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Epidemiology of Fusarium Diseases in Sugarcane
Epidemiology of Fusarium Diseases in Sugarcane
Epidemiology of Fusarium Diseases in Sugarcane
DOI 10.1007/s12355-017-0552-4
RESEARCH ARTICLE
Abstract Sugarcane, an important field crop, is cultivated Keywords Sugarcane Wilt Pokkah boeng
under tropical and subtropical regions around the world. Fusarium sacchari, TEF1-a
Fusarium sacchari causing wilt, is a stalk disease, inflicting
severe damage to the crop in India and other countries.
Similarly, pokkah boeng (PB) a foliar disease caused by Introduction
different species of Fusarium also infects the crop
throughout the world. In India, both the diseases occur in Wilt of sugarcane was recorded more than 100 years ago in
different states in various sugarcane varieties. Although India, since then it caused enormous damage to cane cul-
both diseases occur independently in the field, we recorded tivation in the country (Viswanathan 2013). Recent studies
that they occur together in a plant. Hence, a detailed conducted at the Institute revealed occurrence of the dis-
investigation was conducted to characterize different ease in almost all the sugarcane growing states in the
Fusarium isolates from wilt- and PB-affected sugarcane country to varying intensities. Many of the popular vari-
varieties by sequencing TEF1-a gene. Gene sequencing of eties under cultivation were affected by the disease (Vis-
48 isolates revealed that 44 were of F. sacchari and the wanathan 2012; Viswanathan et al. 2006). Detailed
remaining four belonged to F. proliferatum. Of the four F. characterization of the wilt-associated pathogen in the
proliferatum, three were associated with PB and one with country using cultural, morphological and molecular tools
wilt. Almost all the 41 wilt-associated isolates belonged to clearly established that only Fusarium sacchari is the
F. sacchari. Investigation carried out to identify Fusarium causative organization of the disease (Poongothai et al.
isolates from the plants exhibiting both the wilt and the PB 2014a, b, 2015; Viswanathan et al. 2011, 2012). Earlier
in two varieties Co 0238 and MS 901 revealed that only F. studies in India reported that the disease occurs during
sacchari caused wilt and PB symptoms in both. Further, 4–5 months or later in the crop (Agnihotri 1983; Rao and
several varieties showed progressive disease severity Agnihotri 2000). However, studies of Viswanathan (2013)
through different phases of PB and that resulted in wilt clearly revealed that apart from its severe expression dur-
development. The results clearly established for the first ing grand growth/maturity phases of the crop in the field,
time that the same fungal pathogen systematically infects wilt occurs during germination and tillering phases in
sugarcane plant and exhibits both the diseases. sugarcane. The same study very clearly demonstrated death
of settlings in sugarcane is due to wilt in the mother setts.
Studies of Viswanathan et al. (2015) also revealed wilt
development during germination phase in sugarcane.
& R. Viswanathan Wakker and Went (1896) first observed and character-
rasaviswanathan@yahoo.co.in
ized pokkah boeng (PB) in sugarcane in Java, and the term
1
Division of Crop Protection, ICAR-Sugarcane Breeding ‘pokkah boeng’ is a ‘Javanese term’ that refers to mal-
Institute, Coimbatore 641007, India formed or distorted top. The disease is one of the most
2
ICAR-Sugarcane Breeding Institute Regional Centre, Karnal serious fungal diseases in most, if not all, sugarcane pro-
132001, India ducing areas of the world (Whittle and Irawan 2000). The
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disease is reported to be caused by different species of extraction by this method was better than CTAB method.
Fusarium such as F. sacchari, F. verticillioides, F. Primers targeting Translation elongation factor 1-alpha
andiyazi, F. subglutinans and F. semitectum in different (TEF1-a) gene (forward TCTGCCATCGAAACCCTCAC;
countries (Lin et al. 2014, 2015; McFarlane et al. 2009; reverse GACGGTGACATAGTAGCGGG) were designed
Nordahliawate et al. 2008; Taher Khani et al. 2013; Zain- from the conserved region of the gene, and PCR reactions
udin et al. 2009). In India, also PB occurs in all the sug- were performed in a 25 ll PCR reaction mixture. Ampli-
arcane growing states with different disease severities fication conditions for the TEF gene consisted of an initial
(Viswanathan 2012; Vishwakarma et al. 2013). Recently, denaturation step of 5 min at 94 °C, followed by 35 cycles
severe outbreak of PB was recorded in National of 94 °C for 1 min, 55 °C for 30 s, 72 °C for 1 min and a
Hybridization Garden (NHG) of the Institute which houses final extension step of 10 min at 72 °C (Mastercycler
more than 600 sugarcane parental clones of diverse origin gradient, Eppendorf) followed by electrophoresis on 1.0%
to make biparental crossing. It was also found that apart agarose gels. PCR products were visualized by staining
from independent occurrences of PB and wilt in these with EtBr. PCR-amplified DNA fragments were purified
different parental clones, there were also instances where and sequenced. The sequences of 48 isolates were com-
same cane is affected by both the diseases (Viswanathan pared with GenBank database using BLASTn.
