Epidemiology of Fusarium Diseases in Sugarcane

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DOI 10.1007/s12355-017-0552-4

RESEARCH ARTICLE

Epidemiology of Fusarium Diseases in Sugarcane: A New


Discovery of Same Fusarium sacchari Causing Two Distinct
Diseases, Wilt and Pokkah Boeng
R. Viswanathan1 • C. G. Balaji1 • R. Selvakumar1 • P. Malathi1 • A. Ramesh Sundar1 •

C. Naveen Prasanth1 • M. L. Chhabra2 • B. Parameswari2

Received: 30 June 2017 / Accepted: 5 September 2017


Ó Society for Sugar Research & Promotion 2017

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

Wilt-associated (stalk infecting) isolates


1. Fs419V1 Co 419 Vedapatti, Coimbatore 2014 F. sacchari
2. Fs740V11 Co 740 Vedapatti, Coimbatore 2015 F. sacchari
3. Fs775V17 (15/16) Co 775 Vedapatti, Coimbatore 2015 F. sacchari
4. Fs2174N32 Co 62174 NHG, Coimbatore 2016 F. sacchari
5. Fs219TN3 Co 7219 Vedapatti, Coimbatore 2015 F. sacchari
6. Fs219N39 Co 7219 NHG, Coimbatore 2016 F. sacchari
7. Fs002V21 Co 86002 Vedapatti, Coimbatore 2015 F. sacchari
8. Fs010V19-1 Co 86010 Vedapatti, Coimbatore 2015 F. sacchari
9. Fs010V19-2 Co 86010 Vedapatti, Coimbatore 2016 F. sacchari
10. Fs86032E2 Co 86032 Erode, Tamil Nadu 2015 F. proliferatum
11. Fs032G Co 86032 Bardoli, Gujarat 2004 F. sacchari
12. Fs86032E8 Co 86032 Erode, Tamil Nadu 2015 F. sacchari
13. Fs023N39 Co 87023 NHG, Coimbatore 2016 F. sacchari
14. Fs023V42 Co 87023 Vedapatti, Coimbatore 2016 F. sacchari
15. Fs003H1 Co 89003 Karnal, Haryana 2005 F. sacchari
16. Fs012N11 Co 94012 NHG, Coimbatore 2015 F. sacchari
17. Fs010V8 Co 98010 Vedapatti, Coimbatore 2015 F. sacchari
18. Fs0238N2 Co 0238 NHG, Coimbatore 2015 F. sacchari
19. FsJ70N29 CoJ 70 NHG, Coimbatore 2015 F. sacchari
20. FsJa270V12 CoJaw 270 Vedapatti, Coimbatore 2015 F. sacchari
21. FsJn151N40 CoJn 80151 NHG, Coimbatore 2015 F. sacchari
22. FsM121V23 CoM 88121 Vedapatti, Coimbatore 2015 F. sacchari
23. FsN071V22 CoN 05071 Vedapatti, Coimbatore 2015 F. sacchari
24. FsOr152V6 CoOr 03152 Vedapatti, Coimbatore 2015 F. sacchari
25. FsT201V24 CoT 8201 Vedapatti, Coimbatore 2015 F. sacchari
26. FsPB181N10 CoPb 09181 NHG, Coimbatore 2015 F. sacchari
27. FsS264 N17 CoS 97264 NHG, Coimbatore 2015 F. sacchari
28. FsS423N11 CoSe 92423 NHG, Coimbatore 2015 F. sacchari
29. FsSe422N3 CoSe 95422 Vedapatti, Coimbatore 2014 F. sacchari
30. FsSnk632N26 CoSnk 03632 NHG, Coimbatore 2016 F. sacchari
31. FsC218N38 C 79218 NHG, Coimbatore 2015 F. sacchari
32. FsC218N38 C 79218 Vedapatti, Coimbatore 2016 F. sacchari
33. FsE005T11 EB10005 Kottur, Thanjavur 2015 F. sacchari
34. FsIH41N15 ISH 41 NHG, Coimbatore 2015 F. sacchari
35. FsI100N9 ISH 100 NHG, Coimbatore 2015 F. sacchari
36. FsKAKK3 Kakhai Kannur, Kerala 2015 F. sacchari
37. FsLG04N22 LG 06604 NHG, Coimbatore 2015 F. sacchari
38. Fs901N16 MS 901 NHG, Coimbatore 2015 F. sacchari
39. Fs901V7* MS 901 Vedapatti, Coimbatore 2015 F. sacchari
40. Fs901V9* MS 901 Vedapatti, Coimbatore 2015 F. saccharia
41. FsSi-308T3 SI 308 Theni, Tamil Nadu 2015 F. sacchari
Pokkah boeng-associated (leaf infecting) isolates
42. Fs86027U3 Co 86027 Udumalpet, Tiruppur 2011 F. proliferatum
43. Fs0238N2 Co 0238 NHG, Coimbatore 2016 F. sacchari
44. Fspbj83N19 CoJ 83 NHG, Coimbatore 2016 F. sacchari
45. Fs901V6* MS 901 Vedapatti, Coimbatore 2015 F. saccharib
46. FsSi02P7 Si 2000-02 Palakudi, Thanjavur 2016 F. sacchari

