathogen that affects potato seed and commercial production crops. In recent decades, novel PVY strains have been described that cause necrotic symptoms on tobacco foliage and/or potato tubers. The major PVY strains that affect potato include PVYO and PVYN, which have distinct serotypes that can be differentiated by immunoassay. Other economically important strain variants are derived from recombination events, including variants that cause tuber necrotic symptoms (PVYNTN) and PVYO serotypes that cause tobacco veinal necrosis (PVYN-W, PVYN:O). Although the PVYNTN and PVYN-W variants were first reported in Europe, apparently similar strains have been appearing in North America. Confirmation of the existence of these recombinant strains in North America is important, as is whether they spread from a common source or were derived by independent recombination. Whole genome sequencing can be used to positively identify strain variants and begin to address the issue of origins. Symptomology, serology, RT-PCR, and partial sequencing of the coat protein region were used to identify isolates of the PVYNTN, PVYN, PVYNA-N, and PVYN:O for whole-genome sequencing. Sequencing confirmed the presence of PVYNTN and PVYN isolates that were >99% identical to European sequences deposited in GenBank in the 1990’s. Sequences of the PVYNA-N and PVYN:O types were 99.0% and 99.5% identical to known sequences, respectively. There was no indication that recombinant strains PVYNTN or PVYN:O had different parental origins than recombinant strains previously sequenced. This is the first confirmation by whole-genome sequencing that “European”-type strain variants of PVYN and PVYNTN are present in North America, and the first reported full-length sequence of a tuber necrotic isolate of PVYN:O.

Microbial populations, fungal species diversity and plant pathogen levels in field plots of potato plants expressing theBacillus thuringiensis var.tenebrionis endotoxin

The environmental release of genetically engineered (transgenic) plants may be accompanied by ecological effects including changes in the plant-associated microflora. A field release of transgnic potato plants that produce the insecticidal endotoxin ofBacillus thuringiensis var.tenebrionis (Btt) was monitored for changes in total bacterial and fungal populations, fungal species diversity and abundance, and plant pathogen levels. The microflora on three phenological stages of leaves (green, yellow and brown) were compared over the growing season (sample days 0, 21, 42, 63 and 98) for transgenic potato plants, commercial Russet Burbank potato plants treated with systemic insecticide (Di-Syston) and commercial Russet Burbank potato plants treated with microbialBtt (M-Trak). In addition, plant and soil assays were performed to assess disease incidence ofFusarium spp.,Pythium spp.,Verticillium dahliae, potato leaf roll virus (PLRV) and potato virus Y (PVY). Few significant differences in phylloplane microflora among the plant types were observed and none of the differences were persisent. Total bacterial populations on brown leaves on sample day 21 and on green leaves on sample day 42 were significantly higher on the transgenic potato plants. Total fungal populations on gree leaves on sample day 63 were significantly different among the three plant types; lowest levels were on the commerical potato plants treated with systemic insecticide and highest levels were on the commercial potato plants treated with microbialBtt. Differences in fungal species assemblages and diversity were correlated with sampling dates, but relatively consistent among treatments.Alternaria alternata, a common saprophyte on leaves and in soil and leaf litter, was the most commonly isolated fungus species for all the plant treatments. Rhizosphere populations of the soilborne pathogensPythium spp.,Fusarium spp. andV. dahliae did not differ between the transgenic potato plants and the commercial potato plants treated with systemic insecticide. The incidence of tuber infection at the end of the growing season by the plant pathogenV. dahliae was highest for the transgenic potato plants but this difference was related to longer viability of the transgenic potato plants. This difference in longevity between the transgenic potato plants and the commercial + systemic insecticide potato plants also made comparison of the incidence of PVY and PLRV problematic. Our results indicate that under field conditions the microflora of transgenicBtt-producing potato plants differed minimally from that of chemically and microbially treated commerical potato plants.

