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Simultaneous and Rapid Detection of Four Important Graft\|transmissible Pathogens of Citrus by Multiplex PCR

应用多重PCR技术同步检测柑橘4种重要嫁接传播病原



全 文 :植物病理学报
ACTA PHYTOPATHOLOGICA SINICA  44(3): 295 ̄301(2014)
Received date: 2013 ̄01 ̄07ꎻ Revised date: 2013 ̄09 ̄24
Foundation item: Chang ̄jiang Scholars and Innovative Research Team in University (PCSIRTꎬ IRT0976)ꎬ MOAs Special Fund for Agro ̄Scien ̄
tific Research in the Public Interest (201203076)ꎬ the National Natural Science Foundation of China (30600419)ꎬ and the
Fundamental Research Funds for the Central Universities (XDJK2009C133) .
Correspondence author: Zhou Chang ̄yongꎬ Professorꎬ Specialized in molecular plant pathologyꎻ E ̄mail:zhoucy@swu.edu.cn
First Author: Liu Jin ̄xiangꎬ femaleꎬAssociate professorꎬ Specialized in molecular plant pathologyꎻ Tel:023 ̄68349338ꎬ E ̄mail: Ljinxiang@126.com.
Simultaneous and Rapid Detection of Four
Important Graft ̄transmissible Pathogens of
Citrus by Multiplex PCR
  LIU Jin ̄xiangꎬ ZHOU Chang ̄yong∗ꎬ TANG Ke ̄zhiꎬ LI Ling ̄diꎬ
LIU Ke ̄hongꎬ TIAN Xiaoꎬ LI Zhong ̄an
(Citrus Research Instituteꎬ Southwest Universityꎻ Citrus Research Instituteꎬ
Chinese Academy of Agricultural Sciencesꎬ Chongqing 400712ꎬ China)
Abstract: Citrus tristeza virus (CTV)ꎬ Citrus tatter leaf virus (CTLV)ꎬ Citrus exocortis viroid (CEVd)ꎬ and
Candidatus Liberibacter asiaticus (Ca. L. asiaticus) associated with Huanglongbing (HLB) are important graft ̄
transmissible pathogens of citrus. A rapid multiplex PCR protocol with an internal control was developed for the
detection of these citrus pathogens using a timesaving two ̄temperature cycling for PCR amplification. The assay was
applied for rapid detection of those pathogens in field ̄grown trees. The results indicated that 89.3%ꎬ 10.7%ꎬ 17.9%
and 28.6% of the 28 field ̄grown citrus samples were infected with CTVꎬ CTLVꎬ CEVd and Ca. L. asiaticusꎬ re ̄
spectivelyꎬ and approximately half of the samples were co ̄infected with more than one pathogen. In additionꎬ the
absence of multiple pathogens in shoot ̄tip grafted budlings was evaluated with the multiplex PCR assay.
