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Biochemical and molecular characterization of Alternaria alternata isolates highly resistant to procymidone from broccoli and cabbage

Abstract

Alternaria alternata, a causal agent of leaf blights and spots on a wide range of hosts, has a high risk of developing resistance to fungicides. Procymidone, a dicarboximide fungicide (DCF), has been widely used in controlling Alternaria leaf blights in China for decades. However, the resistance of A. alternata against DCFs has rarely been reported from crucifer plants. A total of 198 A. alternata isolates were collected from commercial fields of broccoli and cabbage during 2018–2019, and their sensitivities to procymidone were determined. Biochemical and molecular characteristics were subsequently compared between the high-level procymidone-resistant (ProHR) and procymidone-sensitive (ProS) isolates, and also between ProHR isolates from broccoli and cabbage. Compared with ProS isolates, the mycelial growth rate, sporulation capacity and virulence of most ProHR isolates were reduced; ProHR isolates displayed an increased sensitivity to osmotic stresses and a reduced sensitivity to sodium dodecyl sulfate (SDS); all ProHR isolates showed a reduced sensitivity to hydrogen peroxide (H2O2) except for the isolate B102. Correlation analysis revealed a positive cross-resistance between procymidone and iprodione, or fludioxonil. When treated with 10 μg/mL of procymidone, both mycelial intracellular glycerol accumulations (MIGAs) and relative expression of AaHK1 in ProS isolates were higher than those in ProHR isolates. Sequence alignment of AaHK1 from ten ProHR isolates demonstrated that five of them possessed a single-point mutation (P94A, V612L, E708K or Q924STOP), and four isolates had an insertion or a deletion in their coding regions. No significant difference in biochemical characteristics was observed among ProHR isolates from two different hosts, though mutations in AaHK1 of the cabbage-originated ProHR isolates were distinct from those of the broccoli-originated ProHR isolates.

Background

A leaf spot and blight disease, caused by the filamentous fungus Alternaria alternata (abbreviated as ALSB), is among the most common diseases of numerous economic crops, including crucifers (such as cabbage, cauliflower and broccoli), bean, cotton, citrus and tomato (Nowicki et al. 2012; Mukesh et al. 2016). The pathogen can infect a wide range of hosts and produce mycotoxins, posing a severe threat to safe food and vegetables worldwide, for instance, the reduced quality of cauliflower heads and brassicaceae oil (Guillemette et al. 2004; Surviliene & Dambrauskiene 2006; Meena & Samal 2019). Owing to few commercially-satisfactory ALSB-resistant varieties of brassicaceae vegetables available, chemical control is relied to control ALSB in the field. Currently, dicarboximide fungicides (DCFs) (Dry et al. 2004), quinol-oxidizing inhibitors (QoIs) (Ma et al. 2003), succinate dehydrogenase inhibitors (SDHIs) (Avenot & Michailides 2007) and sterol demethylation inhibitors (DMIs) (Avenot et al. 2016) are intensively used to control ALSB.

The DCFs, including procymidone and iprodione, have been registered to control ALSB of cabbage and broccoli for decades in China (Ma & Michailides 2004). The biochemical mechanism of DCFs against phytopathogenic fungi is documented to regulate high osmolarity glycerol (HOG) MAP kinases, interfering with the phosphorylation of transduction-associated proteins and glycerol biosynthesis (Cui et al. 2002; Lin & Chung 2010). DCFs and phenylpyrroles are reported to target the same enzyme, a fungal two-component histidine kinase (HK), which belongs to group III hybrid histidine kinases involved in an osmotic-regulatory signal transduction cascade of mitogen-activated protein kinase (MAPK) signaling pathway, i.e., HOG-MAPK (Avenot et al. 2005; Lin & Chung 2010; Ren et al. 2016). This cascade not only perceives extracellular stimuli, but also maintains intracellular osmotic homeostasis. Positive cross-resistance between DCFs and phenylpyrroles is frequently observed in phytopathogenic fungi highly resistant to fludioxonil, including Botrytis cinerea (Sang et al. 2018), Bipolaris maydis (Han et al. 2017), Stemphylium solani (Wu et al. 2015) and Sclerotinia sclerotiorum (Duan et al. 2013). The typical structure of fungal group III HKs from major phytopathogenic fungi is composed of three domains: Histidine kinases-Adenylate cyclases-Methyl accepting proteins and Phosphatases (HAMPs, functionally named as “sensor domain”) at a highly variable N-terminus, a central transmitter domain composed of histidine kinase A (HisKA) and cognate histidine kinase-like ATPase catalytic subdomains (HATPase_c), and a C-terminus receiver domain harboring a three amino-acid signature (DDK) (Herivaux et al. 2016).

