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Article

Origin of Pathogens of Grapevine Crown Gall Disease in Hokkaido in Japan as Characterized by Molecular Epidemiology of Allorhizobium vitis Strains

1
Western Region Agricultural Research Center (WARC) (Kinki, Chugoku, and Shikoku Regions), National Agriculture and Food Research Organization (NARO), 6-12-1 Nishifukatsu-cho, Fukuyama, Hiroshima 721-8514, Japan
2
Research Faculty of Agriculture, Hokkaido University, Kita 9 Nishi 9, Kita-ku, Sapporo 060-8589, Japan
3
Institute of Plant Protection, National Agriculture and Food Research Organization (NIPP), 2-1-18 Kannondai, Tsukuba, Ibaraki 721-8514, Japan
4
Graduate School of Environmental and Life Science, Okayama University, 1-1-1 Tsushima-naka, Kita-ku, Okayama 700-8530, Japan
5
Alson H. Smith, Jr. Agricultural Research and Extension Center, School of Plant and Environmental Sciences, Virginia Polytechnic Institute and State University, Winchester, VA 22602, USA
*
Author to whom correspondence should be addressed.
Life 2021, 11(11), 1265; https://doi.org/10.3390/life11111265
Received: 1 November 2021 / Revised: 16 November 2021 / Accepted: 17 November 2021 / Published: 19 November 2021
(This article belongs to the Collection State of the Art in Plant Science)

Abstract

:
Crown gall is a globally distributed and economically important disease of grapevine and other important crop plants. The causal agent of grapevine crown gall is tumorigenic Allorhizobium vitis (Ti) strains that harbor a tumor-inducing plasmid (pTi). The epidemic of grapevine crown gall has not been widely elucidated. In this study, we investigated the genetic diversity of 89 strains of Ti and nonpathogenic A. vitis to clarify their molecular epidemiology. Multi-locus sequence analysis (MLSA) of the partial nucleotide sequences of pyrG, recA, and rpoD was performed for molecular typing of A. vitis strains isolated from grapevines with crown gall symptoms grown in 30 different vineyards, five different countries, mainly in Japan, and seven genomic groups A to F were obtained. The results of MLSA and logistic regression indicated that the population of genetic group A was significantly related to a range of prefectures and that the epidemic of group A strains originated mainly in Hokkaido in Japan through soil infection. Moreover, group E strains could have been transported by infected nursery stocks. In conclusion, this study indicates that both soil infection and transporting of infected nursery stocks are working as infection source in Hokkaido.

1. Introduction

Grapevine (Vitis vinifera L.) crown gall is caused mainly by tumorigenic Allorhizobium vitis (syn. Rhizobium vitis (Ti), Agrobacterium vitis (Ti), A. tumefaciens biovar 3, where “Ti” means “tumorigenic” or “tumor-inducing”). In this paper, we follow the nomenclature for Allorhizobium species adopted by Mousavi et al. [1] to avoid confusion. This pathogen enters the grapevine through wounds due to a variety of causes, such as cold injury, mechanical damage, and grafting [2]. A. vitis (Ti) causes crown gall by transferring the T-DNA region of the tumor-inducing bacterial plasmid (Ti-plasmid) to the host cell, which subsequently integrates into the plant host genome [3,4,5]. The inserted T-DNA contains genes for biosynthesis of plant growth hormones [6,7]. Subsequent expression of T-DNA genes results in the overproduction of auxins and cytokinins, which eventually leads to abnormal gall formation in the host plant. DNA genes then produce tumor-specific compounds called opines, which serve as nutrients for A. vitis [7]. Invasion of vascular tissue by galls can result in vine death [8,9].
There is no effective method to control grapevine crown gall that can be used in commercial fields so far. Previously, we reported that a nonpathogenic A. vitis strain, VAR03-1, which was isolated from grapevine nursery stock in Japan, inhibited tumor formation in grapevine, rose, tomato, sunflower, and apple [10,11,12,13,14,15]. Moreover, we identified a nonpathogenic strain ARK-1 as a new antagonistic strain [16,17,18,19,20,21,22]. ARK-1 does not have the Ti-plasmid, so ARK-1 neither carries nor causes disease symptoms [16]. It provided better control against grapevine crown gall than VAR03-1 in field trials, and pretreatment of grapevine roots with ARK-1 cell suspension before planting in Ti-contaminated soil effectively suppressed gall formation in roots [16,17,20].
To apply biological control agents ARK-1 and/or VAR03-1 for management of crown gall in commercial vineyards effectively and efficiently, it is essential to know the epidemics of this disease. Crown gall infection takes place not only in vineyards, but also in nurseries [7]. With nursery production, symptoms develop at the site of wounds made by disbudding, at the base of rooted cuttings, and at grafts; however, in many cases, the infected plants remain symptomless until frost or other physical damage initiates the disease [7,23]. Therefore, Ti strains are often transmitted through the vegetative propagation of infected asymptomatic grapevines. When mother vines at a nursery are infected, the pathogen can be spread very quickly through a production and dissemination of nursery stocks. Recently, grapevine crown gall has often occurred in many vineyards in Japan, but it is unclear whether the major infection route of recent outbreaks is soil-borne or transmission of nursery stocks or both.
Thus, the objectives of this study are to classify the genetic diversity of 89 strains of A. vitis obtained from diseased grapevines by multi-locus sequence analysis (MLSA) of the partial nucleotide sequences of housekeeping genes and to clarify the molecular epidemiology of A. vitis strains collected in various locations in Japan and other four countries.