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Table 1 continued
S. no. Isolate Variety Location Year Species

47. FsSi-308T6 SI 308 Andipatti, Theni 2015 F. proliferatum


48. Fs28NGK7 28NG263 Kannur, Kerala 2015 F. proliferatum
a b
* Different isolates from same plant exhbiting wilt and pokkah boeng Fusarium isolated from affected root, Fusarium isolated from affected
leaf sheath

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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Rutherford 2005), F. verticillioides and G. fujikuroi (Gi-


atgong 1980), F. sacchari, F. proliferatum and F. andiyazi
(Govender et al. 2010) and F. verticillioides and F. pro-
liferatum (Lin et al. (2014), was reported as the causal
agents of PB.
Nordahliawate et al. (2008) studied F. sacchari associ-
ated with PB throughout Peninsular Malaysia and identified
the causal organism using morphological characteristics.
They also established pathogenicity of F. sacchari based
on Koch’s postulates. Recently, Taher Khani et al. (2013)
categorized Fusarium spp. associated with PB in Iran into
F. verticillioides, F. proliferatum, F. subglutinans and F.
semitectum with 55, 21.5, 17.6 and 5.9% frequencies,
respectively. Their pathogenicity studies with these fungi
indicated that all the isolates were pathogenic to sugarcane
except isolates of F. semitectum. Among the pathogenic
isolates, F. proliferatum was less pathogenic than F. ver-
ticillioides and F. subglutinans. This is the first report of
the pathogenicity of F. proliferatum on sugarcane in the
world. Recently, Rosas-Guevara et al. (2014) reported
association of F. verticillioides and F. proliferatum with
sugarcane PB samples collected from four states of Mexico
and characterized that 95.7% of the 70 isolates as F. pro-
liferatum and the rest 4.3% as F. verticillioides.
In India, PB was first recorded during 1930s and 1940s.
Severe incidences of the disease were reported from
Maharashtra, and subsequently, PB was reported from
other states like Assam, Karnataka, Uttar Pradesh, Gujarat,
Madhya Pradesh and Andhra Pradesh (Patil et al. 2007;
Viswanathan 2012). Vishwakarma et al. (2013) recently
reported that the PB severity increased in the country based
on detailed surveys during 2007–2013. PB has been
reported as a major threat in sugarcane cultivation in China
(Lin et al. 2014). Studies of Govender et al. (2010) in South
Africa revealed that PB-associated F. sacchari caused
characteristic bend symptoms in sugarcane stalks. Simi-
larly, findings of Taher Khani et al. (2013) revealed that
Fusarium spp. isolated from PB-affected leaves caused
Fig. 2 Development of typical wilt in stalks of sugarcane cv CoN mild-to-moderate symptoms on the stalks as reddish purple
12074 from pokkah boeng-affected internode. The shortened intern- discolouration in Iran. Earlier studies of Nordahliawate
odes are encircled et al. (2008) found that only isolates of F. sacchari caused
PB in sugarcane in pathogenicity studies in Malaysia and
Discussion isolates of F. proliferation and F. subglutinans were not
pathogenic. They also found that F. sacchari inoculation
Initially, Gibberella fujikuroi (Sawada) was reported as the caused death of pathogen-inoculated plants. In these stud-
PB-associated pathogen (Sheldon et al. 1904). Later, in ies, although they did not explore the possibility of wilt
Java, Bolle (1927) reported F. verticillioides (F. monili- development in sugarcane stalks by the PB-associated
forme) as the causative pathogen. In the recent decades, Fusarium, the results showed damages caused by the fun-
association of several species of Fusarium, including F. gal isolates on the stalk tissues. Probably here also the
verticillioides (Martin et al. 1989; Mohammadi et al. plants may have apparent systemic infection caused by F.
2012), F. sacchari (Nordahliawate et al. 2008), F. prolif- sacchari as seen under Indian conditions.
eratum and F. subglutinans (Taher Khani et al. 2013), F. It is well known that acute phase of PB causes death of
verticillioides or F. subglutinans (McFarlane and apical meristem accompanied by dead heart symptoms in

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Fig. 3 Pokkah boeng-affected


canes exhibit knife-cut
symptoms (encircled) and
axillary shoots from bud
sprouts. a cv MS 901, b cv Co
87023

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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Fig. 5 Recovery of Fusarium from the tissues exhibiting both


pokkah boeng and wilt after top rot in the same cane of the sugarcane
cv Co 86027

Fig. 4 Progress of wilt from pokkah boeng-affected internode with


knife-cut phase (encircled) in sugarcane stalks (cv Co 87023)

pathogenicity studies and Koch’s postulates (Viswanathan


et al. 2011). The pathogenicity studies were also supported
by specific RAPD and ISSR markers to confirm the isolates
associated with pathogenicity in sugarcane. Subsequently,
detailed morphological characterization of more than 100
isolates originated from 13 major sugarcane growing states
revealed that majority of them belonged to F. sacchari
Fig. 6 Amplification of 496 bp TEF1-a gene fragment of Fusarium
(Poongothai et al. 2014b). Characterizing a subset 50 of the sacchari isolates from the sugarcane cv MS 901
117 isolates through different molecular markers such as

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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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