Due to the extensive application of DCFs, the resistance against this type of fungicides has been reported in several phytopathogenic fungi, including Alternaria spp. (Dry et al. 2004; Avenot et al. 2005; Luo et al. 2008, 2012), Sclerotinia spp. (Ma et al. 2009; Kuang et al. 2011; Duan et al. 2013), B. cinerea (Fraile et al. 1986; Oshima et al. 2002; Cui et al. 2004; Grabke et al. 2014), Magnaporthe grisea (Motoyama et al. 2005), Stemphylium vesicarium (Alberoni et al. 2010), Neurospora crassa (Fujimura et al. 2000; Miller et al. 2002; Ochiai et al. 2010) and Cochliobolus heterostrophus (Yoshimi et al. 2003, 2004). The molecular mechanisms of DCF-resistance include amino acid substitution in group III HK proteins, deletion or insertion mutations in their coding regions (Cui et al. 2004; Dry et al. 2004; Luo et al. 2008). Mutations in AaHK1 (insertion or deletion) of A. alternata lead to premature termination of the AaHK protein (Dry et al. 2004). Similarly, diverse mutations are found in AbNIK1 of Alternaria brassicicola, including nonsense mutations, a frameshift and a single amino acid substitution (E753K) (Avenot et al. 2005), while deletions and single amino acid substitutions are detected in AlHK1 of Alternaria longipes (Luo et al. 2008, 2012). In brief, it is intriguing to observe a high degree of diversity among mutations in HKs of the DCF-resistant isolates from Alternaria spp..

The mutations of HK1s are involved in the development of resistance to DCFs in fungal pathogens under certain selective pressure (Dry et al. 2004). Recently, growers has raised concerns about the decreased efficacy of DCFs against ALSB on cabbage and broccoli in Jiangsu Province of China. The objectives of this study were to (i) investigate whether procymidone-resistant (ProR) populations of A. alternata has developed in commercial fields of cabbage and broccoli that were repetitively exposed to procymidone; (ii) compare biochemical characteristics between ProS and ProHR isolates, and also between ProHR isolates from broccoli and cabbage; (iii) reveal possible molecular resistant mechanisms of A. alternata against procymidone.

Results

Frequencies of resistance against procymidone in natural populations of A. alternata from broccoli and cabbage

The 198 isolates of A. alternata were obtained during 2018–2019, including 114 isolates from broccoli and 84 isolates from cabbage in Yancheng City, Jiangsu Province, China. Of the 114 isolates from broccoli, 7 high-level procymidone-resistant (ProHR) isolates and 60 low-level procymidone-resistant (ProLR) isolates were detected with resistance frequencies of 6.14 and 52.63%, respectively (Table 1). Of the 84 isolates from cabbage, in contrast, 3 ProHR isolates and 45 ProLR isolates were found with resistance frequencies of 3.57 and 53.57%, respectively (Table 1). The data indicate that DCF-resistant populations of A. alternata has developed in commercial fields of broccoli and cabbage.

Table 1 Sensitivities of Alternaria alternata isolates to procymidone from Yancheng City, Jiangsu Province, China during 2018–2019

The EC50 values of all ProHR isolates from broccoli and cabbage were more than 100 μg/mL, while the values for ProS isolates were less than 1 μg/mL (Table 2).

Table 2 EC50 values of ProS and ProHR isolates of Alternaria alternata from broccoli and cabbage

Fourteen representative single-spore isolates, including ten ProHR isolates (C5, C13, C40, B30, B35, B46, B53, B88, B102 and B108) and four ProS isolates (C10 and C28 from cabbage; B16 and B21 from broccoli), were selected for phylogenetic analyses base on ITS and KOG1058 sequences (Fig. 1) and for further experiments.

Fig. 1
figure1

Phylogram generated from maximum parsimony analysis based on sequences of ITS and KOG1058, showing the phylogenetic relationship of the tested isolates with A. alternata and other Alternaria species

Cross-resistance

All the ProHR isolates from broccoli and cabbage were also highly resistant to fludioxonil and iprodione based on their EC50 values (Table 2). The Spearman’s rank correlation coefficient between the sensitivity against procymidone and fludioxonil, or iprodione was 0.9870 or 0.9824 (P < 0.001), respectively, suggesting a positive correlation (a positive cross-resistance) between procymidone and fludioxonil or iprodione was present in these tested A. alternata isolates.

Mycelial growth, sporulation and virulence in ProHR and ProS isolates of A. alternata

The mycelial growth rates of the ProHR isolates on fungicide-free potato dextrose agar medium (PDA) were significantly reduced compared with those of the ProS isolates (P = 0.05) (Table 3). No significant difference in mycelial growth was observed among the ProHR isolates from cabbage and broccoli (Table 3). Compared with ProS isolates, the sporulation capacity of the ProHR isolates (except for isolates B46 and B88) was significantly reduced (P = 0.05) (Table 3). Furthermore, the virulence of the ProHR isolates (except for isolates B35 and B53) on broccoli detached leaves was also significantly weakened compared with that of the ProS isolates (P = 0.05) (Fig. 2 and Table 3). Intriguingly, all ProHR isolates from cabbage and broccoli fluctuated markedly in sporulation capacity and virulence.