et al. 2014). Earlier also, Viswanathan (2013) recorded wilt
development after PB occurrences in sugarcane and he
opined that the same pathogen might cause both the dis- Results
eases in sugarcane. Hence, further studies were conducted
to characterize Fusarium spp. associated with wilt and PB Expression of PB and Wilt Symptoms in Sugarcane
in sugarcane with an objective of does the same Fusarium
sp. cause both the diseases using conventional and Appearance of PB symptoms in different varieties was
molecular tools. The studies established for the first time noticed 3 months after planting till 1 year or harvest of the
that under Indian scenario, F. sacchari is the major cau- crop. At the time of disease notice, most of the varieties
sative agent of both wilt and PB and the same pathogen exhibited chronic phase of the disease. However, we
causes the two diseases in a sugarcane plant. observed disease progress in a different way such as pro-
gress of the disease from chronic phase of PB to systemic
yellowing followed by wilt in many varieties (Table 1).
Materials and Methods During the chronic phase, only few leaves in the crown
region showed malformation with chlorotic patches and
Epidemiological Studies for Wilt and PB Expression fungal growth on the leaf lamina/sheath (Fig. 1a). Subse-
in Sugarcane Varieties quently, the affected leaves one by one showed complete
yellowing and drying (Fig. 1b). This has resulted in sys-
Observations were made on the status of PB in sugarcane temic yellowing and drying of leaves. Overall, now the
varietal collections maintained at the Institute during the disease phase has changed to wilt from PB (Fig. 1c). The
2015–2016 and 2016–2017 seasons. Occurrences of four process of such shift in the disease occurred between 4 and
different phases of PB incidences viz., chlorotic, acute, 8 months after planting in the field in the varieties such as
knife-cut and top rot phases were recorded up to grand C 79218, Co 86002, Co 86027, Co 86032, Co 89003, Co
growth stages in the field. Simultaneously, appearance of 94008, Co 94012, Co 99004, Co 2000-10, Co 0238, CoC
wilt symptoms in different PB-affected sugarcane varieties 671, CoC 90063, CoJ 72, BO 106 and MS 901 (Table 1).
was recorded. Pathogen isolation was made from both PB- The systemically disease-affected canes with foliage dry-
and wilt-affected tissues by following standard mycologi- ing exhibited typical wilt symptoms of discolouration of
cal procedures. Selected isolates were subjected to Fusar- the stalk tissue with pith cavities. In case of the cv CoN
ium sp. confirmation by PCR assays for termination 12074, downward and upward progress of Fusarium
elongation factor 1-alpha (TEF1-a) gene amplification and infection and wilt from the shortened internodes of PB-
sequencing. affected canes was observed (Fig. 2). Similar to systemic
infection of Fusarium from chronic phase of PB to wilt in
Termination Elongation Factor (TEF) Gene sugarcane, we made detailed studies on Fusarium infection
Amplification and Sequencing from knife-cut phase of wilt and top rot. In the cvs Co
87023 and MS 901, progress of wilt from knife-cut phase
Genomic DNA was extracted from mycelial mats of was documented. These varieties exhibited knife-cut inju-
Fusarium isolates grown on potato dextrose broth for ries of various sizes accompanied by sprouting of axillary
7 days by using SDS extraction buffer. We found DNA buds. The knife cuts had a depth of up to 20 mm, and the
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Table 1 Fusarium isolates recovered from sugarcane and their identity after nucleotide BLAST analysis based on their TEF1-a gene sequences
S. no. Isolate Variety Location Year Species
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Table 1 continued
S. no. Isolate Variety Location Year Species
Fig. 1 Stage shift of foliage infection to systemic wilt in sugarcane cv CoC 671. a Pokkah boeng phase, b leaves in the crown showing infection
and discolouration and c affected plants show systemic yellowing of leaves
cavities on the stalks occupied almost entire core tissues. In results of the isolates revealed that of the 48 isolates, 44
many canes, such bud sprouts appeared as branched canes belonged to F. sacchari and four belonged to F. prolifer-
with robust growth (Fig. 3a, b). In such cane stalks also, we atum (Table 1). The molecular assays very clearly estab-
witnessed progress of wilt from the affected internode lished that most of the wilt- and PB-associated isolates
(Fig. 4). Pathogen isolation has been made from affected belonged to F. sacchari. Among the 41 isolates from the
tissues of leaf lamina, spindle tissue with top rot, stalks, stalk tissues of different sugarcane varieties, 40 were F.
roots, leaf sheath etc. from many varieties to confirm the sacchari and only one isolate from Erode was found to be
pathogen association (Fig. 5). Shift in disease development F. proliferatum. Of the seven PB-associated Fusarium, four
from PB phase to systemic wilt in sugarcane has not been were found to be F. sacchari and three F. proliferatum.