Key words: Citrus tristeza virusꎻ Citrus tatter leaf virusꎻ Citrus exocortis viroidꎻ Candidatus Liberibacter
asiaticusꎻ multiplex PCR
应用多重 PCR技术同步检测柑橘 4种重要嫁接传播病原  刘金香ꎬ 周常勇∗ꎬ 唐科志ꎬ 李玲娣ꎬ
刘科宏ꎬ 田 晓ꎬ 李中安  (西南大学柑橘研究所ꎬ 中国农业科学院柑橘研究所ꎬ重庆 400712)
摘要:柑橘衰退病毒(Citrus tristeza virusꎬCTV)ꎬ柑橘碎叶病毒(Citrus tatter ̄leaf virusꎬCTLV)ꎬ柑橘裂皮病类病毒(Citrus
exocortis viroidꎬCEVd)和柑橘黄龙病(Huanglongbingꎬ HLB)亚洲种病原(Candidatus liberobacter asiaticus)是重要的柑橘嫁
接传播病原ꎮ 本文建立了同时检测 HLB病菌、CTV、CEVd 和 CTLV 4种柑橘嫁接病原的一步法、双温多重 PCR 检测技术
体系ꎬ同时在体系中设置内参基因ꎮ 应用该体系快速评价了 4 种嫁接传播病原在田间侵染情况ꎬ结果表明 28 个田间样品
CTV、CEVd、CTLV和 HLB感染率分别为 89.3 %、17.9 %、10.7 %和 28.6 %ꎬ接近半数样品为混合感染ꎮ 并且将该方法应用
于快速评价茎尖嫁接苗病毒的脱除情况ꎮ
关键词:柑橘衰退病毒ꎻ 柑橘碎叶病毒ꎻ 柑橘裂皮病类病毒ꎻ 柑橘黄龙病菌ꎻ 多重 PCR
中图分类号: S432.4          文献标识码: A          文章编号: 0412 ̄0914(2014)03 ̄0295 ̄07
    Citrusꎬ one of the most widely grown fruit
crops worldwideꎬ is contaminated with graft ̄transmis ̄
sible pathogens by grafting [1] . Citrus tristeza virus
(CTV)ꎬ Citrus tatter leaf virus (CTLV)ꎬ Citrus
 
植物病理学报 44卷
exocortis viroid (CEVd)ꎬ and Candidatus Liberi ̄
bacter asiaticus ( Ca. L. asiaticus) are important
graft ̄transmissible pathogens of citrus in China. Ca.
L. asiaticusꎬ a phloem ̄limited bacteriumꎬ is associ ̄
ated with Huanglongbing (HLB) . Multiple infec ̄
tions of more than one graft ̄transmissible pathogen
often occur in field trees. Thusꎬ it is of great impor ̄
tance to detect these four pathogens in citrus simulta ̄
neously and efficiently.
    Biological indexing is a classic diagnostic
method for the detection of citrus pathogens[2] .
Howeverꎬ it is time ̄consuming and requires
specialized facilitiesꎬ such as a greenhouse or
screenhouse. The polymerase chain reaction (PCR)
is a powerful and the most commonly used detection
technique due to its high sensitivity and specificity.
Multiplex PCR ( mPCR ) has developed for the
detection of multiple pathogens in a single
reaction[3] . Although several multiplex assays for
citrus pathogens have been reported [1ꎬ4] ꎬ no proto ̄
col has been developed for the simultaneous detec ̄
tion of Ca. L. asiaticusꎬ CTVꎬ CTLVꎬ and CEVd.
In the studyꎬ a rapid multiplex PCR protocol for the
detection of these four pathogens by conjunction with
a co ̄amplification of a plant RNA internal control
was introduced.
1  Materials and Methods
1.1  Pathogen sources and sample collection
    Four bud samples of citrus infected with Ca. L.
asiaticus from Guangdong Provincesꎬ CEVd from
Sichuan Provincesꎬ CTV and CTLV from
Chongqing City were collected. The buds were graf ̄
ted onto Carrizo citrange seedlings grown in a
screenhouse at the National Citrus Virus Exclusion
Center located in Beibei district of Chongqing. These
positive samples were used to develop the mPCR
protocol.
    Twenty ̄eight citrus samples were collected
from Chongqing Cityꎬ Guangdongꎬ Yunnanꎬ Zhe ̄
jiangꎬ Jiangxi and Hunan Provinces and the Guangxi
Zhuang Autonomous Regionꎬ Chinaꎬ and subjected
to simultaneous detection of the four above ̄men ̄
tioned pathogens by multiplex PCR. Shoot ̄tip graf ̄
ted budlings were provided by Mrs Ke ̄hong Liu
(Citrus Research Instituteꎬ CAAS) .
1.2  Total nucleic acid extraction
    Leaf and bark or fruit skin (10 ̄15 mg) was
placed in a 1.5 ̄mL microfuge tube immersed in li ̄
quid nitrogen and total nucleic acid was extracted as
described previously[5] . The extracts of total nucleic
acid were used directly for PCR assay.