Table 3 Mycelial growth rate, sporulation and virulence in ProS and ProHR isolates of Alternaria alternata from cabbage and broccoli
Fig. 2
figure2

Virulence analysis of A. alternata ProS and ProHR isolates. The tested isolates were inoculated onto broccoli leaves. Disease lesions were determined at 7 days post-inoculation (dpi). The ProS isolates include C10, C28, B16 and B21. The ProHR isolates include C5, C13, C40, B30, B35, B46, B53, B88, B102 and B108

Sensitivities of ProHR and ProS isolates of A. alternata to stress agents

The group III HK is involved in osmotic-regulatory signal transduction cascade of MAPK signaling pathway (Lin & Chung 2010). To determine whether mutations in AaHK1 affect the sensitivity of A. alternata to osmotic and oxidative stresses, cell membrane permeability or cell wall integrity, the mycelial growth inhibition rates of the ProHR and ProS isolates on PDA supplemented with an osmotic stress agent (1.2 M KCl or 1.2 M NaCl), an oxidative stress agent (10 mM hydrogen peroxide, H2O2), a cell membrane stress agent (0.05% Sodium dodecyl sulfate, SDS) or a cell wall damage agent (0.05% Congo red, CR) were determined.

The data showed that all ProHR isolates were strongly inhibited by 1.2 M KCl or 1.2 M NaCl, with mycelial growth inhibition rates ranging from 84 to 95% or from 85 to 95%, indicating that they were more sensitive to osmotic stresses than ProS isolates (51–78% and 64–78% mycelial growth inhibition by 1.2 M KCl and 1.2 M NaCl, respectively) (P = 0.05) (Fig. 3a, b). However, the mycelial growth rates of the ProHR isolates were higher than those of the ProS isolates when treated with 0.05% SDS (P = 0.05) (Fig. 3c). Under 0.05% CR treatment condition, the radial growth rates of the ProHR isolates displayed different degrees of inhibition relative to those of the ProS isolates (Fig. 3d). Additionally, except for the ProHR isolate B102 (having no mutation in AaHK1), the mycelial growth rates of the ProHR isolates were higher than those of the ProS isolates when treated with 10 mM H2O2 (Fig. 3e). Furthermore, the sensitivity to stress agents varied greatly among the ProHR isolates from broccoli or cabbage.

Fig. 3
figure3

Sensitivity comparison among A. alternata ProS and ProHR isolates to osmotic stress agents generated by 1.2 M KCl (a); 1.2 M NaCl (b); 0.05% SDS (c); 0.05% Congo red (d) and 10 mM hydrogen peroxide (H2O2) (e). Bars denote the standard errors of three repeated experiments. Values on bars followed by the same letter are not significantly different from each other at P = 0.05. The ProS isolates include C10, C28, B16 and B21. The ProHR isolates include C5, C13, C40, B30, B35, B46, B53, B88, B102 and B108

Mycelial intracellular glycerol accumulations (MIGAs) in ProHR and ProS isolates of A. alternata

DCFs are reported to affect glycerol biosynthesis and phosphorylation in HOG-MAPK pathway (Cui et al. 2002). Under procymidone-free condition, no significant difference was observed in MIGAs between the ProS and ProHR isolates (P > 0.05). After treated with 10 μg/mL procymidone for 5 h, MIGAs in ProS isolates increased significantly and were 2.70–3.04 folds of those under procymidone-free condition, higher than that of 1.02–1.27 folds by the ten ProHR isolates under the same conditions (P = 0.05) (Fig. 4). Furthermore, no significant difference was observed in MIGAs among the ProHR isolates from broccoli and cabbage (P > 0.05) (Fig. 4).

Fig. 4
figure4

Comparison of mycelial intracellular glycerol accumulations (MIGAs) among A. alternata ProS and ProHR isolates. The mycelia of each isolate were treated with procymidone at 0 or 10 μg/mL after growth in PDB for 5 h. Bars denote the standard errors of three repeated experiments. The asterisk indicates significant difference between procymidone-treated sample and control. The ProS isolates include C10, C28, B16 and B21. The ProHR isolates include C5, C13, C40, B30, B35, B46, B53, B88, B102 and B108

Sequence alignments of AaHK1 from ProS and ProHR isolates of A. alternata

To characterize mutations in AaHK1 proteins, the complete nucleotide sequences of AaHK1 in all ProHR and 20 arbitrarily selected ProS isolates from broccoli and cabbage were sequenced and aligned. The results showed that the deduced AaHK1 protein is 1330 amino acids (aa) in length, possessing six HAMP repeat domains at N-terminus, followed by a His Kinase A (phospho-acceptor) domain (HisKA), an HK-like ATPase domain (HATPase_c), and a response regulator domain at C-terminus (Fig. 5). The twenty ProS isolates possessed identical AaHK1 sequences with no genetic diversity, as illustrated by the four representative isolates (C10, C28, B16 and B21). No mutation was observed in AaHK1 of all ProLR isolates from broccoli and cabbage (data not show).

