Sugarcane (Saccharum spp. hybrids) is a major field crop grown in India in about 5.2 M ha, under tropical and subtropical conditions. Although sugar and other sweeteners are the major products from the sugar industry, currently more emphasis is given for ethanol production for bioenergy from distilleries attached to sugar industries. In India, sugarcane production and productivity suffers from various biotic and abiotic factors. Red rot caused by Colletotrichum falcatum Went is one of the major constraints affecting sugarcane production both in subtropical and in tropical regions in the country (Viswanathan and Rao 2011). During severe outbreaks, the disease causes large-scale destructions in the field and total crop losses also expected in the field. Many outstanding varieties like Co 1148, Co 6304, Co 7805, CoC 671, CoC 92061, CoJ 64, CoS 8436, CoSe 92423 and CoSe 95422 suffered in the field due to red rot in the recent decades and were removed from cultivation (Viswanathan 2010; Viswanathan et al. 2018). To manage the disease, new resistant varieties are released for cultivation. After each varietal breakdown/epidemics varietal replacements occurred during the last 100 years in India. Though all the varieties released for cultivation are resistant, slowly they succumb to the pathogen and that makes sugarcane breeding in India centering around red rot resistance (Viswanathan 2018). Development of new variants contribute to the varietal breakdown, and the new C. falcatum pathotype has adapted to a ruling variety which was hither to resistant (Viswanathan et al. 2003, 2017). Recently, Viswanathan (2017) reported emergence of a new C. falcatum pathotype CF12 based on its virulent behaviour on a set of sugarcane varieties and its comparatively higher virulence over the former pathotype CF06. This pathotype was able to decimate different varieties (CoV 09356, CoSi 6, CoC 24, Co 92012 and Co 94012) under tropical conditions.

Earlier studies indicated adaptation of C. falcatum to new varieties in causing breakdown effect (Srinivasan 1962; Malathi et al. 2006; Viswanathan 2010; Viswanathan et al. 2003). For this to happen, the pathogenic fungus has to cohabit with the host varieties in the field. Major source of pathogen inoculum freely available is soil borne inoculum, mostly thriving on crop residues. Planting new varieties in fields provides an opportunity for their infection and the pathogen attempts to initiate infection on new varieties probably through repeated attempts. Though the reports on the longevity of pathogen surviving in the soil vary, they agree that soil borne sources of C. falcatum play a crucial role for primary infection along with sett borne inoculum (Viswanathan 2010). The sett borne inoculum directly initiates infection in the host and causes the disease. The released inocula from the dead tissues or conidia spread by rain or irrigation water may serve as sources for new infections. Since there is a lack of information on the role of soil borne inocula of C. falcatum on disease development under tropical conditions, detailed studies were taken up on the impact of this inoculum on infection of buds during germination phase on a set of sugarcane varieties varying in disease resistance and further disease build-up in the field with different pathogenic isolates varying in their virulence. This study has come out with new information on vulnerability of sprouting buds to C. falcatum, and probably, this primary infection may further lead to C. falcatum adaptation in new host varieties. Also we found differential behaviour of soil borne inoculum of C. falcatum against sugarcane varieties for the first time.

