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Molecular Identification of Tilletia controversa KÜhn by Inter-simple Sequence Repeat Marker

基于ISSR标记开发的一种用于小麦矮腥黑穗病菌的分子鉴定方法



全 文 :植物病理学报
ACTA PHYTOPATHOLOGICA SINICA  43(4): 337 ̄343(2013)
Received date: 2012 ̄05 ̄10ꎻ Revised date: 2013 ̄04 ̄19
Foundation item: National Basic Research and Development Program of China (“973” Program: 2002CB111406)ꎻ National Basic Research
and Development Program of China (2002CB111406) and Program for Changjiang Scholars and Innovative Research
Team in University ( IRT1042)
Corresponding author: ZHANG Guo ̄zhenꎬ Professorꎬ specialized in fungal biologyꎻ E ̄mail: zhanggzh@cau. edu. cn.
Biography: LIANG Hongꎬ femaleꎬ Ph. D. ꎬ major in plant pathologyꎻ E ̄mail: lianghong_2004@126. com.
Molecular Identification of Tilletia controversa
Kühn by Inter ̄simple Sequence Repeat Marker
LIANG Hong1ꎬ 2ꎬ ZHANG Guo ̄zhen1∗
( 1 The Key Laboratory of Plant Pathologyꎬ Ministry of Agriculture / Department of Plant Pathologyꎬ China Agricultural Universityꎬ
Beijing 100193ꎬ Chinaꎻ 2 Institute of Microbiologyꎬ Chinese Academy of Sciencesꎬ Beijing 100101ꎬ China)
Abstract:Tilletia controversa Kühn ( TCK)ꎬ causing wheat dwarf buntꎬ is an internationally quarantine
fungal pathogen of economic importance. The aim of the study was to develop a reliable and simple method
suitable for identification of TCK. Inter ̄simple sequence repeat ( ISSR) analysis was performed to reveal the
DNA polymorphism of TCK and its related species. A pair of species ̄specific primers of T. controversaꎬ
TCKF / TCKRꎬ was designed according to the sequence of a unique fragment of 1 113 bp obtained using ISSR
primer P4. An amplicon of 882 bp was detected by PCR with the primer set in 12 isolates of TCK but absent
in 14 isolates of other related pathogenic fungi including T. caries and T. foetida. The sensitivity limit of the
primers TCKF / TCKR was 1 ng of template DNA in a 25 μL PCR reaction mixture. The designed species ̄
specific primers could accurately differentiate TCK from its morphologically similar and phylogenetically close ̄
ly related speciesꎬ especially T. caries. The molecular identification of TCK using ISSR marker established in
the study provides a simple detection system for the quarantine of TCK and is a supplement to the current
molecular identification methods.
Key words: dwarf bunt of wheatꎻ ISSR markerꎻ rapid identification
基于 ISSR标记开发的一种用于小麦矮腥黑穗病菌的分子鉴定方法  梁 宏1ꎬ 2ꎬ 张国珍1∗( 1农业
部植物病理学重点实验室ꎬ 中国农业大学植物病理学系ꎬ 北京 100193ꎻ 2 中国科学院微生物研究所ꎬ 北京 100101)
摘要:小麦矮腥黑穗病菌(Tilletia controversa Kühnꎬ 简称 TCK)是小麦上的一种重要检疫性真菌ꎮ 本研究利用内部简单重
复序列( Inter ̄simple sequence repeatꎬ ISSR)技术研究 TCK及其近缘种的 DNA多态性ꎬ开发了一种可靠而简单的方法用于
TCK的分子鉴定ꎮ 用 ISSR引物 P4 从 TCK 中扩增出一条 1 113 bp 的特异性条带ꎬ据此设计了一对特异性引物 TCKF /
TCKRꎬ在 12 个 TCK菌株中均能扩增得到一条 882 bp的特异性条带ꎬ而其他近缘种包括小麦网腥黑穗病菌(T. caries)和
小麦光腥黑穗病菌(T. foetida)及相关黑粉菌的 14 个菌株均无扩增条带ꎮ 用该特异性引物检测 TCK的下限为 25 μL反应
体系中可检测到 1 ng DNA模板ꎮ 本研究开发的种特异性引物ꎬ可将 TCK与其形态上相似的近缘种尤其是小麦网腥黑穗
病菌准确区分开ꎬ本研究基于 ISSR标记建立的小麦矮腥黑穗病菌的分子鉴定方法为腥黑粉菌的检疫提供了一种便捷的方
法ꎬ是对现有分子鉴定方法的一个补充ꎮ
关键词: 小麦矮腥黑穗病ꎻ ISSR标记ꎻ 快速鉴定
中图分类号: S435. 12          文献标识码: A          文章编号: 0412 ̄0914(2013)04 ̄0337 ̄07
 
植物病理学报 43 卷
    Dwarf bunt of wheatꎬ caused by Tilletia contro ̄
versaꎬ was firstly found in Montana in 1935 and
subsequently has been recorded in many areas world ̄
wide[1]ꎬ including the United States and Canada of
North Americaꎬ Argentina and Uruguay of South
Americaꎬ and several countries of Europe and central
Asia[2] . Dwarf bunt is likely to occur in any wheat ̄
growing areas that have persistent snow cover regu ̄
larly. T. controversa has a low temperature require ̄
ment for teliospores germination optimal between
3℃ to 8℃ [1] . The infected plants are often dwarfed
with an increase in tiller numbers. A kernel in a se ̄
rious infection is converted into a sorus (bunt ball)ꎬ
containing brown to blackꎬ fetid masses of telio ̄
spores[2] . This disease has occasionally caused se ̄
vere losses to winter wheat in the Northwestern Uni ̄
ted States and other countries[2] . The epidemiology
of dwarf bunt is dependent upon teliosporesꎬ which
can keep viability for up to 10 ̄15 years over a wide
range of storage conditions[2] .