2. Materials and Methods

2.1. Multi-Locus Sequence Analysis (MLSA)

The A. vitis including Ti and nonpathogenic strains used in this study are listed in Table 1 and Supplementary Table S1. The sources of the strains and their relevant characteristics have been described in previous papers [16,22,24,25,26,27]. The 89 A. vitis strains were isolated from 19 varieties of grapevine cultivars (including three unknown cultivars), 30 different vineyard locations, 13 different prefectures or states, five different countries (Japan, USA, Iran, Australia, and Greece), and different decades (before 2000, 2000 to 2009, 2010 to 2019, and after 2020) (Table 1). The multiplex polymerase chain reaction (PCR) was performed using a mixture of two primer sets Ab3-F3 ⁄ Ab3-R4 and VCF3 ⁄ VCR3 to identify Ti and non-pathogenic strains of A. vitis according to the procedure of previous reports [11,12,28]. Our previous reports [24,28] have shown that the MLSA approach using three housekeeping genes pyrG (CTP synthetase), recA (recombinase A), and rpoD (RNA polymerase, sigma 70 factor) was useful to reveal the genetic diversity of A. vitis strains. In this study, we followed the experimental methods described in previous reports [24,29]. PCR amplifications of pyrG, recA, and rpoD genes were performed using primers ApyrF1 and ApyrR4, recAF1 and recAR2, and ArpoF1 and ArpoR2, respectively, as reported by Kawaguchi et al. [29] and Kawaguchi [24]. The PCR reactions were conducted using LifeECO ver3.0 (Nippon Genetics Co., Ltd., Tokyo, Japan). The partial nucleotide sequences of pyrG (849 bp), recA (465 bp), and rpoD (733 bp) of the 79 strains of Ti and ten nonpathogenic strains were directly determined from the PCR products using ApyrF1 and ApyrR4, recAF2 and recAR2, and ArpoF3 and ArpoR2 as sequencing primers, respectively (Kawaguchi et al. 2008b; Kawaguchi 2011). The data for the pyrG, recA, and rpoD sequences of 44 strains (accession numbers AB272143 to AB608986) were obtained in previous studies [24,29] and downloaded from the DDBJ database (http://getentry.ddbj.nig.ac.jp) (accessed on 18 October 2021), and those of 45 strains (accession number from LC629040 to LC635338) were newly obtained by sequence analysis using Big Dye Terminator v.3.1 cycle sequencing kit (Applied Biosystems, Foster City, CA, USA) in this study (Supplementary Table S1). The concatenated sequence data for pyrG, recA, and rpoD were aligned with MEGA X software (http://www.megasoftware.net/) (accessed on 18 October 2021) [30]. Maximum likelihood (ML), neighbor-joining (NJ), and minimum-evolution (ME) trees were constructed, and the strength of the internal branches from the resulting tree was tested by bootstrap analysis using 1000 replications.

2.2. Logistic Regression

The A. vitis strains were adequate to perform the statistical analysis due to the large sample size (89 strains) and because they were isolated from various cultivars, locations, countries, and isolation-year histories. In this study, we followed the experimental methods described in a previous report [30]. The A. vitis strains were binary-coded as either 1 (belonging to one specific genetic group) or 0 (belonging to the other genetic groups). The parameters, which were years, cultivars, vineyard locations, prefectures/states, or countries, and when/where A. vitis strains were isolated, were also coded using a binary scale (1 or 0) based on categorical numbers as well as genetic group (Supplementary Table S1).
The logistic regression model was defined as:
ln{P/(1 − P)} = α + β1·x1 + β2·x2 + … + βn·xn,,
where P is the proportion of A. vitis strains belonging to one specific genetic group, α is the y-intercept, and βn is the coefficient associated with predictor variable xn. According to previously described procedures [16,31], the R (ver. 3.6.1, R Development Core Team) package “glm” was used for calculation of logistic regression coefficients. The link function was the logit. The stepwise selection of the explanatory variables was based on the value of Akaike’s information criterion (AIC).

2.3. Odds Ratio

The relationship between the genetic group A and factors was calculated as an odds ratio (OR). An OR was defined as:
OR = {Pa/(1 − Pa)]/[Po/(1/Po)},
where Pa is the proportion of genetic group A strains isolated in Hokkaido and Po is the proportion of genetic group A strains isolated in other prefectures/states (except in Hokkaido). An OR is a measure of association between an exposure and an outcome. The OR represents the odds that an outcome will occur given a particular exposure, compared with the odds of the outcome occurring in the absence of that exposure. In the present study, a high OR indicates a high probability of appearance of genetic group A strains in Hokkaido, and a low OR indicates a low probability of them appearing.

3. Results

3.1. Multi-Locus Sequence Analysis (MLSA)

In the phylogenetic tree constructed by the ML method using the combined sequence data of three housekeeping genes (pyrG, recA, and rpoD), the 89 A. vitis strains separated into six clades (A to F) (Figure 1, Table 1). The 79 Ti strains used in this study comprised four genetic groups, and 35, 5, 18, and 16 strains belonged to genetic groups A, D, E, and F, respectively (Figure 1, Table 1). The ten nonpathogenic strains separated into two genetic groups, with seven and three strains belonging to genetic groups B and C, respectively (Figure 1, Table 1). The topology of the phylogenic tree based on the ML method perfectly coincided with that based on the NJ and ME methods, indicating that the divisions for the six clades in the phylogenic tree were valid (Figure 1, Figures S1 and S2). Five Ti strains (VAT20-8, MAFF211912, MAFF211914, ZEME15, and NCPPB1771) neither belonged to clade A to F and nor formed a clade based on ML, NJ, and ME methods (Figure 1, Figures S1 and S2, Table 1).