Materials and Methods

Field experiments were conducted during 2017–2018 and 2018–2019 seasons at Plant Pathology Farm, ICAR-Sugarcane Breeding Institute, Coimbatore (11.99°N, 76.91°E). The experiments comprised 10 sugarcane varieties varying in red rot resistance according to 0-9 red rot scale developed at ICAR-SBI (Srinivasan and Bhat 1961). As per the scale, the sugarcane clones are classified as resistant (0–2), moderately resistant (2.1–4.0), moderately susceptible (4.1–6.0), susceptible (6.1–8.0) and highly susceptible (8.1–9.0) according to red rot severity. The varieties from moderately resistant (Co 0212, Co 0238 and Co 0403), moderately susceptible (Co 86032, Co 06022, Co 06027, Co 06030 and CoV 09356) and highly susceptible (Co 94012 and CoC 671) categories were included in this study. At Plant Pathology Lab of the institute, C. falcatum isolates isolated from many field-grown varieties are being maintained and viability of them is assessed every year on their respective hosts. From this C. falcatum repository, 11 isolates, viz. Cf671 (Pathotype CF06), Cf94012 (Pathotype CF12), Cf0323-Petta, Cf99006-MPM, CfV09356-ENGR, Cf671-Tuhili, Cf86027-NKU, Cf2001-13-PPM, Cf06022-KUT, Cf86032-SKPM and Cf0323-TNV, representing different host varieties and locations in Tamil Nadu state were selected for this study (Table 1). Before the conduction of experiment, the field was left fallow for 1 year with 3–4 ploughings with a short green manure crop of sun hemp (Crotalaria juncea) to augment soil organic matter. This is a regular practice to eradicate red rot pathogen inoculum remaining in the soil and to prevent decline in crop vigour due to monocropping.

Table 1 Details of Colletotrichum falcatum isolates used in the study
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In total, 12 blocks comprising 10 varieties each were planted in 3-m rows and each block was treated with individual isolate. Each block was separated from other block by three empty rows to prevent and mix up of other isolates from adjacent plots through irrigation or rain water. About 20 two budded healthy setts from each sugarcane variety free from red rot and other stalk diseases were planted in a row. Each pathogenic isolate was multiplied in the laboratory on sorghum grains as reported earlier (Mohanraj et al. 2012). The individual isolate of C. falcatum was mixed with sand to have uniform distribution of the inoculum, and the concentration of inoculum was maintained at the rate of 105 per gram of sand before application in the soil. At the time of planting, the individual isolates of C. falcatum were applied on the setts at 100 g per row ensuring the availability of inoculum in the soil around the germinating buds. After the application of the inoculum, the setts were covered with soil from both sides of ridges and irrigated. The crop was raised following the standard package of practices for a tropical sugarcane. Under tropical conditions, bud germination starts 10 days after planting and therefore bud sprouting was recorded from 15 days after planting and disease development on main stalks and tillers was recorded at regular intervals. Impact of C. falcatum on bud germination and post-emergent death of sprouts was assessed as death of buds and drying of germinated sprouts, respectively. Germination in the C. falcatum inoculated plots was compared with pathogen-free control plots. In control plots, all the 10 test varieties were planted at rate of 20 two budded setts per row each obtained from healthy canes without pathogen inoculum. The disease development in the form of yellowing or orange discoloration of sprouts/shoots, death of stalks/tillers was recorded in the pathogen inoculated plots and control healthy plots remained free from red rot infections. At the time of harvest (360 days) surviving total cane population in the trial plots were recorded and compared with the population of the respective varieties in the pathogen-free healthy plots to assess impact of the pathogen inoculum on cane survival.