described earlier, and it is the first such report on occur- Three isolates of F. proliferatum associated with PB were
rence of both diseases together in this crop. originated from Theni and Tiruppur Districts in Tamil
Nadu and Kannur in Kerala. Similarly, another F. prolif-
PCR Assays and Identifying Associated Fusarium eratum isolate associated with wilt in Co 86032 was iso-
sp. lated from Erode District. These studies indicated that all
the pathogenic isolates associated with wilt or PB from
PCR assays conducted with TEF1-a gene primers specifi- Coimbatore belonged to F. sacchari. Both stalk and leaf
cally amplified predicted 496-bp amplicons from the isolates of Fusarium from the cvs Co 0238 and MS 901
purified Fusarium isolates. Both stalk and leaf isolates of were found to be F. sacchari. The study also established
Fusarium from the cvs Co 0238 and MS 901 exhibited that almost all the wilt-associated pathogenic fungal iso-
amplicons of 496 bp in the gel (Fig. 6). Similarly, a set of lates from diverse locations in the country belonged to F.
44 Fusarium isolates from stalk and leaf were subjected to sacchari.
PCR assays and confirmed amplification of the PCR
product. Further studies were conducted to sequence the
amplicons to identify the associated Fusarium sp. with the
two diseases. Sequencing of the amplicons and BLASTn
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the whorl. Such damages during grand growth phase of the 901 which displayed occurrence of both wilt and PB dis-
crop lead to top rot symptoms accompanied by sprouting of eases in the field. We established that the pathogen isolates
axillary buds in the top nodes (Viswanathan 2013). We also from the symptomatic stalk, root and leaf sheath tissues
witnessed under field conditions that the pathogen causing were found to be the same F. sacchari. Similarly, in this
top rot symptoms further invades stalk tissues systemically study we also found the cause of both wilt and PB by the
and causes typical wilt symptoms on the top internodes. same F. sacchari in the cv Co 0238. After recovery of PB
This clearly indicates that the same F. sacchari isolate symptoms, remnants of the pathogen infection/damage can
causes PB at first and then depending on the prevailing be seen as knife-cut and ladder-like damages in the stalks
environment and/or host variety causes wilt. Earlier, Vis- (Patil 2002, Whittle and Irawan 2000). However, no reports
wanathan et al. (2014) reported inoculation of Fusarium are available on stalk infection of the pathogen from such
isolates associated with PB from the varieties Co 8371, Co knife cut-damaged tissues as well as from the top rot-af-
99004 and CoC 671 caused systemic yellowing of leaves fected canes. The present study revealed that many sug-
suggesting that inoculated pathogen from the crown region arcanes cvs Co 0238, MS 901, CoJ 83, CoC 671, Co 94012,
progressed into stalk and caused yellowing of leaves as has Co 62174, ISH 100 etc. exhibited partial or complete
been witnessed in the present study. Furthermore, planting wilting of canes after PB occurrence (Table 1).
of wilt-affected seed canes results in systemic infection of Earlier different causative agents were reported to cause
the pathogen in the plant and first exhibited PB symptoms, sugarcane wilt in India. Detailed studies conducted earlier
subsequently wilt during grand growth phases. This was at the Institute clearly established that F. sacchari is the
validated by planting of wilt-affected canes of the cv MS causative agent of wilt. This was done based on
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RAPD, ISSR, IGS-RFLP and ITS sequencing clearly throughout the year may facilitate infection of the crop, and
established that majority of the isolates belonged to F. the crop phase and prevailing weather may decide severity
sacchari. The F. sacchari isolates grouped together in of the disease. However, further studies are required on
different phylogenetic tree, and other species such as F. influence of host resistance and role of environmental
proliferatum, F. verticillioides, F. napiforme and F. subg- conditions favouring stage shift from PB to wilt in sugar-
lutinans separated in a different cluster. The present study cane in different agro-climatic conditions in the country.
with TEF1-a gene sequencing confirmed that F. sacchari is
associated with wilt in different states in the country. Acknowledgements The authors are grateful to the Directors of the
Institute for providing facilities and acknowledge Dr. R. Jothi, Shri K.
TEF gene has become the marker of choice as a single- Manivannan and Shri. R. Nithyanandan for their technical support in
locus identification tool in Fusarium. This gene appears to carrying out field and laboratory studies. The research work was
be consistently single copy in Fusarium, and it shows a partly supported by ICAR under Outreach project on PHYTOFURA.
high level of sequence polymorphism among closely rela-
Compliance with Ethical Standards
ted species, even in comparison to the intron-rich portions
of protein-coding genes such as calmodulin, beta-tubulin Conflict of interest The authors declare that they have no conflict of
and histone H3 (Geiser et al. 2004). Due to these attributes, interest
TEF1-a gene was found to be a useful genetic marker for
phylogenetic and taxonomic studies in different Fusarium Funding This study was partly funded by Outreach project of ICAR,
ALCOCERA.
spp. McFarlane et al. (2009) earlier identified F. sacchari
isolates associated with sugarcane by sequencing TEF1-a Ethical Standard This article does not contain any studies with
fragments. In this study, we have clearly demonstrated the human participants or animals performed by any of the authors.
use of TEF1-a as a marker to identify F. sacchari and F.
proliferatum associated with PB and wilt in sugarcane
under Indian conditions. However, earlier studies at the References
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