Relative resistances of potato clones in response to new and old populations of Phytophthora infestans

Potato cultivars and clones were evaluated in Washington and New York in 1993 and 1994 for field reaction to recent immigrant genotypes of Phytophthora infestans. Plants were visually evaluated at regular intervals for percent blighted foliage. Relative cultivar susceptibilities were compared by ranking the values obtained for areas under disease progress curves (AUDPC) of each line tested. Cultivar rankings in response to infection by new, immigrant isolates of P infestans were nearly identical to rankings obtained previously with isolates prevalent prior to 1990. The cultivars Norchip, Hilite, Russet Norkotah, Goldrush, Superior, and Shepody were more susceptible than Russet Burbank. White Rose and Ranger Russet were similar in susceptibility to Russet Burbank. C008-3008-1, ND-2438-7R, Kennebec, and Elba were less susceptible than Russet Burbank. Comparisons of the number of blighted tubers at harvest showed that foliage and tuber susceptibilities differed among cultivars. Shepody and Russet Norkotah tubers were most susceptible to tuber blight of those tested.

Aggressiveness of isolates of Phytophthora infestans from the Columbia Basin of Washington and Oregon

ABSTRACT The aggressiveness of 22 isolates of Phytophthora infestans collected from naturally infected potato plants in the Columbia Basin of Washington and Oregon was determined on detached potato leaflets at 18 degrees C in an incubator. Selected isolates were evaluated on whole plants in a greenhouse. Aggressiveness was measured by using the area under the lesion expansion curve (AULEC), incubation period, latent period, sporulation capacity, and lesion size on detached leaflets and the area under the disease progress curve and sporulation capacity on whole plants. The detached-leaflet assay was useful in that a large number of isolates were tested, several components of aggressiveness were studied, and significant differences were found among isolates. Significant variation for components of aggressiveness was found within and among isolates classified according to genotype. Significant interactions among isolates and cultivars were found for some components of aggressiveness, so results were pooled according to cultivar. On average, US-8 and US-11 isolates had higher AULEC scores, indicating aggressiveness higher than that of US-7, US-6, and US-1 genotypes. One US-8 genotype isolate had a higher standardized sporulation capacity than isolates of the other genotypes. US-6 genotype isolates were the least aggressive group, as indicated by low AULEC, sporulation capacity, and lesion size values. The replacement of the US-1 genotype by the US-8 genotype in the Columbia Basin may be partially explained by the increased aggressiveness of US-8 isolates. Additionally, potato growers may need to shorten intervals between fungicide applications and begin applications earlier.

Potato Late Blight in the Columbia Basin: An Economic Analysis of the 1995 Epidemic

The cost of managing late blight in potatoes during a severe epidemic caused by new, aggressive strains of Phytophthora infestans in the Columbia Basin of Washington and Oregon in 1995 was documented. The mean number of fungicide applications per field varied from 5.1 to 6.3 for early- and midseason potatoes, and from 8.2 to 12.3 for late-season potatoes in the northern and southern Columbia Basin, respectively. In 1994, a year when late blight was not severe, the mean number of fungicide applications per field made to early- and midseason potatoes was 2.0; whereas late-season potatoes received a mean of 2.5 applications. The mean per acre cost of individual fungicides applied varied from

Characterization of the Phytophthora infestans Population in the Columbia Basin of Oregon and Washington from 1992 to 1995.

4.90 for copper hydroxide to

The Occurrence of PVYO, PVYN, and PVYN:O Strains of Potato virus Y in Certified Potato Seed Lot Trials in Washington and Oregon

36.00 for propamocarb + chlorothalonil. Total per acre expenses (application costs plus fungicide material) for protecting the crop from late blight during 1995 ranged from

Coat protein transgenic resistance to watermelon mosaic and zucchini yellows mosaic virus in squash and cantaloupe.

106.77 to

First Report of the Necrotic Strain of Potato virus Y (PVYN) on Potatoes in the Northwestern United States

110.08 for early and midseason potatoes in different regions of the Columbia Basin and from

Cost of Fungicides Used to Manage Potato Late Blight in the Columbia Basin: 1996 to 1998

149.30 to