Results and Discussion

Impact of Soil Borne Inoculum on Sett Germination

During 2017–2018 season, overall germination in healthy control plots was 74.0%, whereas the pathogen inoculated plots recorded a mean germination of only 43.6%, indicating a drastic reduction of 41.4% in bud sprouting due to the pathogen presence in the soil (Table 2). Among the 10 varieties tested, all of them showed reduced sett germination in the range of 59.2–16.2%, the highest being in the cv CoC 671 and least in case of Co 0403. The cvs Co 86032, Co 94012 and Co 06022 recorded more than 50% mean germination loss in the trial plots. Apart from the cv Co 0403, only two other cvs Co 0238 and Co 06027 recorded mean germination of more than 50% and other varieties recorded less than 50% mean germination. The cv Co 06030 recorded the lowest mean germination of 29.1% and followed by Co 94012, CoC 671 and Co 86032 and other varieties. When germination in plots against C. falcatum isolates was seen, the cvs Co 0403 and Co 0238 recorded highest germination with six and four isolates, respectively. However, the cv CoV 09356 recorded highest germination in case of the isolate Cf99006-MPM. The cv Co 06030 recorded lowest germination against five isolates, whereas the cvs Co 86032 and CoC 671 recorded least germination against two isolates each (Table 2). Among all the varieties, the cv Co 0238 was not affected by the presence of C. falcatum in the soil, where germination of more than 50% was recorded against each of the 11 C. falcatum isolates. Two cvs Co 94012 and Co 06030 recorded germination of less than 50% against all the isolates, the cvs Co 86032 and CoC 671 recorded > 50% germination against one isolate each, whereas the cv Co 06022 had > 50% germination against two isolates, cv CoV 09356 against five and the cvs Co 0212 and Co 06027 against seven isolates each (Table 2). Overall, C. falcatum isolates caused ~ 41.4% reduction in germination in 10 varieties, the C. falcatum isolate Cf0323-TNV caused least impact on germination (53.0%), whereas the isolate Cf86032-SKPM caused highest impact on germination (35.5%). The other isolates with higher impact on germination were Cf06022-KUT (36.3%) followed by Cf2001-13-PPM (39.3%) and Cf86027-NKU (40.5%). In case of other isolates mean germination ranged from 47.8 to 42.3%. When interaction of C. falcatum isolates and their host varieties in germination was studied, it was found that two isolates, viz. Cf671-Tuhili and Cf86032-SKPM, caused maximum germination loss against the host varieties, CoC 671 (20.0%) and Co 86032 (22.5%), respectively. Although the isolates Cf671, Cf94012, CfV09356-EGNR and Cf06022-KUT had matching host varieties in the trial, their potential to reduce germination was highest in other varieties (Table 2).

Table 2 Impact of C. falcatum inoculum applied to the soil on sett germination (%) in different sugarcane varieties (2017–2018 and 2018–2019 seasons)
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The trial was repeated with the same set of host varieties and C. falcatum isolates during 2018–2019. The pathogen inoculated plots had an overall mean germination of 46.0% as compared to 75.3% in uninoculated control plots, indicating a drastic reduction of 39.0% in sett germination (Table 2). Sett germination across the varieties revealed that Co 0238 recorded the highest mean germination (57.5%), whereas the cv Co 94012 recorded the least germination (31.1%) in the pathogen inoculated plots. The other cvs Co 0212, Co 0403 and Co 06027 recorded mean germination of more than 50% and the susceptible cvs CoC 671 and Co 94012 recorded mean germination of 36.6% and 31.1%, respectively (Table 2). When germination across the isolates was seen, in the cv Co 0238, germination of more than 50% recorded against nine isolates, whereas in other varieties such as Co 0403 (7 isolates), Co 06027 (6 isolates) and CoV 09356 (3 isolates) germination of more than 50% was recorded. The cvs Co 0212, Co 06022 and Co 06030 recorded more than 50% germination against five isolates each, whereas the cvs Co 86032 and CoC 671 recorded against only one isolate CfV09356-ENGR and Cf671-Tuhili, respectively. The cv Co 94012 recorded least germination against seven isolates, whereas other cvs Co 86032, CoC 671, Co 06022 and Co 06030 recorded least germination against one isolate each. Data on reduction in sett germination revealed that the cv Co 86032 recorded the highest reduction in germination of 50.9% and the cv Co 0238 recorded the least reduction of 25.8% (Table 2). The cvs Co 0212, CoC 671, Co 94012 and CoV 09356 recorded higher loss in mean germination than the overall mean reduction of 39.0%. Among the C. falcatum isolates, the isolates and Cf06022-KUT caused more impact on sett germination as indicated by least mean germination of 40.0% and was followed by Cf86027-NKU, Cf0323-Petta, Cf671, Cf671-Tuhili, Cf86032-SKPM, Cf99006-MPM, Cf2001-13-PPM and Cf94012. The isolates CfV09356-ENGR and Cf0323-TNV exhibited least impact on sett germination (Table 2). When impact of sett germination by the isolates on their host varieties was analysed, none of the five isolates Cf671, Cf671-Tuhili, Cf94012, CfV09356-ENGR and Cf06022-KUT caused highest impact on the respective host cvs CoC 671, Co 94012, CoV 09356 and Co 06022 (Table 2).