1.3  Single PCRs
    Single RT ̄PCR for CEVd and PCR for Ca. L.
asiaticus were performed in accordance with the
methods of Wang et al. [6] and Ding et al.[7]ꎬ
respectively. Single RT ̄PCR for CTV and CTLV
was performed using the selected primers (Table 1)
according to Tang et al.[11] .
Table 1  PCR primers used in the multiplex and single reaction
Target pathogen Primer name Sequence (5′– 3′) Product size / bp Target gene Reference
Ca. L. asiaticus OI1 GCGCGTATGCAATACGAGCGGCA 1 160 16S rDNA [8]
OI2c GCCTCGCGACTTCGCAACCCAT
CTV ARISF ATGTCAGGCAGCTTGGGAAATT 511 P18 [1]
ARISR TTCGTGTCTAAGTCRCGCTAA CA
CEVd CEVF GGAAACCTGGAGGAAGTCGAG 371 Complete genome [9]
CEVR CCGGGGATCCCTGAAGGACTT
CTLV TLVF TGAAAACCTTTGCTGCCACTTCT 309 Partial coat protein gene [1]
TLVR TACTCTCCGAACCTGCCTCGA AA
Internal control UBQF∗ GATCTTCGCCTTAACGTTGTCAAT 194 Ubiquitin [10]
UBQR GTTGATTTTTGCTGGGAAGCA
  R: Antisense primerꎻ F: Sense primer.
692
 
  3期 刘金香ꎬ等:应用多重 PCR技术同步检测柑橘 4种重要嫁接传播病原
1.4  Multiplex PCR assay
    In the multiplex PCR assayꎬ One ̄Step RT ̄PCR
System ( Invitrogen) was used. The reaction mixture
( total volume 10 μL) comprised 1μL of total nucleic
acid and 9 μL of the PCR mixtureꎬ which contained 5
μL of 2× bufferꎬ 0.3 μL of 50 mM MgSO4ꎬ 0.3 μL
of 10 mM dNTPsꎬ 0.6 μL of 100 mM DTTꎬ 0.4 μL
of RT / Platinum Taq Mix (Invitrogenꎬ USA) ꎬ 0.97
μL of sterile water and 1.43 μL of each primer mix ̄
tures (Table 1) at a final concentration of 0.16 μM
for CTLVꎬ 0.5 μM for CEVdꎬ 0.4 μM for HLB and
0.13 μM for CTV. Primers to the Ubiquitin gene were
used as an internal control (UBQ ̄Fꎬ  ̄Rꎬ each at 0.24
μM) . The mixture was incubated at 55°C for 30 min
for cDNA synthesisꎬ followed by a denaturation step
at 94℃ for 5 min. Then a total of 35 PCR cycles were
runꎬ by using a two ̄temperature PCR cycle with de ̄
naturation at 94℃ for 30 s and primer annealing and
extension at 68℃ for 80 sꎬfollowed by final extension
at 68℃ for 7 min. The amplified PCR products were
analysed on a 1. 5% agarose gel and stained with
ethidium bromide.
1.5  Cloning and sequencing
    To determine the specificity of the multiplex
PCR protocolꎬ PCR products were purifiedꎬ ligated
into the pMD19 ̄T vector (TaKaRa)ꎬ and sequenced
(BGIꎬ China) . The identity of the sequences was
verified by a BLAST search of the National Center
for Biotechnology Information databases ( http: / /
www.ncbi.nlm.nih.gov / blast) .
1.6   Sensitivity of the single and multiplex
PCR assays
    To determine the detection limits of the assayꎬ ex ̄
tracts from pathogen ̄infected trees were diluted serially
in a ten ̄fold in extracts from uninfected trees and tested
in both the single and multiplex PCR formats.
2  Results
2.1  Single PCR assay
    With the single PCR assaysꎬ expected frag ̄
ments specific to each of target pathogens were
amplified from infected samplesꎬ whereas no
unsepecific band was detected in healthy citrus
tissues. The amplification of CTV ̄ and CTLV ̄spe ̄
cific fragments by uniplex ̄PCR was shown in Fig. 1.