Dwarf bunt of wheat is an important internation ̄
ally quarantine disease. The accurate identification
of T. controversa has the important application val ̄
ue. Several methods based on microscopicꎬ serologi ̄
calꎬ biochemical and molecular techniques have been
developed to differentiate T. controversa from other
smut fungi[1] . Howeverꎬ the methods such as germi ̄
nation assay of teliospores[3ꎬ 4]ꎬ morphological iden ̄
tification of teliospores[5ꎬ 6]ꎬ characterization of au ̄
tofluorescence of teliospores[7] and immunological
detection[8ꎬ 9] have the following disadvantages: in ̄
convenientꎬ time ̄consuming and lack of accuracy.
Furthermoreꎬ it is difficult to differentiate T. contro ̄
versa from its morphologically similar and phyloge ̄
netically closely related speciesꎬ especially T.
cariesꎬ using these conventional methods. There ̄
foreꎬ methods based on molecular identification have
obvious advantages over the conventional ones be ̄
cause of their convenienceꎬ accuracy and time ̄sav ̄
ing aspects.
Polymerase chain reaction (PCR) with species ̄
specific primers is served and widely used as a po ̄
werful tool for identification and detection of plant
pathogensꎬ especially those quarantine ̄listed fungi.
Several molecular techniques such as RAPD (random
amplified polymorphic DNA) [10ꎬ 11]ꎬ SSR ( simple
sequence repeat) [12]ꎬ ISSR ( inter ̄simple sequence
repeat) [13ꎬ 14] and AFLP ( amplified fragment length
polymorphism) [15] have been widely used to develop
PCR ̄based markers. Among these techniquesꎬ ISSR
can reveal high polymorphism and there is no intricate
procedure. The ISSR method uncovers polymorphism
by amplifying the inter ̄microsatellites sequence
throughout the genome with a single primer of 16 ̄18
bp longꎬ composed of a repeated sequence flanked at
the 3′ or 5′ end by 2 ̄4 arbitrary nucleotides[14] . ISSR
shows relatively better repeata ̄bility and reliability
than RAPDꎬ and simpler procedure and lower
operating expense than SSR and AFLP.
In this studyꎬ ISSR was performed to find poly ̄
morphisms between T. controversa and its related
species. The purpose of the study was to develop a
rapid PCR ̄based method to differentiate T. contro ̄
versa from other related smut fungi of wheatꎬ espe ̄
cially T. caries and T. foetida.
1  Materials and Methods
1. 1  Fungal isolates
Twelve isolates of T. controversaꎬ three iso ̄
lates of T. cariesꎬ seven isolates of T. foetidaꎬ one
isolate of T. bromiꎬ one isolate of T. barclayana
and two isolates of Ustilago maydis were used in this
study. Isolates of T. controversa were obtained from
Prof. Chen Wan ̄quan ( Institute of Plant Protectionꎬ
Chinese Academy of Agricultural Sciences)ꎻ other
isolates were kindly provided by Prof. Chen Xiu ̄
rong (Gansu Agricultural University) and HAMS
( Herbarium Mycologicum Academiae Sinicaeꎬ
Institute of Microbiologyꎬ Chinese Academy of
Sciences) .