Among the two seasons, 2017–2018 showed relatively more impact on bud germination than 2018–2019 season. The resistant varieties such as Co 0212, Co 0238 and Co 0403 recorded more than 50% germination during both the seasons against different isolates (Table 2). The cv Co 0238 exhibited more than 50% germination against all the 11 isolates during 2018–2019, whereas germination in the susceptible cvs Co 94012 and CoC 671 and moderately susceptible cvs Co 86032 and Co 06030 was affected due to C. falcatum inoculum in the soil (Table 2). This observation suggests that although C. falcatum tries to affect bud sprouting in the resistant varieties, the impact is not visible in the field and crop establishment appears to be normal. Both the susceptible and MS varieties suffer to a larger extent probably due to direct killing of buds by the pathogen (Mohanraj et al. 2012; Mohanraj and Kaverinathan 2011).

Disease Development in the Trial Plots

Red rot Incidence 60 DAP

Infectivity of the soil borne inocula of 11 C. falcatum isolates on the 10 sugarcane varieties varying in disease resistance revealed that two resistant varieties Co 0238 and Co 0403 and one MS cv Co 06027 remained disease-free by 60 DAP during 2017–2018 (Table 3). Unexpectedly, all the isolates did not cause disease even in the known susceptible cvs Co 94012 and CoC 671. The Co 94012 was free from infections to four isolates, and the cv CoC 671 was free from six isolates. In case of other MS cvs, Co 86032 picked up infection from an isolate, three each in Co 06022 and CoV 09356 and six in Co 06030. The MR cv Co 0212 picked up infection from one isolate (Table 3). The C. falcatum isolates exhibited a differential behaviour in causing infection across the varieties. The isolates, Cf671-Tuhili and Cf2001-13-PPM, did not exhibit disease on any of the varieties, whereas the isolates Cf671, Cf94012, Cf99006-MPM and Cf0323-Petta caused disease on at least one variety each, Cf06022-KUT and Cf86027-NKU caused disease on six varieties each followed by Cf86032-SKPM on five, and Cf0323-TNV and CfV09356-ENGR on three each during 2017–2018 season.

Table 3 Per cent incidence of red rot on sugarcane varieties varying in red rot resistance to soil borne inoculum of C. falcatum—60 days after planting (2017–2018 and 2018–2019 seasons)
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Unlike the previous season, during 2018–2019, the soil borne inoculum of all the C. falcatum isolates exhibited red rot in the susceptible cvs CoC 671 and Co 94012; however, the MR cv Co 0238 remained free from the disease for all the pathogenic isolates. The cvs Co 86032 and Co 0212 remained free from C. falcatum infections except to the isolates Cf671 and Cf0323-Petta, respectively, with limited infections (Fig. 1a, b), whereas many of the varieties with MS reaction to C. falcatum exhibited moderate to severe infections against different isolates and the cvs Co 0403, CoV 09356, Co 06027, Co 06022 and Co 06030 infected by five, six, eight, nine and ten isolates, respectively. The isolates Cf0323-Petta, Cf671-Tuhili and Cf86027-NKU caused the disease in maximum of eight varieties each, followed by seven varieties by Cf2001-13-PPM, six by CfV09356-ENGR, Cf06022-KUT and Cf0323-TNV, five by Cf671, Cf99006-MPM and Cf86032-SKPM and four by Cf94012 (Table 3). The susceptible cvs Co 94012 and CoC 671 recorded very high incidences of more than 75% disease against 3–4 isolates. The isolates, Cf99006-MPM and Cf06022-KUT, caused severe disease on both these varieties. The other isolates Cf0323-TNV, Cf671-Tuhili and Cf86027-NKU also caused severe disease on one or two varieties. The MS cvs Co 06030 and CoV 09356 exhibited severe disease incidence of more than 75% against Cf0323-TNV and Cf06022-KUT, respectively. Overall, during 2018–2019 season disease incidence was very high as compared to the previous season. The cvs Co 403 and Co 06027 which were free from infections against all the isolates during previous season 2017–2018 picked up red rot from four and eight isolates, respectively, during 2018–2019 (Table 3).