The sizes of the amplified products were 511 bp for
CTV and 309 bp for CTLV.
Fig. 1  Amplification of CTV and CTLV by sin ̄
gle RT ̄PCR
(a) Lane 1 ̄3: CTV ̄infectedꎻ Lanes 4 and 5: Healthy con ̄
trol. (b) Lanes 1 ̄3: CTLV ̄infectedꎻ Lanes 4 and 5: Healthy
control.
2.2  Multiplex PCR assay
    Various parameters were tested to optimize the
mPCR conditionsꎬ especially with respect to primer
concentration. At firstꎬ in the multiplex systemꎬ at a
final concentration of 0.2 μM primer for all genesꎬ
except for 0.4 μM primer for Ca. L. asiaticusꎬ the
lowest level of amplification was achieved for
CEVdꎬ whereas CTV gave the highest amount of
792
 
植物病理学报 44卷
amplification. To achieve efficient amplification of
all targetsꎬ the concentration of the primers for CTV
was decreased to 0.13 μM and those for CEVd am ̄
plification were increased to 0.5 μM. The effect of
different primer concentrations on CTV amplification
by multiplex PCR is illustrated in Fig. 2. At a CTV
primer concentration of 0.1 μMꎬ little product was
amplified. In the final multiplex mixtureꎬ the con ̄
centration of the CTLV primers was 0. 16 μM and
that of the Ca. L. asiaticus primers was 0. 4 μM.
Nonspecific bands were not detected in any of the
samples tested. The internal control fragment was
amplified consistently in all citrus samples analysed.
When a mixture of four single ̄infection extracts was
subjected to multiplex PCRꎬ the expected fragments
were amplified specifically by the mixture of primers
for Ca. L. asiaticusꎬ CTVꎬ CTLVꎬ CEVd and the
internal control (Fig. 3ꎬ Lane 1) .
Fig. 2   Effect of different primer concentra ̄
tions on the amplification of CTV by
multiplex PCR
Lanes 1 ̄4 represent a mix of total nucleic acids and different
primer concentrations. Lane 1: 0.02 μMꎻ Lane 2: 0.06 μMꎻ
Lane 3: 0.1 μMꎻ Lane 4: 0.13 μMꎻ Lane 5: Healthy con ̄
trolꎻ M: 100 bp molecular marker.
    To determine the specificity of the multiplex
PCR protocolꎬ all the PCR products were purifiedꎬ
clonedꎬ and sequenced. Their sequencing confirmed
both the expected size and the corresponding
genomic region sequence.
2.3   Sensitivity of the single and multiplex
PCR assays
    The sensitivity of the mPCR was determined u ̄
sing 10 ̄fold serial dilution of a mix of total nucleic
acids. Pathogen ̄specific bands were detected in total
nucleic acid at dilutions 10 ̄4for CTVꎬ 10 ̄3 for Ca. L.
asiaticusꎬ CEVd and CTLV (Fig. 4) . The sensitivi ̄
ties of the single and multiplex PCR assay were simi ̄
lar for all four pathogens upon serial dilution testing.
Fig. 3  Multiplex PCR analysis of single infec ̄
tion extracts
Lane 1: Mix of total nucleic acids tested in Lanes 2 ̄5ꎻ Lane 2:
Ca. L. asiaticusꎻ Lane 3: CTVꎻ Lane 4: CEVdꎻ Lane 5: CTLVꎻ
Lane 6: Healthy controlꎻ M: 100 bp molecular marker.
Fig. 4  Sensitivities of multiplex (a) and sin ̄
gle PCR (b) for the detection of Can ̄
didatus L. asiaticusꎬ CTVꎬ CTLV and
CEVd
Lane 1 ̄5: 10 ̄fold serial dilutions of total nucleic acids of the
pathogens positive controlꎻ Lane 6: Water controlꎻ M: 100
bp molecular marker.