Fig. 5
figure5

Schematic representation of the AaHK1 protein coding region, including histidine kinase, adenylyl cyclase, methyl-accepting chemotaxis protein, and phosphatase domain repeats (HAMPs); His kinase A (phospho-acceptor) domain (HisKA); HK-like ATPase domain (HATPase_c); and response regulator domain (Rec)

All mutations in the coding regions of AaHK1 from ProHR isolates are presented in Table 4. Except for the isolate B102, all broccoli-originated ProHR isolates contained abundant amino acid mutations in AaHK1, which could be divided into two groups. Groups I possessed an amino acid substitution: E708K (a substitution of glutamic acid by lysine at codon708 within the HAMP6 domain) in isolates B88 and B108; V612L (a substitution of valine by leucine at codon612 within the HAMP6 domain) in isolate B30; Q924STOP (a precocious stop of translation at codon924 within the HATPase_c domain) in isolate B35. Group II had a 2-bp deletion between domains of HATPase_c and Rec in isolate B53 (which caused a frame-shift, leading to premature termination at codon1104 of AaHK1), or a 381-bp deletion (from nt1707 to nt2089, causing a 127-AA deletion from HAMP4 to HAMP6) in isolate B46. In contrast, mutations in AaHK1 from three cabbage-originated ProHR isolates could be categorized into three groups: group I presented an amino acid substitution (P94A, proline was changed to alanine at codon94 localized between N-terminus and HAMP1) in isolate C5; group II had an 8-bp insertion at the Rec domain in isolate C40, resulting in a premature termination at codon1204; group III had a 552-bp deletion, causing a 184-AA deletion from HAMP1 to HAMP3 in isolate C13. In brief, diverse mutations were found in ProHR isolates, and the resistant genotypes of ProHR isolates from cabbage were distinct from those from broccoli. Nucleotide sequence accession numbers corresponding to AaHK1 from the tested ProHR and ProS isolates are presented in Table 5.

Table 4 Mutations in the coding regions of AaHK1 from Alternaria alternata ProHR and ProS isolates
Table 5 Nucleotide sequence accession numbers corresponding to AaHK1 from ProHR and ProS isolates of Alternaria alternata in this study

The relative expression level of AaHK1 in ProS and ProHR isolates of A. alternata

The relative expression level of group III HK gene in B. cinerea is correlated with its resistance against histidine kinase inhibitors (Ren et al. 2016). Here, we investigated changes of AaHK1 expression in ProS and ProHR isolates against procymidone. In the absence of procymidone, the expression of AaHK1 was relatively low in the ProS and ProHR isolates (Fig. 6). When treated with procymidone at 10 μg/mL for 12 h, the relative expression level of AaHK1 in the ProS isolates was 3.36–3.65 folds of that of untreated ProS isolates, much higher than that of 0.89–1.22 folds in the ten ProHR isolates under the same condition (Fig. 6). Furthermore, no significant difference in the relative expression of AaHK1 was observed among ProHR isolates from two different hosts (broccoli and cabbage).

Fig. 6
figure6

The expression of AaHK1 gene in A. alternata ProS and ProHR isolates. The mycelia of each isolate were treated with procymidone at 0 or 10 μg/mL after growth in PDB for 12 h. Bars denote the standard errors of three repeated experiments. The asterisk indicates significant difference between procymidone-treated sample and control. The ProS isolates include C10, C28, B16 and B21. The ProHR isolates include C5, C13, C40, B30, B35, B46, B53, B88, B102 and B108

Discussion

Procymidone, a DCF fungicide for ALSB control, has been extensively used for decades in China, however, there is a growing concern about its decreased efficacy nowadays. Our data in this study indicate that DCF-resistance has developed in natural populations of A. alternata from commercial fields of broccoli and cabbage in Yancheng, Jiangsu Province, China. ProLR populations developed faster than ProHR populations in these fields during 2018–2019, and ProHR populations from broccoli were larger than those from cabbage, which may be attributed to different selective pressures exerted by the use of a fungicide in different ways in the field. Long-term monitoring of population change should be performed to detect the dynamic of ProHR population and formulate corresponding management strategy in time. To our knowledge, there has been no report so far on DCF-resistance in A. alternata from commercial fields of broccoli and cabbage.

DCF-resistance has been reported in several Alternaria species, including A. alternata (Dry et al. 2004), A. longipes (Luo et al. 2008), A. brassicicola (Avenot et al. 2005) and A. arborescens (Ma & Michailides 2004). However, the resistance mechanism of these fungal pathogens to DCFs and phenylpyrroles has not yet been determined. To elucidate the possible molecular mechanism of DCF-resistance, the nucleotide sequences of AaHK1 of A. alternata ProHR isolates from broccoli and cabbage were sequenced and aligned in this study. The results demonstrate that a high level of nucleotide sequence homology exists between AaHK1 and os-1 from N. crassa (Ochiai et al. 2010), B. cinerea (Ren et al. 2016), A. brassicicola (Avenot et al. 2005) and A. longipes (Luo et al. 2008).