Fig. 1
figure 1

a Sugarcane varieties exhibiting death of plants by 60 days after planting by C. falcatum CF12 inoculum. b Healthy crop stand of sugarcane varieties, 60 days after planting. From left—cvs Co 86032, Co 0212, Co 0238 and Co 0403 against C. falcatum CF12 inoculum

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Red Rot Incidence 240 DAP

During 2017–2018 season, the disease development was less in the trial where six of the 10 varieties remained free from the disease by 240 DAP. The susceptible cvs CoC 671 and Co 94012 and MS cvs Co 06022 and Co 06027 exhibited red rot against one isolate each; however, the MS cv CoV 09356 exhibited the disease against three isolates. C. falcatum isolates Cf671, Cf94012, CfV09356-ENGR, Cf671-Tuhili, Cf2001-13-PPM and Cf86032-SKPM did not exhibit the disease across the varieties during 240 DAP during 2017–2018 season (Table 4).

Table 4 Per cent incidence of red rot on sugarcane varieties varying in red rot resistance to soil borne inoculum of C. falcatum 240 days after planting (2017–2018 and 2018–2019)
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During the maturity stage of the crop in 2018–2019, the cvs Co 0212, Co 0238 and Co 0403 were free from the disease infections and the cv Co 86032 recorded 9.4% red rot against Cf671-Tuhili, and except this isolate, none of the other isolates caused disease in Co 86032. The two susceptible cvs CoC 671 and Co 94012 exhibited very severe red rot incidences of 71.4–100%, across the isolates. The MS cv Co 06030 also exhibited disease against 10 of 11 isolates with a mean disease incidence of 83.3%. The other MS cvs Co 06022, Co 06027 and CoV 09356 exhibited disease against 5–7 isolates with mean disease incidences of 23.4%, 47.5% and 27.1%, respectively. The C. falcatum-Cf86027-NKU isolate caused death of almost all the plants in rows of cvs Co 06022, Co 06027 and Co 06030 (Fig. 2). Among the isolates Cf06022-KUT appeared to be more virulent in causing disease on six varieties with a mean disease incidence of 49.3%, followed by Cf2001-13-PPM, Cf0323-Petta, Cf86027-NKU, Cf671-Tuhili and others (Table 4).

Fig. 2
figure 2

Death of plants in rows of sugarcane cvs Co 06022, Co 06027 and Co 06030 (left to right) to C. falcatum-Cf86027-NKU isolate by 240 days after planting

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Total Cane Population at the Time of Harvest

Total cane population in the trial plots at the time of harvest (360 days) revealed that in all the varieties, cane population showed a reduction except in the cv Co 0403 during 2017–2018 season. In the cv Co 0238 the loss in population was just 5.3% only, and in other varieties the loss was in the range of 26.3–40.9%. The population loss was ~ 30% in the cvs Co 86032 (29.2%), Co 06027 (26.5%), CoC 671 (26.3%), Co 94012 (28.7%), Co 0212 (30.6%) and CoV 09356 (34.7%); ~ 40 in the cvs Co 06022 (39.12%) and Co 06030 (40.89%) (Table 5). However, comparatively a low population count in the trial plots was recorded during 2018–2019 which reflected loss of canes due to red rot during the preceding months. It was found that during 2018–2019 season, the two susceptible cvs CoC 671 and Co 94012 recorded a mean reduction of 80.1% and 86.1%, respectively. Similarly, the MS cvs Co 06030, Co 06022, CoV 09356 and Co 06027 recorded a loss of 63.1%, 52.6%, 48.0% and 42.5%, respectively. The other MS cv Co 86032 recorded a loss of 31.6%. The cane population reduction in the MR cvs Co 0212, Co 0238 and Co 0403 was in the range of 17.9–26.8% (Table 5).