892
 
  3期 刘金香ꎬ等:应用多重 PCR技术同步检测柑橘 4种重要嫁接传播病原
2.4   Simultaneous detection of four patho ̄
gens by multiplex PCR in field ̄grown
trees and shoot ̄tip grafted budlings
    The multiplex PCR protocol was applied for the
rapid detection of Ca. L. asiaticusꎬ CTVꎬ CTLVꎬ and
CEVd in field ̄grown samples ( Fig. 5 ̄a ).
Approximately half of the samples were co ̄infected
with more than onepathogen and three plants contained
up to three pathogens (Fig. 5 ̄aꎬ Lane 5). In additionꎬ
shoot ̄tip grafted budlings were assayed rapidly by this
methodꎬ over 80% samples were confirmed to be virus ̄
free (Fig. 5 ̄b). Detection of the four pathogens in 28
representative citrus trees comprised sweet orangeꎬ
lemonꎬ mandarinꎬ and mandarin hybrid cultivars is
summarized in Table 2. The results indicated that
89.3%ꎬ 17.9%ꎬ 10.7%ꎬ and 28.6% of the field ̄grown
citrus samples were infected with CTVꎬ CEVdꎬ
CTLVꎬ and Ca. L. asiaticusꎬ respectively.
3  Discussion
    The citrus pathogens CTVꎬ CTLVꎬ CEVd and
Ca. L. asiaticus are all systemically infectiousꎬ dis ̄
tributed worldwideꎬ and cause high losses to citrus
production. Consequentlyꎬ we selected these patho ̄
gens as the targets for the establishment of a patho ̄
gen ̄specific detection system. In the developed multi ̄
plex assays for citrus pathogens[12]ꎬ two ̄step RT ̄
PCR wtih three ̄temperature cycling was appliedꎬ and
no more than three pathogens were simultaneously de ̄
tected. Hereꎬ a one ̄step protocol for the simultaneous
detection of the four targets was developedꎬin which
a two ̄temperature cycling for PCR amplification was
adopted. Compared with the two ̄step assayꎬ the protocol
is more timesaving and could decrease contamination.
    Although target fragments with a short length
often give efficient detection for pathogens by multi ̄
plex PCRꎬ long target fragments of approximately
1 000 bp had been used successfully to detect patho ̄
gens[13] . In this multiplex PCR procedureꎬ primers
for Ca. L. asiaticus was used that gave a longer
product (1 160 bp) because Ca. L. asiaticus was i ̄
dentified consistently by the amplification product. In
additionꎬ the Ubiquitin gene was selected as an inter ̄
nal control to validate the effectiveness of the nucleic
acid extractions and the mPCR assays[11] . Moreoverꎬ
to achieve efficient amplification of this internal con ̄
trolꎬ a pair of internal primers for amplification of a
partial sequence of the Ubiquitin gene was rede ̄
signed on the basis of the primer sequences reported
by Brunner et al. [10] .
    A rapid mini ̄prep protocol for total nucleic acid
extraction was used in this study. Both RNA and
DNA were isolated simultaneouslyꎬ which met the
demand for the simultaneous detection of RNA
and DNA were pathogens. In additionꎬ though the
four pathogens are all systemically infectiousꎬ their
Fig. 5  Multiplex PCR analysis of Ca. L. asiaticusꎬ CTVꎬ CTLV and CEVd in field ̄grown citrus
samples (a) and shoot ̄tip grafted budlings (b)
(a) Lanes 1 ̄6 correspond to six samples listed in Table 2. Lane 1: no. 7ꎻ Lane 2: no. 22ꎻ Lane 3: no. 10ꎻ
Lane 4: no. 26ꎻ Lane 5: no. 23ꎻ Lane 6: no. 18ꎻ Lane 7: Healthy controlꎻ M: 100 ̄bp molecular marker.
(b) Lanes 1 ̄6:Shoot ̄tip grafted budlingsꎻ Lane 7: Mix of total nucleic acids testedꎻ Lane 8: Healthy controlꎻ
M: 100 bp molecular marker.