3.2. Logistic Regression

Genetic groups A, E, or F have more A. vitis strains (35, 18, and 16, respectively) than those B, C, and D (Figure 1, Table 1). The relationship with the records of isolation history, which were years, cultivars, vineyard locations, prefectures/states, and countries of the strains belonging to A, E, or F were investigated. In genetic group A, a logistic regression with a stepwise selection method based on AIC was conducted; two factors “Yoichi” (in the category “location of vineyards”) and “Hokkaido” (in “prefecture/state”) were selected as variables, but a variable of “Hokkaido” was only significantly correlated with the objective variable (p = 4.5 × 10−4, Table 2). In genetic groups E and F, no factor was significantly selected as a variable by a logistic regression with a stepwise selection method based on AIC (data not shown).

3.3. Odds Ratio

The odds ratio, which was obtained from the logistic regression used to predict the proportion of genetic group A strains isolated from grapevines in Hokkaido, was 10.52 (95% confidence interval = 3.68 to 30.68, p = 0.048). This result indicated that there was a significantly high probability of appearance of genetic group A strains in Hokkaido.

4. Discussion

In our previous report (Kawaguchi 2011), 35 Ti strains were separated into five (previous clades A to E) groups and six nonpathogenic strains into two (previous clades F and G) groups. However, previously determined clades D and E had two Ti strains MAFF211912 (IS552-1) and MAFF211914 (UK-2), respectively [24]. In this study, these two Ti strains were not grouped as clades because different nodes were obtained from ML, NJ, and ME phylogenetic trees and low bootstrap values (<50%, Figure 1, , Figures S1 and S2, Table 1). Moreover, a new genetic group D, which had five Ti strains isolated from V. vinifera cv. Kerner and cv. Zweigeltrebein in Urausu, Hokkaido, Japan, was revealed (Figure 1, Table 1). All Ti strains belonging to group D were isolated from two different cultivars in the same vineyard in 2020, but it was unclear where these strains came from because logistic regression could not be carried out using only five strains.
The genetic groups B and C in this study coincided with previous groups F and G, respectively (Figure 1) [24]. The group B strains, which were nonpathogenic strains including VAR03-1 and ARK-1, were antagonistic against Ti strains [10,11,12,13,14,15,16,17,18,19,20,21,22,29,32], but the nonpathogenic strains belonging to group C were not. This result suggests that the housekeeping genes pyrG, recA, and rpoD in A. vitis strains, which are antagonistic to grapevine crown gall, are genetically dissimilar from those of non-antagonistic strains.
The genetic groups A, E, and F in this study coincided with previous groups C, A, and B, respectively (Figure 1) [24]. Groups A, E, and F have many Ti strains derived from various districts of Japan (Figure 1, Table 1). Group E has 18 Ti strains isolated in Japan and Virginia, USA. Japanese strains in group E were isolated from various districts in nine different prefectures, indicating that Ti strains of group E could be widely distributed around Japan. It is still unclear that these strains originally lived in the soil in each district or were moved by circulation of infected nursery stocks. Although no factors were significantly selected as variables by a logistic regression, these strains were isolated in two different countries—Japan and the USA (Table 1). In Japan, there are large nursery production vineyards in several prefectures including group E, and nursery stocks of various grapevine cultivars are distributed from some prefectures to all areas of Japan. These results indicate that strains in group E could have been moved by circulation of infected nursery stocks.
Group F has 16 Ti strains isolated in Japan alone. These strains were also isolated from various districts in six different prefectures, indicating that Ti strains in group F could be as widely distributed around Japan as group E. Many strains in group F (12/16) were isolated from V. labrusca × V. vinifera cv. Kyoho, which is grown in all over Japan because it is very common as a table grape in Japan, and some strains in group E were also isolated from cv. Kyoho (Table 1). However, various cultivators were not significantly selected as variables by a logistic regression. The small sample size (n = 16) might be insufficient for logistic regression. In our future studies, more strains are needed to certify the relationship between genetic groups and cultivar varieties.
Group A has 35 Ti strains (including with type strain NCPPB3554T) isolated in Japan, USA, Australia, and Greece, indicating that Ti strains of group A could be widely distributed around many countries. In the results of the stepwise regression analysis focusing on the group A strains, only the variable “Hokkaido” was selected as a significantly correlated parameter explaining the group A population. According to the OR results, there is also a significantly high probability of the appearance of group A strains in Hokkaido. These results indicate that group A population is significantly related to Hokkaido. Growers usually buy nursery stocks from grapevine nursery production vineyards in prefectures other than Hokkaido because nursery stocks are rarely produced in Hokkaido. In this study, however, group A strains were never isolated in these three nursery production prefectures (Table 1). Thus, these findings indicate that the group A strains would have been already disseminated in Hokkaido before 2000 and that crown gall could have been mainly caused by group A strains not via circulation of infected nursery stocks but by soil infection at each vineyard after 2000.
In this study, some Ti strains collected in various locations in other four countries except Japan, some Ti strains (including the type-strain NCPPB3554T) isolated from USA, Australia, and Greece belonged to genetic group A, indicating that group A might be one of the major genetic groups around the world. On the other hand, two Ti strains ACME15 and HNVR15 collected in USA were belonging to genetic group F, which had also 17 Ti strains collected in Japan. To verify whether the group F is a specific group be distributed between Japan and Virginia, an additional study of investigation of more varieties of A. vitis Ti strains collected in various countries is needed.
Five Ti strains (VAT20-8, MAFF211912, MAFF211914, ZEME15, and NCPPB1771) did not belong to genetic groups A to F using sequences data of pyrG, recA, and rpoD (Figure 1, Table 1). These five strains might be formed a clade by other housekeeping genes instead of pyrG, recA, and rpoD. Moreover, the authors should try with other genes such as additional housekeeping genes RNA genes for further confirmation of MLSA.
In general, freeze injuries provide sites for initiating crown gall [7,33]. Severe winter weather, as well as recent trends in extreme temperature fluctuations during late winter and early spring, tend to damage grapevine trunks, which allows the entry of A. vitis (Ti) [7]. Hokkaido is a cold region, and vines are also exposed to freeze injuries. Grapevine crown gall has been increasing in Hokkaido since 1990 [34,35]. Recently, grapevines in many vineyards were damaged by crown gall disease in Hokkaido, and many Ti strains belonging into three genetic groups (A, D, and E) have been isolated after 2020 (Figure 1, Table 1). Our results indicate that the occurrence of crown gall in Hokkaido could be due to both soil infection caused by group A strains and entry of infected nursery stocks by group E strains. If biological control agents ARK-1 and/or VAR03-1 are applied to control crown gall in Hokkaido, the roots of pathogen-free nursery stocks should be treated with ARK-1 and/or VAR03-1 (e.g., dipping into cell suspension of antagonists) before planting to prevent soil infection. To produce pathogen-free nursery stocks, moreover, antagonistic strains should be applied in nurseries in prefectures other than Hokkaido.
The genetic diversity of A. vitis (Ti) isolated in some countries has previously been reported [22,36,37]. The results from cluster analysis based on repetitive sequence-based (rep)-PCR and inter-simple sequence-repeat (ISSR)-PCR data concurrently showed a potential genomic diversity that separates the Virginia strains from the Japanese strains using a total of 12 strains [22]. However, results from MLSA showed some Virginia strains and Japanese strains formed the same cluster (strain LCCH15 belonging to group A, DCCS15B to group B, ACME15 and HNVR15 to group E) (Figure 1, Table 1). Kuzmanović et al. [36] reported that genetic varieties of A. vitis (Ti) of 29 strains isolated in European countries and the USA were analyzed by random amplified polymorphic DNA (RAPD) PCR, and sequence analysis of housekeeping genes of dnaK, gyrB, and recA. RAPD divided them into 17 groups, but a phylogenetic tree based on recA gene divided them into four clades [36]. It seems that PCR-based analysis tends to divide into more groups than partial sequence analysis. However, concurrently amplifying many PCR fragments of different lengths is sometimes unreliable and strains should be compared among using results of the band patterns obtained from concurrent PCR reactions and in the same gel. Thus, genetic performing diversity analysis using PCR and gel electrophoresis for many strains isolated in several countries is sometimes difficult. On the other hand, although the results would not reflect the whole genome information, partial sequence analysis is robust and could be used on the deposited sequence data in the public DNA databases (e.g., DDBJ/EMBL/GenBank), even strains conserved in each country. Recently, whole genome sequences of three A. vitis strains used in this study (MAFF211676 (former name VAT03-9), VAR03-1, and VAR06-30) are already available [38,39,40]. If complete genome sequence data of A. vitis strains obtained by a next generation sequencing system are accumulated, assessment of genetic diversity using them could become easy. By knowing the diversity of A. vitis, we can now select representative strains to determine the effectiveness of disease control strategies. For example, the effectiveness of biological controls can be determined for a diverse group of strains that are representative of the different genetic groups. Our group has already reported that the nonpathogenic A. vitis strain ARK-1 inhibited formation of galls caused by representative Ti strains in group A, E, and F in this study, which coincided with previous groups C, A, and B, respectively [15,18,22]. We plan to test group D and non-clustered Ti strains in biological control experiments.