1. 2  DNA extraction
The teliospores of tested isolates were scraped
and mechanically disrupted by grinding to a fine
powder under liquid nitrogen. Total DNA from
teliospores of each fungal isolate was extracted
according to a previously published protocol[16] . DNA
833
 
  4 期 LIANG Hong,et al.: Molecular Identification of T. controversa Kühn by Inter ̄simple Sequence Repeat Marker
samples were visualized under UV light on 0. 8%
(w / v) agarose gel stained with ethidium bromide
and quantified using a NanoDrop ND ̄1000 spectro ̄
photometer (Thermoꎬ USA) . The extracted DNA
from all these isolates were stored at - 20℃ and
used as template for PCR.
1. 3  ISSR
Six ISSR primers ( P4: 5′ ̄ KVRVRV(CT) 6  ̄
3′ꎬ P5: 5′ ̄ KHFHFH (AC) 6  ̄3′ꎬ P890: 5′ ̄ VHV
(GT) 7  ̄3′ꎬ P884: 5′ ̄ HBH (AG) 7  ̄3′ꎬ P859: 5′ ̄
(TG) 8 RC ̄3′ and P835: 5′ ̄ (AG) 8 YC ̄3′) were
used in ISSR analysis. All PCRs were performed in
25 μL reaction mixture that contained 30 ng DNA
templatesꎬ 1 × PCR buffer (plus Mg2 + )ꎬ 50 μmol /
L each dNTPsꎬ 0. 3 μmol / L ISSR primer and 1 U of
Taq DNA polymerase (TaKaRa) . The PCRs were
performed in a PTC ̄100 thermocycler (MJ Re ̄
searchꎬ Inc. ) using the following program: 5 min at
94℃ꎻ 34 cycles of 50 s at 94℃ꎬ 1 min at 49℃ꎬ 2
min at 72℃ꎻ and then a 10 min final extension at
72℃. Control reactionꎬ in which no DNA template
was presentꎬ was performed to test for possible con ̄
tamination of the reagents with fungal DNA. Ampli ̄
fied PCR products (10 μL) were separated by hori ̄
zontal gel electrophoresis in 1. 5% agarose gel at
room temperature in 1 × TAE (40 mmol / L Trisꎬ 20
mmol / L acetate acidꎬ 1 mmol / L EDTAꎬ pH 8. 0)
running buffer. Gels were stained in dilute ethidium
bromide (0. 5 μg / mL)ꎬ and DNA was visualized
under UV light and photographed using the ALPHA
Electrophoresis Documentation and Analysis Sys ̄
tem. DNA ladder DL2 000 (TaKaRa) was used as
a size marker.
1. 4  Species ̄specific primers
The specific amplified fragment was gel purified
using the Gel DNA extraction kit ( SBS Genetech
Co. Ltdꎬ China) according to the manufacturer’ s
instructions. The purified PCR fragment was cloned
into the pMD18 ̄T (TaKaRa) vector. Ligated pro ̄
duct was transformed into the Escherichia coli DH5α
competent cells. The cloned fragment was sequenced
by Invitrogen using M13 forward and M13 reverse
primers. The sequence was analyzed and the
BLASTN / BLASTX search was performed to check
for potential homologous sequences. Based on the
sequencesꎬ a pair of primers was designed with the
Oligo 6. 0 software. The primers were synthesized
by company ( Invitrogen) .
1. 5   Universality and specificity of the de ̄
signed primers
The universality and specificity of the designed
primers were tested by PCR. Specific primers for T.
controversa were designed based on the unique se ̄
quence. The forward primer was named TCKF (5′ ̄
TCA AGA CGA AAG TAG CCG AAG  ̄3′) and the
reverse primer was named TCKR (5′ ̄ CCG TCC
TCG TCT TTG TGA TCC  ̄3′) . PCRs were per ̄
formed in a 25 μL reaction volume that contained 30
ng DNA templatesꎬ 1 × PCR buffer (plus Mg2 + )ꎬ
50 μmol / L each dNTPsꎬ 0. 2 μmol / L each primer
and 1 U of Taq DNA polymerase (TaKaRa) . The
PCR conditions were consisted of an initial denatu ̄
rizing step at 94℃ for 5 min followed by 35 cycles
of denaturizing at 94℃ for 1 minꎬ annealing at 65℃
for 50 secꎬ elongation at 72℃ for 1 minꎬ and a final
elongation step of 72℃ for 5 min. PCR products
were electrophoresed through 1. 5% agarose gelꎬ
stained with ethidium bromideꎬ and visualized under
ultraviolet light. The specificity of primers was eva ̄
luated using the extracted DNA of the 12 isolates of
T. controversa and 14 isolates of other related fungi.
1. 6   Determination of sensitivity of T. con ̄
troversa ̄specific primers
To determine the sensitivity of the PCR with T.
