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Clarke 2019
Clarke 2019
1094/PHYTO-09-18-0368-R
Bacteriology
ABSTRACT
Common scab of potato is a superficial tuber disease caused by and identified cultivars that were resistant or susceptible to all three species
Streptomyces species that produce the phytotoxin thaxtomin. Because and cultivars that had widely varying resistance dependent on the pathogen
common scab development is highly dependent on the effects of this species. Overall lower virulence was associated with the strain that produces
single toxin, the current operating paradigm in common scab pathology is the least thaxtomin. This result showcases several cultivars of potato that are
that a potato cultivar resistant to one strain of the common scab pathogen is expected to be resistant to the majority of common scab populations but also
resistant to all strains. However, cultivar resistance to common scab disease highlights that many potato cultivars are resistant to only specific species of
identified in one breeding program is often not durable when tested in other the pathogen. These results demonstrate that extension specialists and
potato breeding programs across the United States. We infected 55 potato growers must consider their local population of the common scab pathogen
cultivar populations with three distinct species of the common scab pathogen when selecting which cultivars to plant for common scab resistance.
Common scab disease of potato is characterized by raised or isolated from diseased tubers, followed by S. stelliscabiei and
pitted scabby lesions on tuber surfaces that reduce the marketability Streptomyces sp. IdahoX (Wanner 2009).
of tubers but not total yield (Braun et al. 2017a). The etiological The one known commonality of all Streptomyces strains that cause
agents of common scab are several soilborne species of Streptomy- common scab is that they produce the phytotoxin thaxtomin A (Kers
ces. There are more than 800 named species of Streptomyces et al. 2005; Loria et al. 2008). The thaxtomin A biosynthetic gene
(bacterio.net 2019). Most Streptomyces species isolated from soil cluster is located on a mobile pathogenicity island (Bignell et al.
are harmless saprophytes. Several species are known to promote 2010; Kers et al. 2005). Horizontal gene transfer of this pathogenicity
plant growth or are intensively studied because of their value as island was potentially the driver for the emergence of several lineages
antibiotic-producing organisms (Chater 2016; Sousa and Olivares of Streptomyces common scab pathogens (Bukhalid et al. 2002;
2016). Only a few species of Streptomyces include major plant Zhang et al. 2016). Conjugation of the thaxtomin biosynthetic cluster
pathogens (Francis et al. 2010). Thus, one must assess subspecies- can convert nonpathogenic Streptomyces species into pathogens
level diversity to understand the ecological impact of local field (Bukhalid and Loria 1997; Healy et al. 2000; Zhang et al. 2016).
population of Streptomyces species. The species known to cause Deletion of genes in the thaxtomin biosynthetic cluster or associated
common scab on potato in North America are S. stelliscabiei, regulatory elements from thaxtomin-producing Streptomyces path-
S. scabiei, S. europaeiscabiei, Streptomyces sp. IdahoX, S. acidiscabiei, ogens eliminates pathogenicity (Joshi et al. 2007; Kers et al. 2004).
and S. turgidiscabiei (Braun et al. 2017a; Goyer and Beaulieu 1997; The genes in the thaxtomin A biosynthetic cluster are used as a marker
Wanner 2006, 2009; Zhou et al. 2017). In addition, S. ipomoea causes for pathogenicity in Streptomyces strains (Qu et al. 2008). Identifying
common scab of sweet potato (Clark and Matthews 1987) and potatoes resistant to the effects of thaxtomin is considered necessary
S. reticuliscabiei causes the related but less severe netted scab for developing common scab-resistant cultivars. Indeed, resistance to
disease (Bouchek-Mechiche et al. 2000). In North America, thaxtomin has been used as a selective agent in somatic selection of
S. scabiei and S. europaeiscabiei are the species most commonly scab-resistant plantlets (Wilson et al. 2009, 2010). It is also generally
accepted that a potato cultivar resistant to one strain of common scab-
causing Streptomyces is likely to be resistant to most other strains as
well because all strains primarily rely on the same virulence factor.
†Corresponding author: C. R. Clarke; [email protected] Several potato cultivars are resistant to common scab (Braun et al.