Table 5 Total cane population in different sugarcane varieties in the trial plots with soil borne inoculum of C. falcatum at the time of harvest—360 days (2017–2018 and 2018–2019)
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Influence of Weather on Disease Severity

As compared to 2017–2018, the disease severity was high during the 2018–2019 and 2017–2018 season was warmer compared to the second and there was more variation between maximum (34–37.8 °C) and minimum (23–24 °C) temperature in the former (Fig. 3), whereas the latter had less variation between maximum (28–35 °C) and minimum (21–25 °C) temperature (Fig. 4). Between the two seasons, night temperature did not show much change, whereas there was an increase in day temperature during 2017–2018 as compared to 2018–2019. During the germination phase, we have recorded rain during 2nd, 3rd and 4th week of March and 1st week of April in 2017 and subsequently the climate became dry. However, in 2018, the rain started from 3rd week of March and continued at regular intervals till September (Fig. 2). In this study, continuous rainfall accompanied by a comparatively low day temperature from germination to grand growth phase favoured higher disease incidences during 2018–2019, whereas higher day temperature during 2017–2018 season with drought during grand growth phase did not favour disease development.

Fig. 3
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Weather conditions prevailed in the experimental farm during 2017–2018

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Fig. 4
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Weather conditions prevailed in the experimental farm during 2018–2019

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Surviving pathogen inocula of C. falcatum in the soil plays an important role in primary infection and epidemiology of red rot in sugarcane. The previous workers differed in their opinion on survival C. falcatum in soil and that depends on type of inocula, viz. conidial suspension, inoculum multiplied on sorghum grains/cane bits and naturally infected cane debris (Agnihotri 1983). Mohanraj et al. (2012) assessed efficacy of C. falcatum inoculum on its infectivity on sugarcane setts using fresh red rot-affected cane debris. Although they found fresh red rot-affected cane debris causes red rot in sugarcane varieties, there were inconsistencies in its efficacy in causing the disease. Hence, they have standardized C. falcatum inoculum multiplied on a mixture of sand and sorghum grains. This 10-day-old culture sporulated profusely and had consistent in disease initiation on the planted setts and further disease development in different sugarcane varieties. Earlier, Mohanraj and Kaverinathan (2011) assessed C. falcatum inoculum multiplied on sorghum/sand mixture and found 1–2 g per bud in the setts was ideal to cause red rot to a satisfactory level in the susceptible variety like CoC 671, and this inoculum load is comparable to a highly infected preceding sugarcane crop. Further, the applied inoculum was found to have 108 propagules per bud. However, they found that the inoculum load gradually declines and it loses its survival in a month after application in the soil, whereas inoculum as pathogen-infected cane debris remained active for comparatively a longer period.

Longevity of C. falcatum in soil under field conditions is influenced by various factors (Chona 1950; Singh and Agnihotri 1995). Singh et al. (1977) reported that C. falcatum survives in soil for two months when 1-cm-long pieces of affected diseased stalks and midribs were used. Subsequently Singh et al. (1986) reported survival of the fungus in the soil for nine months with red rot-affected nodal and intermodal tissues bits on soil surface and found the presence of different types of fungal structures, viz. appressoria, conidia, thick-walled hyphae, setae and chlamydospores for two months after burial. C. falcatum survival in the soil varies according to the conditions such as soil moisture, soil depth, natural soil or sterilized, nature of infected canes like split or unsplit, etc. It is also clear from the reports that C. falcatum survival as saprophyte remains low (Viswanathan, 2010). It is understood that the pathogen inoculum as infected cane survives for longer duration in soil. Further, under field conditions, the first author has found survival of C. falcatum for more than 1 year in crop residues and in stubbles. Such inoculum readily infected when susceptible varieties such as Co 6304, Co 7717, Co 94012, Co 95020, Co 2001-15 and CoC 671 were grown even after 1-year fallow at Coimbatore (Viswanathan unpublished).