992
 
植物病理学报 44卷
Table 2  Multiplex PCR analysis of the presence of CTVꎬ CEVdꎬ CTLV and
Candidatus L. asiaticus in 28 field samples of sweet orangeꎬ
mandarinꎬ mandarin hybridꎬ and lemon collected in China
No. Cultivar
Multiplex PCR
Origin of sample CTV CEVd CTLV
Candidatus
L. asiaticus
1 Shatangju mandarin Yunnan +  ̄  ̄  ̄
2 Shatangju mandarin Yunnan +  ̄  ̄ +
3 Eureka lemon Yunnan  ̄  ̄  ̄  ̄
4 Eureka lemon Yunnan +  ̄  ̄ +
5 Xingguo sweet orange Jiangxi + +  ̄  ̄
6 Newhall navel orange Jiangxi + +  ̄  ̄
7 Hamlin sweet orange Jiangxi +  ̄  ̄  ̄
8 Newhall navel orange Jiangxi  ̄  ̄  ̄ +
9 Miyagawa wase unshiu Hunan +  ̄  ̄  ̄
10 Ehime kashi No. 22 Hunan +  ̄  ̄  ̄
11 Ehime kashi No. 28 Hunan +  ̄  ̄  ̄
12 Nankan unshiu No. 20 Hunan +  ̄  ̄  ̄
13 Amakusa Tangor Zhejiang +  ̄  ̄  ̄
14 Oita unshiu Zhejiang  ̄  ̄  ̄  ̄
15 AmakusaTangor Chongqing +  ̄  ̄  ̄
16 Taroco blood orange Chongqing + + +  ̄
17 Yuhong sweet orange Chongqing +  ̄  ̄  ̄
18 Fengyuan No. 72 ̄1 navel orange Chongqing + +  ̄  ̄
19 Powell navel orange Chongqing +  ̄ +  ̄
20 Taroco blood orange Chongqing +  ̄  ̄  ̄
21 Xinhui sweet orange Guangdong + +  ̄ +
22 Anliu sweet orange Guangdong +  ̄  ̄ +
23 Shatangju mandarin Guangdong +  ̄ + +
24 Shatangju mandarin Guangdong +  ̄  ̄  ̄
25 Anliu sweet orange Guangxi +  ̄  ̄  ̄
26 Seike navel orange Guangxi +  ̄  ̄ +
27 Seike navel orange Guangxi +  ̄  ̄  ̄
28 Anliu sweet orange Guangxi +  ̄  ̄ +
Number of positive samples (%) 25(89.3) 5(17.9) 3(10.7) 8(28.6)
distribution in citrus plant is different. The highest
levels of Ca. L. asiaticus are detected in the midrib
of mature leaves[14]ꎬ whereas CTV is more abundant
in bark than in roots or leaves and the efficiency of
detection is higher in young tissues than in old
tissues[15] . Thusꎬ the samples for simultaneous de ̄
tection of the four pathogens included the midrib of
both mature and young leavesꎬ in addition to tender
barks.
    In the present studyꎬ the mPCR assay was applied
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  3期 刘金香ꎬ等:应用多重 PCR技术同步检测柑橘 4种重要嫁接传播病原
for the detection of graft ̄transmissible pathogens of cit ̄
rus in China. Of the four pathogensꎬ CTV was the pre ̄
dominant speciesꎬ whereas the distribution of CEVd
and CTLV in the field in China was sporadic. Of the
samples collected from coastal areasꎬ co ̄infection by
CTV and HLB was frequentꎬ whereas co ̄infection by
CTV and CTLV occurred seldomly.
    Citrus production needs rapid and reliable
diagnostic methods to detect pathogens. The rapid
multiplex PCR assay described herein is an effective
method for the detection of these four important
pathogens of citrus in nurseries or in fieldꎬ and for
the evaluation of the exclusive effect of multiple
pathogens in shoot ̄tip grafted budlingsꎬ which
would be used for virus ̄free propagation.
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