controversa ̄specific primer TCKF / TCKRꎬ the ge ̄
nomic DNA was diluted serially until the final DNA
concentration was 400 pg / μL. A 1μL aliquot of
each dilution was used in the PCR. The PCR condi ̄
tions were an initial denaturizing step at 94℃ for 5
min followed by 35 cycles of denaturizing at 94℃
for 1 minꎬ annealing at 65℃ for 50 secꎬ elongation
at 72℃ for 1 minꎬ and a final elongation step at
933
 
植物病理学报 43 卷
72℃ for 5 min. The PCR products were electropho ̄
resed through 1. 5% agarose gelꎬ stained with ethi ̄
dium bromideꎬ and then visualized under ultraviolet
light. The initial DNA concentration was measured
using NanoDrop ND ̄1000 spectrophotometer (Ther ̄
moꎬ USA) .
2  Results
2. 1  ISSR assay
A total of six ISSR primers were used in this
study. Among theseꎬ primer P4 generated differential
polymorphic patterns between T. controversa and its
closely related species such as T. caries and T. foe ̄
tida. A DNA fragment of about 1 100 bp was only
amplified from the isolates of T. controversa but not
the isolates of its related species (Fig. 1)ꎬ sugges ̄
ting that the amplified fragment was specific to T.
controversa. For the other five ISSR primersꎬ
similar DNA polymorphism between T. controversa
and its closely related species was observed. In addi ̄
tionꎬ the polymorphic profile of U. maydis was
distinct from T. controversa and its closely related
species.
Fig. 1   Amplified DNA polymorphic pattern
generated by ISSR primer P4
Lane M: DNA markerꎻ Lanes 1 ̄4: T. controversaꎻ Lanes 5 ̄
6: T. cariesꎻ Lanes 7 ̄8: T. foetidaꎻ Lanes 9 ̄10: U. may ̄
disꎻ Lane 11: Negative controlꎻ Lane 12: No template con ̄
trol. The specific amplified fragment was indicated.
2. 2  Sequence analysis of the 1 113 bp DNA
fragment from T. controversa
A fragment of about 1 100 bp was identified
using ISSR analysis with an ISSR primer P4 from
four isolates of T. controversa. The resulting frag ̄
ments from each isolates were cloned and se ̄
quenced. The fragments were of 1 113 bp and used
for sequence alignment. No differences were found
among the 1 113 bp nucleotide sequencesꎬ indicating
the sequences were conserved in T. controversa.
The 1 113 bp DNA sequence did not reveal any sig ̄
nificant sequence identity in either nucleotide or pro ̄
tein sequence databases using BLASTN or BLASTP.
The sequence obtained in the study was deposited in
GenBank under the accession number JF965635.
2. 3  Development of species ̄specific primers
and PCR assay
A pair of specific primers of T. controversaꎬ
TCKF / TCKRꎬ was designed according to a unique
fragment identified by ISSR using the Oligo 6. 0
computer software. A fragment of 882 bp was am ̄
plified from T. controversa using the primers
TCKF / TCKR. In order to verify the specificity of
the designed primersꎬ DNA extracts were obtained
from 12 isolates of T. controversa and 14 isolates of
other related smut fungi and tested with the designed
primer set TCKF / TCKR. The 882 ̄bp fragment was
found in all isolates of T. controversa but absent
from other isolates of related smut fungi (Fig. 2) .
2. 4   Sensitivity of the species ̄specific pri ̄
mers
To determine the sensitivity limit of the species ̄
specific primers of T. controversaꎬ dilutions of puri ̄
fied total DNA from T. controversa isolates were ex ̄
amined. The results of PCR amplification indicated
that 1 ng of total DNA produced detectable band in a
25 μL PCR reaction mixture ( Fig. 3 ) . Primers
TCKF / TCKR was proved to be sensitive to detect
very low quantities of the fungal DNA.
043
 
  4 期 LIANG Hong,et al.: Molecular Identification of T. controversa Kühn by Inter ̄simple Sequence Repeat Marker
Fig. 2  Amplification of genomic DNA of T. controversa and other smut fungi
by PCR using the designed specific primers TCKF / TCKR
(A) Lane M: DNA markerꎻ Lanes 1 ̄6: T. controversaꎻ Lanes 7 ̄8: T. cariesꎻ Lanes 9 ̄14: T. foetidaꎻ Lane 15:
T. bromiꎻ Lane 16: T. barclayanaꎻ Lane 17: U. maydisꎻ Lane 18: Negative control. (B) Lane M: DNA markerꎻ
Lanes 1 ̄6: T. controversaꎻ Lane 7: T. cariesꎻ Lanes 8 ̄9: T. foetidaꎻ Lane 10: Negative control.