5. Conclusions

The results of MLSA of the partial nucleotide sequences of pyrG, recA, and rpoD and of logistic regression analyses indicated that the population of genetic group A was significantly related to a range of prefectures and that the epidemic of group A strains could have originated in the Hokkaido region mainly through soil infection. Moreover, group E strains could have been moved by circulation of infected nursery stocks. In conclusion, this study indicated that both soil infection and transporting of infected nursery stock were working as infection sources in Hokkaido. This study will be applicable to future studies of the molecular epidemiology of grapevine crown gall occurring in several countries.

Supplementary Materials

The following are available online at https://www.mdpi.com/article/10.3390/life11111265/s1, Figure S1: Phylogenetic tree of Rhizobium vitis strains based on the neighbor-joining (NJ) method using the concatenated sequence data for pyrG, recA, and rpoD, Figure S2: Phylogenetic tree of Allorhizobium vitis strains based on the minimum-evolution (ME) method using the concatenated sequence data for pyrG, recA, and rpoD. Bootstrap values from 1000 samplings are indicated, Table S1: List of each category and sequence information.

Author Contributions

Conceptualization, A.K., T.S., Y.N. and M.N.; methodology, A.K. and M.N.; investigation, A.K., T.S., S.O. and Y.M.; formal analysis, A.K.; writing—original draft preparation, A.K. and Y.N.; writing—review and editing, A.K. and Y.N.; validation, A.K. and Y.N.; supervision, A.K.; data curation, A.K. and M.N.; resources, A.K., T.S. and M.N. All authors have read and agreed to the published version of the manuscript.

Funding

This research was supported by Japan Society for the Promotion of Science, KAKENHI Grant 20K20572 from the Ministry of Education, Culture, Sports, Science and Technology of Japan to A.K. and Y.N.

Institutional Review Board Statement

Not applicable.

Informed Consent Statement

Not applicable.

Data Availability Statement

The data presented in this study are available on request from the corresponding author.

Acknowledgments

The authors are grateful to Shoya KItabayashi (WARC/NARO) for his technical support.

Conflicts of Interest

The authors declare no competing financial interests.