Abundant mutation types were detected in AaHK1 of the ProHR isolates from cabbage and broccoli, including deletions at HAMPs or between HATPase_c and Rec domains, an insertion at the Rec domain, amino acid substitutions at HAMPs or HATPase_c domain. The observed premature termination mutations in AaHK1 were generated by a 2-bp deletion, an 8-bp insertion or C to T transition. Intriguingly, no mutation was detected in AaHK1 of B102 (a ProHR isolate from broccoli), with the same situation occurring in DCF-resistant isolates of A. alternata (from pistachio), A. arborescens (Ma & Michailides 2004) and A. brassicicola (Avenot et al. 2005). Additionally, in DCF-resistant A. alternata isolates from passionfruit, frameshift mutations caused by a 4-bp and an 11-bp insertion at HAMP5 and HAMP1 of AaHK1, respectively, confer resistance to DCFs (Dry et al. 2004). The diverse mutations are also found in homologous HK1s of other Alternaria species. The iprodione-resistant A. brassicicola isolates possess an amino acid substitution (E to K) at the HisKA domain, a frameshift caused by a 2-bp deletion at HAMP4, or nonsense mutations at HAMPs or HATPase_c domains in AbNIK1 (Avenot et al. 2005), while the dimethachlon-resistant A. longipes isolates possess amino acid substitutions at HAMPs, nonsense mutation generated by amino acid substitution at HAMP5, or a 321-bp deletion between HAMP5 and HAMP6 of AlHK1 (Luo et al. 2008). All the mutations detected at different domains of HKs in DCF-resistant isolates might affect their corresponding biochemical characteristics, including the resistance against DCFs. In this study, although not all A. alternata ProHR isolates possessed mutation in AaHK1, this might be the dominant mechanism involved in their DCF-resistance.

In yeast and B. cinerea, cellular responses to osmotic stress are controlled by the HOG-MAPK signaling pathway through which a range of osmotic responses including glycerol synthesis are regulated (Brewster et al. 1993; Cui et al. 2002). In this study, when treated with 10 μg/mL procymidone, MIGAs and the expression level of AaHK1 were significantly increased in the ProS isolates compared with those under procymidone-free conditions, while this increase in the ten ProHR isolates was at a relatively low level, the same as that observed in fludioxonil-resistant B. cinerea isolates (Ren et al. 2016). The results indicate that AaHK1 plays a role in the HOG-MAPK pathway, and a negative correlation exists between the resistance level of A. alternata to procymidone and the increase of MIGAs under procymidone-stressed condition. It was reported that the high level iprodione- or fludioxonil-resistant isolates of A. alternata from passionfruit exhibited moderate sensitivity to osmotic stress, identical to that of A. brassicicola (Dry et al. 2004; Avenot et al. 2005). Nevertheless, in this study, all the ProHR isolates from broccoli and cabbage were highly sensitive to osmotic stresses. The difference in sensitivity to osmotic stress agents in Alternaria spp. suggest that mutations in HK1s might affect signal transduction of the HOG-MAPK signaling pathway, consequently resulting in distinct responses to stress agents.

For other regulatory functions of HK1s in the development of DCF-resistance, Steel (Steel 1996) reported that the resistance to DCFs is positively correlated with the activity of an anti-oxidant enzyme, catalase. Compared with ProS isolates, the sensitivity of ProHR isolates (with mutations in AaHK1) to oxidative stress (H2O2) was reduced significantly, whereas, no significant difference in sensitivity to H2O2 was observed in B102, a ProHR isolate having no mutations in AaHK1. This suggests that mutations leading to inactivation of HK1 may result in constitutive induction of catalase, as observed in DCF-resistant B. cinerea and A. alternata isolates from passionfruit (Steel & Nair 1995; Steel 1996). In contrast, the sensitivity to oxidative stress in HK mutants of A. longipes from tobacco was not affected (Luo et al. 2012). These results indicate that HKs from A. alternata and A. longipes have a different regulatory function in signal transduction during oxidative stress. In addition, all ProHR isolates were more resistant to cell membrane agent (0.05% SDS) than those of ProS isolates, indicating that the group III HK of A. alternata is probably associated with membrane permeability. The enhanced tolerance to H2O2 and SDS in ProHR isolates is suggested to protect their cells from the deleterious effects of DCFs.