Fig. 3   Detection limits of T. controversa
DNA in the PCR assay using pri ̄
mers TCKF / TCKR
Lane M: DNA markerꎻ Lanes 1 ̄6: 5 ngꎬ 2. 5 ngꎬ 2 ngꎬ
1 ngꎬ 800 pgꎬ 400 pg DNAꎻ Lane 7: Negative control.
3  Discussion
PCR ̄based detection assays are extremely sensi ̄
tiveꎬ highly specificꎬ relatively quick and simple to
perform. In the current studyꎬ a PCR ̄based method
for detecting and identifying T. controversa was es ̄
tablished as an alternative to traditional methods of
morphological characterization that were time ̄consu ̄
ming and sometimes inconclusive. PCR with spe ̄
cies ̄specific primers TCKF / TCKR designed in this
work accurately differentiated T. controversa from
the other related smut fungal speciesꎬ especially T.
caries. The main practical significance of this work
was to develop a strategy for detecting T. controver ̄
sa quickly and accurately.
We had previously analyzed internal transcribed
spacer ( ITS) [17] and intergenic spacer ( IGS) of ri ̄
bosome DNA[18] of T. controversa and its related
species. The variations in ITS and IGS sequences of
Tilletia species are limited. Thusꎬ T. controversa
could not been differentiated from its related species
by comparing the sequences of ITS and IGS. The
ISSR method used in this study was obviously effec ̄
tive and sensitive to reveal the genetic diversity of
143
 
植物病理学报 43 卷
Tilletia. The longer primers and higher annealing
temperatures made ISSR a more stable and repeat ̄
able technique than RAPD.
Several studies on molecular identification and
detection of TCK had been reported. Gao et al. [19]
established a method for identifying TCK by real ̄
time fluorescent PCR. Howeverꎬ Nian and his group
could not repeat the method described by Gao et al.
to differentiate TCK and TCT ( Tilletia cariesꎬ
Tul. ) isolates[20] . Insteadꎬ they selected a 1 322 bp
specific fragment of TCK based on RM ̄PCR
(RAPD primer mediated hemi ̄specific PCR)ꎬ es ̄
tablished universal PCR[20] and real time PCR[21] to
identify TCKꎬ respectively. Liu et al. [22] developed
an approach for distinguishing TCK from similar
species based on AFLP (Amplified fragment length
polymorphism) . The detection limit of the specific
primer set was 10 ng DNA in a 25 μL PCR reaction.
In a study performed by Cai et al. [23]ꎬ it was stated
that the detection system developed by Nian et al[20]
could only identify TCK but not its related speciesꎬ
TCT. Based on 1 322 bp marker selected by Nian et
al. [20] Cai et al. established HRCA (hyperbranched
rolling cycle amplification) to detect TCK with de ̄
tection limit of 10 pg / μL of genomic DNA[23] . Re ̄
al ̄time PCR offers distinct advantage over regular
PCR due to its extremely high sensitivity. Howeverꎬ
it requires expensive equipments and reagents.
In the current workꎬ we identified a unique spe ̄
cies ̄specific DNA fragment from T. controversa by
ISSR and designed a pair of species ̄specific primers
used for PCR ̄based detection and identification of
T. controversa. The detection limit by ISSR marker
in the present study was 1 ng of DNA in a 25 μL
PCR reaction mixtureꎬ which was lower than that by
AFLP marker described by Liu et al. [22] but higher
than that by HRCA approach performed by Cai
et al. [23] . The ISSR ̄PCR method capable of detec ̄
ting T. controversa was developed and could be a
supplement to the current molecular identification
methods. Actuallyꎬ the work was finished in 2006
and applied for a patent in China based on the results
subsequently. The patent ( ZL200610114229. 3 )
was granted in Juneꎬ 2011.
Acknowledgments
We thank Prof. Chen Wan ̄quan ( Institute of
Plant Protectionꎬ Chinese Academy of Agricultural
Sciences) for providing isolates of T. controversaꎬ
Prof. Chen Xiu ̄rong (Gansu Agricultural Universi ̄
ty) for providing the isolates of T. caries and T.
foetida and HAMS (Herbarium Mycologicum Aca ̄
demiae Sinicaeꎬ Institute of Microbiologyꎬ Chinese
Academy of Sciences) for providing isolates of smut
fungi.
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