References

  1. Mousavi, S.A.; Willems, A.; Nesme, X.; de Lajudie, P.; Lindstrom, K. Revised phylogeny of Rhizobiaceae: Proposal of the delineation of Pararhizobium gen. nov., and 13 new species combinations. Syst. Appl. Microbiol. 2015, 38, 84–90. [Google Scholar] [CrossRef]
  2. Burr, T.J.; Otten, L. Crown gall of grape: Biology and disease management. Annu. Rev. Phytopathol. 1999, 37, 53–80. [Google Scholar] [CrossRef]
  3. Chilton, M.D.; Drummond, M.H.; Merlo, D.J.; Sciaky, D.; Montoya, A.L.; Gordon, M.P.; Nester, W. Stable incorporation of plasmid DNA into higher plant cells: The molecular basis of crown gall tumorigenesis. Cell 1997, 11, 263–271. [Google Scholar] [CrossRef]
  4. Gelvin, S.B. Traversing the cell: Agrobacterium T-DNA’s journey to the host genome. Front. Plant Sci. 2012, 3, 52. [Google Scholar] [CrossRef] [PubMed][Green Version]
  5. Pitzschke, A.; Hirt, H. New insights into an old story: Agrobacterium-induced tumor formation in plants by plant transformation. EMBO J. 2010, 29, 1021–1032. [Google Scholar] [CrossRef]
  6. Morris, R. Genes specifying auxin and cytokinin biosynthesis in phytopathogens. Annu. Rev. Plant Physiol. 1986, 37, 509–538. [Google Scholar] [CrossRef]
  7. Burr, T.J.; Bazzi, C.; Süle, S.; Otten, L. Crown gall of grape: Biology of Agrobacterium vitis and the development of disease control strategies. Plant Dis. 1998, 82, 1288–1297. [Google Scholar] [CrossRef][Green Version]
  8. Wächter, R.; Langhans, M.; Aloni, R.; Götz, S.; Weilmünster, A.; Koops, A.; Temguia, L.; Mistrik, I.; Pavlovkin, J.; Rascher, U.; et al. Vascularization, high-volume solution flow, and localized roles for enzymes of sucrose metabolism during tumorigenesis by Agrobacterium tumefaciens. Plant Physiol. 2003, 133, 1024–1037. [Google Scholar] [CrossRef][Green Version]
  9. Gohlke, J.; Deeken, R. Plant responses to Agrobacterium tumefaciens and crown gall development. Front. Plant Sci. 2014, 5, 155. [Google Scholar] [CrossRef][Green Version]
  10. Kawaguchi, A. Studies on the diagnosis and biological control of grapevine crown gall and phylogenetic analysis of tumorigenic Rhizobium vitis. J. Gen. Plant Pathol. 2009, 75, 462–463. [Google Scholar] [CrossRef]
  11. Kawaguchi, A.; Inoue, K.; Nasu, H. Inhibition of crown gall formation by Agrobacterium radiobacter biovar 3 strains isolated from grapevine. J. Gen. Plant Pathol. 2005, 71, 422–430. [Google Scholar] [CrossRef]
  12. Kawaguchi, A.; Inoue, K.; Nasu, H. Biological control of grapevine crown gall by nonpathogenic Agrobacterium vitis strain VAR03-1. J. Gen. Plant Pathol. 2007, 73, 133–138. [Google Scholar] [CrossRef]
  13. Kawaguchi, A.; Inoue, K.; Ichinose, Y. Biological control of crown gall of grapevine, rose, and tomato by nonpathogenic Agrobacterium vitis strain VAR03-1. Phytopathology 2008, 98, 1218–1225. [Google Scholar] [CrossRef] [PubMed][Green Version]
  14. Kawaguchi, A.; Kondo, K.; Inoue, K. Biological control of apple crown gall by nonpathogenic Rhizobium vitis strain VAR03-1. J. Gen. Plant Pathol. 2012, 78, 287–293. [Google Scholar] [CrossRef]
  15. Saito, K.; Watanabe, M.; Matsui, H.; Yamamoto, M.; Ichinose, Y.; Toyoda, K.; Kawaguchi, A.; Noutoshi, Y. Characterization of the suppressive effects of the biological control strain VAR03-1 of Rhizobium vitis on the virulence of tumorigenic R. vitis. J. Gen. Plant Pathol. 2018, 84, 58–64. [Google Scholar] [CrossRef]
  16. Kawaguchi, A.; Inoue, K. New antagonistic strains of non-pathogenic Agrobacterium vitis to control grapevine crown gall. J. Phytopathol. 2012, 160, 509–518. [Google Scholar] [CrossRef]
  17. Kawaguchi, A. Biological control of crown gall on grapevine and root colonization by nonpathogenic Rhizobium vitis strain ARK-1. Microbes Environ. 2013, 28, 306–311. [Google Scholar] [CrossRef][Green Version]
  18. Kawaguchi, A. Reduction in pathogen populations at grapevine wound sites is associated with the mechanism underlying the biological control of crown gall by Rhizobium vitis strain ARK-1. Microbes Environ. 2014, 29, 296–302. [Google Scholar] [CrossRef] [PubMed][Green Version]
  19. Kawaguchi, A. Biological control agent Agrobacterium vitis strain ARK-1 suppresses expression of the virD2 and virE2 genes in tumorigenic A. vitis. Eur. J. Plant Pathol. 2015, 143, 789–799. [Google Scholar] [CrossRef]