Fitness is an extremely essential parameter for evaluation of the potential risk of fungicide-resistant populations. Many DCF-resistant isolates display a fitness penalty relative to DCF-sensitive isolates, as those found in S. sclerotiorum (Kuang et al. 2011), B. cinerea (Ren et al. 2016) and Penicillium expansum (Li & Xiao 2008). Although most ProHR isolates of A. alternata in current study was also reduced in mycelial growth rate, sporulation capacity and virulence, the ProHR isolates B46, B35 and B53 were increased significantly in sporulation capacity or pathogenicity compared with ProS isolates. This suggests that ProHR populations of A. alternata from commercial fields of broccoli and cabbage as a whole possessed no superiority over ProS populations (wild type), and was in a stage of slow development in these fields during 2018–2019. However, the ProHR isolates with high fitness may have the potential to develop into a large group if no reasonable control methods are adopted. Therefore, the growers should be encouraged to use mixed fungicides with different modes of action (e.g., QoIs, DMIs or SDHIs) to delay the development of DCF-resistant A. alternata populations in these fields.

Conclusions

The resistance to procymidone has developed in natural populations of A. alternata infecting broccoli and cabbage crops in Jiangsu Province of China. Most ProHR isolates displayed a fitness penalty in mycelial growth rate, sporulation and virulence compared with ProS isolates. The ProHR isolates were highly sensitive to osmotic stress. In addition, a positive cross-resistance was observed between procymidone and fludioxonil or iprodione. Mutations in AaHK1 were involved in the resistance of A. alternata isolates to DCFs. No significant differences in biochemical characteristics was observed between ProHR isolates from broccoli and cabbage.

Methods

Sample collection, causal agent isolation and identification

All the 198 isolates of A. alternata were isolated from symptomatic leaves during 2018–2019. Diseased leaves were collected from different commercial fields of broccoli and cabbage at Yancheng City, Jiangsu Province, China, where procymidone (a member of DCFs), alone or mixed with other fungicides with different mode of action, had been extensively used to control ALSB twice or three times in a growing stage since 1980s. Any two neighboring samples were separated from each other at least 50 m, with each sample placed in an individual envelope. To obtain A. alternata isolates, small tissue pieces cut from lesion edges were sterilized in 1% NaClO for 3 min, washed three times with sterile distilled water, and transferred onto Petri dishes containing PDA medium supplemented with 100 μg/mL streptomycin sulfate (Solarbio Science & Technology Co., Ltd.) (Ren et al. 2016). After incubation at 25 °C for 6 days, a mycelial plug was cut from the margin of an actively growing colony, and transferred to the center of a fresh PDA plate. Conidia were harvested using sterile distilled water after 6 days of incubation at 25 °C, and the single-spore isolate was obtained by picking a single conidium under a microscope (Zhang et al. 2017). In total, 198 single-spore isolates were obtained. The representative isolates were further identified by polymerase chain reactions (PCR) with two primer pairs ITS1/ITS4 and KOG1058F/KOG1058R (Table 6) (Woudenberg et al. 2015). The ITS and KOG1058 sequences of each isolate were blasted and congeneric sequences were obtained from the National Center for Biotechnology Information (NCBI) GenBank database. Phylogram analysis was processed by MEGA7 software based on ITS and KOG1058 sequences to further identify the isolates.

Table 6 Primers used in this study

Fungicides

All fungicides used are technical grade. Fludioxonil and iprodione (98% active ingredient; generously provided by Yangzhou Younuo Chemicals Co., Ltd., Yangzhou, China) were dissolved in methanol to obtain a stock solution of 2 × 104 mg/L. Procymidone (99.2% active ingredient; provided by Jiangsu Xinyi Chemical Co., Ltd., Xuzhou, China) was dissolved in acetone to obtain a stock solution of 2 × 104 mg/L. All stock solutions were kept at 4 °C before use.

Determination of resistance frequencies of A. alternata isolates to procymidone

Sensitivities of 198 single-conidium isolates of A. alternata to procymidone were determined by discriminatory doses of mycelial growth inhibition method. In brief, procymidone at 0, 10, 50 and 100 μg/mL were used to determine sensitivities of all isolates for low-resistance (LR), moderate-resistance (MR) and high-resistance (HR). The isolate was considered procymidone-sensitive (ProS) when the MIC (minimum inhibitory concentration) value was less than 10 μg/mL. Similarly, 10 < MIC< 50 μg/mL for low-level procymidone-resistant (ProLR) isolates, 50 < MIC< 100 μg/mL for moderate-level procymidone-resistant (ProMR) isolates, and MIC> 100 μg/mL for high-level procymidone-resistant (ProHR) isolates. Mycelial plugs (5 mm in diameter) were cut from the margin of a 6-day-old colony, and transferred to the center of Petri dishes containing PDA medium (one plug per dish) amended with procymidone at the above-mentioned concentrations. At 6 days of incubation, the sensitivity of each isolate to procymidone was determined based on the mycelial colony growth inhibited by procymidone. The resistance frequency was determined using the following formula: resistance frequency (%) = (the number of resistant isolates/the number of the total isolates tested) × 100%. The experiment was performed three times with three replications for each isolate.