2017a), and markers for common scab resistance were identified in a
Funding: This study was supported by U.S. Department of Agriculture-Agricultural Research
Service Current Research Information System (CRIS) project number 8042-21000-283. breeding population (Braun et al. 2017b). However, common scab
resistance is lacking from many elite cultivars. Resistance to common
L. A. Wanner is deceased. scab is often screened during cultivar development in many of the
*The e-Xtra logo stands for “electronic extra” and indicates that two supplementary potato breeding programs in the United States. However, clones that
figures and six supplementary tables are published online. exhibit resistance to common scab in one program often are
The author(s) declare no conflict of interest. susceptible to the disease when they are released for testing by other
breeding programs. This instability of resistance may be driven by
This article is in the public domain and not copyrightable. It may be freely
environmental variables or differences in the pathogen populations.
reprinted with customary crediting of the source. The American Phytopathological Here we test the hypothesis that defining a potato cultivar as resistant
Society, 2019. or susceptible to common scab is pathogen specific.
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MATERIALS AND METHODS Infection of potato with Streptomyces pathogens in
greenhouse pot assays. Streptomyces inoculum was prepared
Potato cultivars/clones and Streptomyces pathogens used by growing strains on standard yeast malt extract (YME; 4 g of yeast
in this study. All potato cultivars tested in this study are listed in extract, 10 g of malt extract, and 4 g of dextrose per liter of ddH2O)
Table 1. The three species of common scab-causing Streptomyces tested plates at 28°C for 14 days, suspending spores in sterile H2O, and
in this study were Streptomyces sp. IdahoX strain ID01-12C, S. scabiei then using this spore suspension to inoculate 30 ml of liquid YME.
strain ME01-11h, and S. stelliscabiei strain NY02-1C or NY02-3A. Spore suspensions in YME were then grown at 28°C with 190 rpm
These strains were originally isolated from common scab-infected shaking. After 3 days of incubation, bacterial cells were pelleted
tubers in Idaho, Maine, and New York, respectively (Wanner 2006, 2009). through centrifugation at 4,000 rpm at 4°C for 15 min, and cells
were resuspended in sterile H2O to a final concentration of 0.15 g/ml.
TABLE 1. Potato cultivars and clones tested in this work Two milliliters of this cell suspension was then inoculated into
Cultivar/clonea Testingb individual bags of approximately 45 g of vermiculite that had
previously been autoclaved three times at 3-day intervals. The
AF4013-3 Year 2 only
AF4157-6 Year 2 only
vermiculite bags were then incubated at 28°C for 14 days with
Alturas Both years kneading of the bags to mix the inoculum every 2 to 3 days. After
Atlantic Both years 11 days, a small quantity of vermiculite from each bag was sampled,
B2727-2 Year 2 only weighed, and vortexed in sterile H2O to release bacteria. A dilution
Bannock Year 2 only series was plated onto YME plates and the number of CFU per gram
Blazer Both years of vermiculite was calculated 3 days later. All bags were then
BNC-182-5 Year 2 only
Burbank Both years
standardized to approximately 1 × 108 CFU/g vermiculite as the
Burbank (ID) Both years; no data for final inoculum.
at least one pathogen Cold-stored tubers were rinsed with H2O, dipped in 1.5% sodium
Canela Both years hypochlorite for 2 min, and then rinsed with H2O again. Tubers were
Chieftan Year 2 only then stored in the dark at room temperature for 3 to 6 days before
Chippewa Year 2 only planting. At planting, tubers were cut to include at least two sprouts
Classic Year 2 only
Dakota Pearl Both years
on each seed piece. Pots were prepared by mixing 1:1 sand/potting
Dark Red Norland Both years mix (Sungrow professional growth mix; Sun Gro, Seba Beach, AB,
Green Mountain Year 2 only Canada) with Streptomyces-containing vermiculite inoculum,
Dakota Crisp Year 2 only added to an 8-inch pot, and then burying the seed pieces 1 to 2
GoldRush Both years inches under the soil line. Three replicate pots were included for
Ivory Crisp Year 2 only each pathogen–cultivar combination in each year.