  20. Kawaguchi, A.; Inoue, K.; Tanina, K.; Nita, M. Biological control for grapevine crown gall using nonpathogenic Rhizobium vitis strain ARK-1. Proc. Jpn. Acad. Ser. B Phys. Biol. Sci. 2017, 93, 547–560. [Google Scholar] [CrossRef][Green Version]
  21. Kawaguchi, A.; Nita, M.; Ishii, T.; Watanabe, M.; Noutoshi, Y. Biological control agent Rhizobium (=Agrobacterium) vitis strain ARK-1 suppresses expression of the essential and non-essential vir genes of tumorigenic R. vitis. BMC Res. Notes. 2019, 12, 1–6. [Google Scholar] [CrossRef][Green Version]
  22. Wong, A.T.; Kawaguchi, A.; Nita, M. Efficacy of a biological control agent Rhizobium vitis ARK-1 against Virginia R. vitis isolates, and relative relationship among Japanese and Virginia R. vitis isolates. Crop Prot. 2021, 146, 105685. [Google Scholar] [CrossRef]
  23. Burr, T.J.; Katz, B.H. Grapevine cuttings as potential sites of survival and means of dissemination of Agrobacterium tumefaciens. Plant Dis. 1984, 68, 976–978. [Google Scholar] [CrossRef]
  24. Kawaguchi, A. Genetic diversity of Rhizobium vitis strains in Japan based on multilocus sequence analysis of pyrG, recA and rpoD. J. Gen. Plant Pathol. 2011, 77, 299–303. [Google Scholar] [CrossRef]
  25. Sawada, H.; Ieki, H. Phenotypic characteristics of the genus Agrobacterium. Annu. Phytopathol. Soc. Jpn. 1992, 58, 37–45. [Google Scholar] [CrossRef]
  26. Sawada, H.; Ieki, H.; Takikawa, Y. Identification of grapevine crown gall bacteria isolated in Japan. Annu. Phytopathol. Soc. Jpn. 1990, 56, 199–206. [Google Scholar] [CrossRef][Green Version]
  27. Sawada, H.; Imada, J.; Ieki, H. Serogroups of Agrobacterium tumefaciens biovar 3 determined using somatic antigens. Annu. Phytopathol. Soc. Jpn. 1992, 58, 52–57. [Google Scholar] [CrossRef][Green Version]
  28. Kawaguchi, A.; Sawada, H.; Inoue, K.; Nasu, H. Multiplex PCR for the identification of Agrobacterium biover 3 strainsI. J. Gen. Plant Pathol. 2005, 71, 54–59. [Google Scholar] [CrossRef]
  29. Kawaguchi, A.; Sawada, H.; Ichinose, Y. Phylogenetic and serological analyses reveal genetic diversity of Agrobacterium vitis strains in Japan. Plant Pathol. 2008, 57, 747–753. [Google Scholar] [CrossRef]
  30. Kumar, S.; Stecher, G.; Li, M.; Knyaz, C.; Tamura, K. MEGA X: Molecular evolutionary genetics analysis across computing platforms. Mol. Biol. Evol. 2018, 35, 1547. [Google Scholar] [CrossRef]
  31. Kawaguchi, A.; Tanina, K.; Takehara, T. Molecular epidemiology of Pseudomonas syringae pv. syringae strains isolated from barley and wheat infected with bacterial black node. J. Gen. Plant Pathol. 2017, 83, 162–168. [Google Scholar] [CrossRef]
  32. Kawaguchi, A.; Inoue, K.; Tanina, K. Evaluation of the nonpathogenic Agrobacterium vitis strain ARK-1 for crown gall control in diverse plant species. Plant Dis. 2015, 99, 409–414. [Google Scholar] [CrossRef][Green Version]
  33. Stover, E.W.; Swarz, H.J.; Burr, T.J. Eondophytic Agrobacterium in crown gall-resistant and susceptible Vitis genetypes. Vitis 1997, 36, 21–26. [Google Scholar]
  34. Misawa, T. A field survey of crown gall of grapevine (Vitis vinifera) caused by Agrobacterium vitis in Hokkaido. Annu. Rept. Plant Prot. N. Jpn. 2004, 55, 82–83. (In Japanese) [Google Scholar]
  35. Misawa, T. Infection and disease development of crown gall in pathogen-free grapevine seedlings replanted in infested vineyard. Annu. Rept. Plant Prot. N. Jpn. 2004, 55, 84–86. (In Japanese) [Google Scholar]
  36. Gan, H.M.; Szegedi, E.; Fersi, R.; Chebil, S.; Kovács, L.; Kawaguchi, A.; Hudson, A.O.; Burr, T.J.; Savka, M.A. Insight into the microbial co-occurrence and diversity of 73 grapevine (Vitis vinifera) crown galls collected across the northern hemisphere. Front. Microbiol. 2019, 13, 1896. [Google Scholar] [CrossRef][Green Version]
  37. Kuzmanović, N.; Biondi, E.; Bertaccini, A.; Obradović, A. Genetic relatedness and recombination analysis of Allorhizobium vitis strains associated with grapevine crown gall outbreaks in Europe. J. Appl. Microbiol. 2015, 119, 786–796. [Google Scholar] [CrossRef] [PubMed][Green Version]
  38. Noutoshi, Y.; Toyoda, A.; Ishii, T.; Saito, K.; Watanabe, M.; Kawaguchi, A. Complete genome sequence data of tumorigenic Rhizobium vitis strain VAT03-9, a causal agent of grapevine crown gall disease. Mol. Plant Microbe Interact. 2020, 33, 1280–1282. [Google Scholar] [CrossRef]