Determination of sensitivities of A. alternata isolates to procymidone

To determine the sensitivity of A. alternata isolates to procymidone, the fungicide was prepared in a serial concentrations of 0, 25, 50, 100, 200, 400 and 800 μg/mL for ProHR isolates, and another serial concentrations of 0, 0.03, 0.1, 0.3, 1, 3 and 9 μg/mL for ProS isolates. The 6-day-old mycelial plugs (5 mm in diameter) were separately transferred to the center of PDA plates with above-mentioned concentrations of procymidone. Percentage of inhibition was evaluated and EC50 (effective concentration for 50% mycelial inhibitive growth) was calculated for each tested isolate using Data Processing System (DPS 7.05). The experiment was performed three times with three replications for each isolate.

Cross-resistance test among different fungicides

The sensitivity of A. alternata isolates to fludioxonil and iprodione were determined by measuring mycelial growth rate. One serial concentrations (0, 25, 50, 100, 200, 400 and 800 μg/mL) were set up to test the sensitivity of resistant isolates to fludioxonil or iprodione, and another serial concentrations (0, 0.025, 0.05, 0.1, 0.2, 0.4, 0.8 and 1.6 μg/mL) for sensitive isolates. EC50 values were determined with the same method as above-mentioned. Spearman’s rank correlation coefficient for the log10-transformed EC50 values was used to analyze cross-resistance pattern between procymidone and fludioxonil or iprodione. The experiment was performed three times with four replicates per concentration.

Determination of radial growth rates and sporulation capacities of A. alternata isolates

Six-day-old mycelial plugs (5 mm in diameter) of A. alternata isolates were transferred to the center of Petri dishes containing PDA medium (one plug per dish), then placed in an incubator at 25 °C in darkness. At 6 days of incubation, the average colony diameter for each isolate was measured in two perpendicular directions. The experiment was performed three times with three replications for each isolate.

For sporulation test, conidia were harvested from the surface of six-day-old PDA colonies washed with 10 mL sterile water (containing 0.1% Tween 20), filtered through four layers of sterile lens papers, and centrifuged at 5000 rpm for 1 min. The pellets were re-suspended in 1 mL sterile distilled water. The concentrations of conidial suspensions were measured with a hemacytometer under microscope. Six replicates were performed for each isolate, and the experiment was repeated three times.

Virulence assay

Broccoli (var. Hanxiu) leaves were used to determine the pathogenicity of A. alternata isolates. Leaves were surface-disinfected with 75% alcohol for 10 s, and inoculated with six-day-old hyphal plugs (5 mm in diameter) of each isolate. Before inoculation, a sterilized needle was used to produce wound. All the inoculated leaves were transferred onto three layers of moistened filter paper, and incubated at 25 °C with 85% relative humidity (RH) and a 12-h light/12-h dark cycle. The lesion areas were calculated at 7 dpi (days post-inoculation). The experiment was performed three times.

Determination of responses of A. alternata isolates to various environmental stresses

To evaluate responses of A. alternata isolates to different stress agents, all isolates were incubated at 25 °C for 6 days. Then, mycelial plugs (5 mm in diameter) were cut from the edge of actively growing colonies, and transferred onto PDA plates amended with 0.05% sodium dodecyl sulfate (SDS) (w/v), 0.05% Congo red (CR) (w/v), 1.2 M KCl, 1.2 M NaCl or 10 mM hydrogen peroxide (H2O2) (v/v). The isolates incubated in PDA plates without stress agents were served as controls. All treatments were incubated for 6 days at 25 °C, with three replicate plates for each agent. The inhibition percentages of mycelial growth by these stress agents were determined for each tested isolate. This experiment was performed three times.

Determination of intracellular glycerol accumulations in A. alternata isolates

A commercial assay kit (Applygen Technologies Inc., Beijing) was used to determine intracellular glycerol accumulations in mycelia of A. alternata isolates in accordance with the manufacturer’s instruction. In brief, all isolates were incubated in potato dextrose broth (PDB) in a shaker (175 rpm) at 25 °C for 2 days. At 5 h after treatment with 10 μg/mL procymidone, mycelia of each isolate were collected with sterile distilled water, lyophilized and grounded in mortars amended with liquid nitrogen (Ren et al. 2016). Mycelial powder (0.1 g) was then transferred into a 2 mL centrifuge tube, and mixed in 1 mL glycerol extraction buffer (Applygen Technologies Inc., Beijing, China). The mixture was vortexed for 5 min and centrifuged at 5000 rpm for 20 min, and the supernatants were used to analyze mycelial intracellular glycerol concentrations (Duan et al. 2013). This experiment was repeated three times with four replicates for each isolate.