Katahdin Year 2 only
Kennebec Year 2 only
Scoring of severity of common scab disease and
Megachip Year 1 only statistical analysis. Daughter tubers were collected and rinsed
Modoc Year 2 only 14 weeks after planting. All tubers were defined as market grade or
Norkotah Year 2 only below market grade based on the type of lesion present on the tuber
Norkotah-3 Both years and the total coverage of the tuber in lesions using the criteria
Norkotah-8 Both years defined in Figure 1. Our data analyses were based on the proportion
Norkotah-112 Year 2 only
Norkotah-278 Year 2 only
of below market grade tubers. To test for interactions and main
Norkotah-296 Both years
Norkotah (ID) Year 1 only
Norkotah (ND) Year 1 only
Norland Both years; no data for
at least one pathogen
NY150 Year 2 only
NYE106-4 Year 2 only
Pike Both years
Premier Both years
Ranger Both years
Ranger Amisk Year 2 only; no data for
at least one pathogen
Reba Year 2 only
Red LaSoda Both years
Red Maria Year 2 only
Rio Grande Both years
Shepody Both years
Silverton Year 1 only
Snowden Both years
Superior Both years
Superior (NY) Year 2 only
Umatilla Year 2 only
Western Year 2 only
Yukon Gem Year 2 only
Yukon Gold Year 2 only; no data for
at least one pathogen
Yukon Gold (ID) Year 1 only; no data for
at least one pathogen
Yukon Gold (ME) Year 1 only
Yukon Gold (WI) Year 1 only; no data for
at least one pathogen
a ID = Idaho, ND = North Dakota, NY = New York, ME = Maine, and WI = Fig. 1. Examples of common scab lesion types on Chippewa tubers. Per-
Wisconsin. centages indicate the maximum percent surface coverage of each lesion to be
b Year 1 = 2012, year 2 = 2013. considered “market grade” in the scab scoring system.
1546 PHYTOPATHOLOGY
based on the presence of multiple amplicons. Relative txtAB (Cai et al. 2016) was used, because this transformation both removes
expression was calculated for each biological group across all the dependence of standard deviations on their means and allows
technical replicates using Bio-Rad CFX Maestro software. txtAB for testing in a parametric framework because the transformed data
expression data required transformation prior to analysis because will satisfy normality assumptions. Analysis was conducted using
standard deviations (calculated from technical replicates) were analysis of variance (ANOVA) (base R) followed by tests of linear
clearly a function of the mean. A rank-inverse normal transformation contrasts of interest (using the emmeans R package). No P value
Fig. 2. Susceptibility of potato cultivars to strain Streptomyces sp. IdahoX strain ID01-12C. Black points represent the mean estimate of the percentage of tubers
that were classified as below market grade for each cultivar after infection of Streptomyces sp. IdahoX strain ID01-12C. Shaded gray bars represent the 95%
confidence interval. For cultivars with no indicated 95% confidence, all tubers were ranked as either market grade or below market grade uniformly, so the variance
was zero (no confidence interval possible).
Fig. 3. Susceptibility of potato cultivars to Streptomyces scabiei strain ME01-11h. Black points represent the mean estimate of the percentage of tubers that were
classified as below market grade for each cultivar after infection of S. scabiei strain ME01-11h. Shaded gray bars represent the 95% confidence interval. For
cultivars with no indicated 95% confidence, all tubers were ranked as either market grade or below market grade uniformly, so the variance was zero (no
confidence interval possible).
1548 PHYTOPATHOLOGY
RESULTS scab: Streptomyces sp. IdahoX strain ID01-12C, S. scabiei strain
ME01-11h, and S. stelliscabiei strain NY02-1C or NY02-3A. An
The susceptibility of 55 potato cultivar populations to additional two cultivars were challenged with Streptomyces sp.
three species of Streptomyces that cause common scab. IdahoX strain ID01-12C and S. scabiei strain ME01-11h only. Four
Thirty-eight distinct potato cultivars were individually challenged cultivars (Yukon Gold, Russet Norkotah, Superior, and Russet
with three different species of Streptomyces that cause common Burbank) were tested with tubers sourced from different geographic
Fig. 4. Susceptibility of potato cultivars to Streptomyces stelliscabiei strain NY02-1C and NY02-3A. Black points represent the mean estimate of the percentage of
tubers that were classified as below market grade for each cultivar after infection of S. stelliscabiei strain NY02-1C (year 1) or NY02-3A (year 2). Shaded gray bars
represent the 95% confidence interval. For cultivars with no indicated 95% confidence, all tubers were ranked as either market grade or below market grade
uniformly, so the variance was zero (no confidence interval possible).