  39. Noutoshi, Y.; Toyoda, A.; Ishii, T.; Saito, K.; Watanabe, M.; Kawaguchi, A. Complete genome sequence data of nonpathogenic and nonantagonistic strain of Rhizobium vitis VAR06-30 isolated from grapevine rhizosphere. Mol. Plant Microbe Interact. 2020, 33, 1283–1285. [Google Scholar] [CrossRef]
  40. Noutoshi, Y.; Toyoda, A.; Ishii, T.; Saito, K.; Watanabe, M.; Kawaguchi, A. Complete genome sequence data of nonpathogenic Rhizobium vitis strain VAT03-1, a biological control agent for grapevine crown gall disease. Mol. Plant Microbe Interact. 2020, 33, 1451–1453. [Google Scholar] [CrossRef]
Figure 1. Phylogenetic tree of Allorhizobium vitis strains based on the maximum likelihood (ML) method using concatenated sequence data for pyrG, recA, and rpoD. Bootstrap values from 1000 samplings are indicated. The bar represents a phylogenetic distance of 1%.
Figure 1. Phylogenetic tree of Allorhizobium vitis strains based on the maximum likelihood (ML) method using concatenated sequence data for pyrG, recA, and rpoD. Bootstrap values from 1000 samplings are indicated. The bar represents a phylogenetic distance of 1%.
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Table 1. List of Allorhizobium vitis strains analyzed.
Table 1. List of Allorhizobium vitis strains analyzed.
Strains (Former Name)Ti or N aCultivar bLocation of VineyardPrefcture/StateCountryIsolated YearGenetic Group c
MAFF663001 (G-Ag-27)TiKyohoMatsumotoNaganoJapanBefore 2000E
MAFF212292 (YGAt32-3)TiGarnet AYamanashiYamanashiJapanBefore 2000E
MAFF663017 (G-Ag-4)TiKyohoShimaneShimaneJapanBefore 2000E
MAFF663004 (G-Ag-9)TiKyohoYokotaShimaneJapanBefore 2000E
MAFF211676 (VAT03-9)TiSeto GiantsAsaguchiOkayamaJapan2000 to 2009E
MAFF211944 (G-Ag-62)TiKyohoSagaeYamagataJapanBefore 2000E
MAFF211889 (G-Ag-52)TiKyohoHanamakiIwateJapanBefore 2000E
At-90-23TiKyohoShimaneShimaneJapanBefore 2000E
FZ-3-1TiZweigeltrebeFuranoHokkaidoJapan2000 to 2009E
VAT20-30TiPinot NoirChitoseHokkaidoJapanAfter 2020E
VAT21-9TiZweigeltrebeYoichiHokkaidoJapanAfter 2020E
VAT21-10TiKernerYoichiHokkaidoJapanAfter 2020E
VAT21-14TiCambell EarlyYoichiHokkaidoJapanAfter 2020E
VAT21-15TiCambell EarlyYoichiHokkaidoJapanAfter 2020E
ACME15TiMerlotWinchesterVirginiaUSA2010 to 2019E
HNVR15TiViognierGordonsvilleVirginiaUSA2010 to 2019E
MAFF211909 (FM-3-2)TiMüller-ThurgauFuranoHokkaidoJapan2000 to 2009E
MAFF211913 (UM-1)TiMüller-ThurgauUrausuHokkaidoJapan2000 to 2009E
MAFF211301 (At-5)TiKyohoShimaneShimaneJapanBefore 2000F
MAFF211674 (A5-1)TiKyohoYokoteAkitaJapan2000 to 2009F
MAFF211675 (A5-2)TiKyohoYokoteAkitaJapan2000 to 2009F
MAFF211677 (A5-4)TiKyohoYokoteAkitaJapan2000 to 2009F
A5-7TiKyohoYokoteAkitaJapan2000 to 2009F
MAFF211302 (A5-8)TiKyohoYokoteAkitaJapan2000 to 2009F
VAT06-11TiAurora BlackUkanOkayamaJapan2000 to 2009F
MAFF663006 (G-Ag-19)TiRizamatShiojiriNaganoJapanBefore 2000F
MAFF663007 (G-Ag-21)TiKyohoShiojiriNaganoJapanBefore 2000F
MAFF663008 (G-Ag-23)TiKyohoShiojiriNaganoJapanBefore 2000F
9-1-5TiKyohoHanamakiAkitaJapan2000 to 2009F
9-3-1TiKyohoHanamakiAkitaJapan2000 to 2009F
9-3-5TiKyohoHanamakiAkitaJapan2000 to 2009F
MAFF211943 (G-Ag-61)TiBeniizuSannoheAomoriJapanBefore 2000F
MAFF211949 (G-Ag-67)TiKyohoYokoteAkitaJapanBefore 2000F
MAFF211910 (ISP-2)TiPinot NoirIkedaHokkaidoJapan2000 to 2009F
MAFF212306 (VAR03-1)NSeto GiantsOkayamaOkayamaJapan2000 to 2009B
ARK-1NPioneOkayamaOkayamaJapan2000 to 2009B
MAFF212307 (VAR03-3)NSeto GiantsOkayamaOkayamaJapan2000 to 2009B
MAFF212308 (VAR03-4)NSeto GiantsOkayamaOkayamaJapan2000 to 2009B
ARK-2NPioneOkayamaOkayamaJapan2000 to 2009B
ARK-3NPioneOkayamaOkayamaJapan2000 to 2009B
MAFF212313 (VAR7-1)NSeto GiantsOkayamaOkayamaJapan2000 to 2009B
VAR06-30NAurora BlackUkanOkayamaJapan2000 to 2009C
VAR06-31NAurora BlackUkanOkayamaJapan2000 to 2009C
DCCS15BNCabernet SauvignonEtlanVirginiaUSA2010 to 2019C
NCPPB3554TTiUnknownUnknownUnknownAustraliaBefore 2000A
DCCS15TiCabernet SauvignonEtlanVirginiaUSA2010 to 2019A
MAFF211942 (G-Ag-60)TiCambell EarlyNanbuAomoriJapan2000 to 2009A
MAFF211918 (YHsM-2)TiMüller-ThurgauYoichiHokkaidoJapan2000 to 2009A
VAT07-1TiAurora BlackAsaguchiOkayamaJapan2000 to 2009A
NCPPB2562TiUnknownUnknownUnknownGreeceBefore 2000A