DNA extraction and sequence analysis of AaHK1

Genomic DNAs were extracted from mycelia of A. alternata isolates with a commonly used cetyltrimethylammonium bromide (CTAB) method. Based on the sequence of AaHK1 (GenBank accession No. GQ414508.1) deposited in NCBI GenBank database, five primer pairs (Table 6) were designed to amplify the complete nucleotide sequence of AaHK1. Polymerase chain reactions (PCR) were conducted in a 25 μL volume, containing 0.25 μL of high-fidelity LA polymerase (5 U/mL) (TaKaRa, Japan), 1 μL of each primer (10 mM), 2.5 μL of 10× LA polymerase buffer (Mg2+ free), 50 ng of genomic DNA, 2.5 μL of MgCl2 (25 mM), 4 μL of dNTP mixture (2.5 mM of each dNTP) and 12.75 μL of ddH2O. The PCR program consisted of an initial denaturation at 94 °C for 5 min; followed by 35 cycles of denaturation at 94 °C for 30 s, annealing at 56 °C for 30 s, and extension at 72 °C for 50s; and a terminal extension at 72 °C for 10 min. Each PCR product was purified using the QIAquick PCR Purification Kit (Qiagen, MD, USA), and sequenced by the Sangon Biotech Co., Ltd. (Shanghai, China). The amino acid sequences were analyzed by DNAMAN software (version 6.0; Lynnon Biosoft Bioinformatic Solutions). PCR amplifications were performed three times for each isolate to avoid sequence mismatches during PCR amplification and sequencing.

Determination of the gene expression level of AaHK1

To analyze the relative gene expression level of AaHK1 in A. alternata isolates, mycelial plugs were incubated in flasks containing PDB, with six replicate flasks for each isolate. After 2 days of incubation at 25 °C in a shaker, three flasks were treated with 10 μg/mL of procymidone, and the other three were added with the same volume of sterile water and used as controls. After 12 h, the mycelia of each isolate were harvested for RNA extraction using Total RNA Isolation kit (Promega, USA). Further, cDNA was synthesized using PrimeScript RT reagent kit with gDNA Eraser (TaKaRa, Japan). Primers used for quantitative PCR (qPCR) are shown in Table 6. qPCR was performed in an ABI 7500 Real-Time Detection System (Applied Biosystems) using SYBR Green I fluorescent dye detection. Amplification was performed in a 20-μL volume containing 10 μL of iTaq Universal SYBR Green Supermix (Bio-Rad Laboratories), 1 μL of each of the forward and reverse primers (10 μM), 0.4 μL of 50 × ROX Reference Dye 2, 1 μL of reverse transcription product, and 6.6 μL of ddH2O. The expression of AaHK1 was normalized to that of β-tubulin gene. The transcription level of AaHK1 in each isolate relative to that of β-tubulin gene was calculated using the 2- ΔΔCt method (Wei et al. 2019). The experiment was repeated three times.

Statistical analysis

The SIGMA-STAT Statistical Software Package (SPSS Science, version 11) was used to analyze the data. Fisher’s protected least significant difference (P = 0.05) test was calculated to evaluate statistical significance.

Availability of data and materials

Not applicable.

Abbreviations

ALSB:

Alternaria leaf spots and blights

DMIs:

Sterol demethylation inhibitors

DCFs:

Dicarboximide fungicides

DDK:

C-terminus receiver domain harboring a three amino-acid signature

EC50 :

Effective concentration for 50% mycelial inhibitive growth

HAMPs:

Histidine kinases-Adenylate cyclases-Methyl accepting proteins and Phosphatases

HATPase_c:

Cognate histidine kinase-like ATPase catalytic subdomains

HisKA:

Histidine kinase A

HK:

Histidine kinase

MAPK:

Mitogen-activated protein kinase

MIGAs:

Mycelial intracellular glycerol accumulations

ProHR :

High-level procymidone-resistant

ProLR :

Low-level procymidone-resistant

ProMR :

Moderate-level procymidone-resistant

ProR :

Procymidone-resistant

ProS :

Procymidone-sensitive

QoIs:

Quinol-oxidizing inhibitors

RH:

Relative humidity

SDHIs:

Succinate dehydrogenase inhibitors

MIC:

Minimum inhibitory concentration

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Acknowledgements

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Funding

This work was supported by National Science Foundation of China (No.31801778 & No.31672065), Chinese Key R & D Plan (2018YFD0201201, 2016YED0201007 & 2018YFD0201000), Agricultural Science and Technology Projects of Jiangsu Province, China {PZCZ201715, CX [19]3003, BE2018378, BA2018039, & CX (18)2005}.

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BRW, TCL, LLW and WCC conducted the experiments. All authors analyzed the data. BRW, TCL and CCJ wrote and revised the manuscript. All authors read and approved the final manuscript.

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Correspondence to Changjun Chen or Kai Wang.

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Wang, B., Lou, T., Wei, L. et al. Biochemical and molecular characterization of Alternaria alternata isolates highly resistant to procymidone from broccoli and cabbage. Phytopathol Res 3, 15 (2021). https://doi.org/10.1186/s42483-021-00092-z

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Keywords

  • Alternaria alternata
  • Broccoli
  • Cabbage
  • Resistance
  • Dicarboximide fungicides
  • Fitness
  • AaHK1