Fig. 5. Relationship of mean severity and consistency (standard deviation) of common scab disease caused by the three tested pathogen species for each potato
cultivar. Each cultivar is plotted by the mean and standard deviation estimates of the percentage of tubers that are below market grade across all tested pathogens.
1550 PHYTOPATHOLOGY
pots (Table 2, last column), representing tuber-to-tuber variability of S. stelliscabiei being the least aggressive pathogen. In contrast,
within a plant (Table 2). the S. stelliscabiei strains were highly virulent on most of the tested
For each pathogen, the response of the tested cultivars ranged clones of the Norkotah cultivar, whereas Norkotah was, in general,
from fully resistant (defined as all tubers being market grade) to resistant to Streptomyces sp. IdahoX strain ID01-12C.
fully susceptible (defined as all tubers being below market grade) Resistance to common scab is pathogen specific for
with numerous intermediate phenotypes (Figs. 2, 3, and 4; the error several potato cultivars. To better understand the extent to
bars represent 95% confidence intervals on the proportions, which common scab resistance is pathogen specific, we plotted the
calculated on the logit scale and back-transformed to the original mean against the standard deviation estimates of the percentage of
scale). S. scabiei strain ME01-11h was the most aggressive tubers that were below market grade for all 55 cultivar populations
pathogen (Fig. 3) and S. stelliscabiei strains NY02-1C and NY02- across all tested pathogens (Fig. 5). Cultivars with low standard
3A were the least aggressive (Fig. 4) for the majority of cultivars. deviation across all of the pathogens can more consistently be
For most cultivars, resistance or susceptibility to one pathogenic defined as susceptible or resistant to common scab. Cultivars with
species was a good predictor of resistance or susceptibility to the notable discrepancies in predicted susceptibility to different
other pathogens. However, there are several notable exceptions. The pathogen species (discussed above) and a high variance estimate,
cultivars Yukon Gold, Reba, NY150 (now Upstate Abundance), and such as Yukon Gold, Reba, and NY150 (Fig. 5; Supplementary
Katahdin were resistant to the S. stelliscabiei strains but highly Table S3), are hypothesized to have pathogen-specific resistance or
susceptible to Streptomyces sp. IdahoX strain ID01-12C and susceptibility determinants. Although all four tested pathogens had
S. scabiei strain ME01-11h. This is in line with the general trend similar variances across all tested potato cultivars (Table 3), a
Fig. 6. Streptomyces stelliscabiei strain NY02-3a produces significantly less thaxtomin than S. scabiei strain ME01-11h and Streptomyces sp. IdahoX strain ID01-
12c. A, Thaxtomin present in cell-free extract after 7 days of growth of the indicated strain in oat bran broth (OBB) medium. B, Amount of thaxtomin after column
purification of thaxtomin from cell-free extracts from the indicated strain for 7 days in OBB medium. C, Relative expression of txtAB in the three pathogens grown
in either OBB (thaxtomin-inducing) or yeast malt extract (YME; not thaxtomin-inducing) medium. Data represent the average of three biological and four
technical replicates. Error bars are the standard error. Asterisks indicate a significant difference in group means using one degree of freedom linear contrasts
following an analysis of variance that included the main effects of medium (P < 0.001), pathogen (P = 0.011), and their interaction (P < 0.001). The full analysis is
shown in Supplementary Table S6. txtAB gene expression was normalized to two reference genes (see the Materials and Methods). ns = not significant.
1552 PHYTOPATHOLOGY
DISCUSSION LITERATURE CITED
1554 PHYTOPATHOLOGY