MAFF211919 (YMK-1)TiKernerYoichiHokkaidoJapan2000 to 2009A
MAFF211920 (NKZ-2)TiZweigeltrebeNikiHokkaidoJapan2000 to 2009A
MAFF211908 (FK-2-2)TiKernerFuranoHokkaidoJapan2000 to 2009A
MAFF211915 (MM-2)TiMüller-ThurgauMikasaHokkaidoJapan2000 to 2009A
LCCH15TiChardonnayCharlottesvilleVirginiaUSA2010 to 2019A
VAT20-1TiZweigeltrebeUrausuHokkaidoJapanAfter 2020A
VAT20-2TiZweigeltrebeUrausuHokkaidoJapanAfter 2020A
VAT20-3TiKernerUrausuHokkaidoJapanAfter 2020A
VAT21-4TiKernerUrausuHokkaidoJapanAfter 2020A
VAT21-5TiKernerUrausuHokkaidoJapanAfter 2020A
VAT20-11TiZweigeltrebeYoichiHokkaidoJapanAfter 2020A
VAT20-12TiKernerYoichiHokkaidoJapanAfter 2020A
VAT20-13TiZweigeltrebeYoichiHokkaidoJapanAfter 2020A
VAT20-21TiKernerNisekoHokkaidoJapanAfter 2020A
VAT20-22TiKernerNisekoHokkaidoJapanAfter 2020A
VAT20-23TiKernerNisekoHokkaidoJapanAfter 2020A
VAT20-24TiKernerNisekoHokkaidoJapanAfter 2020A
VAT20-25TiKernerNisekoHokkaidoJapanAfter 2020A
VAT20-26TiKernerNisekoHokkaidoJapanAfter 2020A
VAT20-31TiPinot NoirChitoseHokkaidoJapanAfter 2020A
VAT20-32TiPinot NoirChitoseHokkaidoJapanAfter 2020A
VAT21-1TiZweigeltrebeYoichiHokkaidoJapanAfter 2020A
VAT21-2TiZweigeltrebeYoichiHokkaidoJapanAfter 2020A
VAT21-3TiZweigeltrebeYoichiHokkaidoJapanAfter 2020A
VAT21-4TiZweigeltrebeYoichiHokkaidoJapanAfter 2020A
VAT21-5TiZweigeltrebeYoichiHokkaidoJapanAfter 2020A
VAT21-6TiZweigeltrebeYoichiHokkaidoJapanAfter 2020A
VAT21-7TiZweigeltrebeYoichiHokkaidoJapanAfter 2020A
VAT21-8TiZweigeltrebeYoichiHokkaidoJapanAfter 2020A
VAT20-7TiZweigeltrebeUrausuHokkaidoJapanAfter 2020D
VAT20-9TiZweigeltrebeUrausuHokkaidoJapanAfter 2020D
VAT21-11TiZweigeltrebeUrausuHokkaidoJapanAfter 2020D
VAT21-12TiZweigeltrebeUrausuHokkaidoJapanAfter 2020D
VAT21-13TiKernerUrausuHokkaidoJapanAfter 2020D
VAT20-8TiZweigeltrebeUrausuHokkaidoJapanAfter 2020nc
ZEME15TiMerlotHamiltonVirginiaUSA2010 to 2019nc
MAFF211912 (IS552-1)TiPinot NoirIkedaHokkaidoJapan2000 to 2009nc
MAFF211914 (UK-2)TiKernerUrausuHokkaidoJapan2000 to 2009nc
NCPPB1771TiUnknownUnknownUnknownIranBefore 2000nc
a Ti: Tumorigenic. N: Nonpathogenic. b indicates cultivar name of grapevine; Vitis labrusca × V. vinifera cv. Kyoho; V. vinifera cv. Garnet A; V. vinifera cv. Seto Giants; V. labrusca × V. vinifera cv. Cambell Early; V. vinifera × V. labrusca cv. Pione; V. vinifera cv. Kerner; V. vinifera cv. Zweigeltrebe; V. vinifera cv. Müller-Thurgau; V. vinifera cv. Rizamat; V. vinifera × V. labrusca cv. Seibel5279; Vitis sp. cv. Aurora Black; Vitis sp. cv. Beniizu; V. vinifera cv. Merlot; V. vinifera cv. Cabernet Sauvignon; V. vinifera cv. Chardonnay; V. vinifera cv. Viognier; V. vinifera cv. Pinot Noir. c nc: not clustered.
Table 2. Parameter estimates a for the logistic regression model used to predict the proportion of A. vitis strains in genetic group A.
Table 2. Parameter estimates a for the logistic regression model used to predict the proportion of A. vitis strains in genetic group A.
VariableParameter EstimateStandard Errorz Valuep Value b
CategoryFactor
Location of vineyardYoichi0.9710.6831.4220.155
Prefecture/stateHokkaido2.0270.5773.5124.5 × 10−4
y-Intercept −1.8190.440−4.1333.6 × 10−5
a AIC (Akaike’s information criterion) = 99.19. b p values < 0.05 indicate significance.
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Kawaguchi, A.; Sone, T.; Ochi, S.; Matsushita, Y.; Noutoshi, Y.; Nita, M. Origin of Pathogens of Grapevine Crown Gall Disease in Hokkaido in Japan as Characterized by Molecular Epidemiology of Allorhizobium vitis Strains. Life 2021, 11, 1265. https://doi.org/10.3390/life11111265

AMA Style

Kawaguchi A, Sone T, Ochi S, Matsushita Y, Noutoshi Y, Nita M. Origin of Pathogens of Grapevine Crown Gall Disease in Hokkaido in Japan as Characterized by Molecular Epidemiology of Allorhizobium vitis Strains. Life. 2021; 11(11):1265. https://doi.org/10.3390/life11111265

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Kawaguchi, Akira, Teruo Sone, Sunao Ochi, Yosuke Matsushita, Yoshiteru Noutoshi, and Mizuho Nita. 2021. "Origin of Pathogens of Grapevine Crown Gall Disease in Hokkaido in Japan as Characterized by Molecular Epidemiology of Allorhizobium vitis Strains" Life 11, no. 11: 1265. https://doi.org/10.3390/life11111265

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