Among the MS varieties the cvs Co 06027 and CoV 09356 exhibited more than 50% germination against 3–7 isolates, whereas other C. falcatum isolates caused severe loss to germination and this probably indicates a differential interaction between these varieties and the pathogenic isolates. Existence of differential interaction in sugarcane against C. falcatum isolates is well established based on the pathogenic reaction on the stalk tissues after plug method of inoculation (Viswanathan et al. 2003, 2017, 2018). The other MS varieties, Co 06022 and Co 06030, also exhibited more tolerance during 2017–2018 season, probably due to the influence of prevailing weather. Prevalence of drought and higher day temperature in the 2017–2018 season did not favour the pathogen to cause more infections on the buds. Soil moisture plays a critical role in C. falcatum infection for the surviving inoculum in the soil. High soil moisture favours red rot development, spread and development of epiphytotics in sugarcane. However, behaviour of different sugarcane varieties differs under varying soil moisture regimes (Viswanathan 2010). Earlier, it was reported that drought causes more dead parenchyma cells in the plants and that facilitates the pathogen spread in the stalks. Probably the resistance offered by host tissue against the pathogen may be less during drought, which accelerates the pathogen invasion and colonization in the host (Singh et al. 1991; Pappelis and Katasanos 1965). In Louisiana, conditions of desiccation increase disease severity in stalks and drought conditions during early growth phase increase red rot severity (Yin and Hoy 1997). These studies assessed drought conditions on progress of the disease after stalk infection, whereas our studies focused on primary source of C. falcatum infection, viz. soil borne inoculum on disease development in young sugarcane.

The results very clearly indicated that MR variety like Co 0238 does not suffer due to C. falcatum and S varieties CoC 671 and Co 94012 suffered heavily in both the seasons. In different occasions, most of the MS varieties succumbed to C. falcatum under field conditions. Though the disease incidence is less or limited as compared to severe disease outbreaks in cases of S varieties, the present study illustrates that MS varieties do pick up infection from the soil borne inoculum, during germination phase, leading to disease development in the standing canes (Fig. 5). Different tissues in nodal region, viz. bud, leaf scar and root primordia, are reported to harbour more pathogen colonization and serve as portals of pathogen entry (Singh and Singh 1989; Viswanathan et al. 1998, 2000). The inoculum in the soil may readily infect these portals on the nodal region and colonizes the nodal region. Availability of soil borne inoculum is very common in red rot endemic regions, and such inoculum gradually adapts to the varieties in due course of time and causes varietal breakdown under field conditions (Viswanathan 2010). Hence to manage red rot, addressing soil borne inoculum sources is important to prevent varietal breakdown and sustainable management of elite sugarcane varieties under field conditions.

Fig. 5
figure 5

Complete death of plants in an entire sugarcane clump due to C. falcatum inoculum applied to soil at the time of planting (cv Co 06022, 120 days after planting)

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Apart from disease build-up in S/MS varieties, the study has given new information on field tolerance to red rot in the cv Co 86032 (Fig. 6). Unlike other MS varieties, it maintained a healthy crop stand in the trial plots though it suffered to an extent of ~ 50% loss in germination. Probably, the buds that escaped the pathogen infection remained free from the pathogen infection and continue to maintain a healthy crop stand. This reiterates its field tolerance potential demonstrated earlier (Viswanathan 2010; Padmanaban et al. 2010). The first author has witnessed survival of this variety under severe epiphytotic situation caused by the cvs CoC 671, CoC 92061, Co 6304, CoSi 96071, etc., in late 1990s and early years of the last decade in the states of Tamil Nadu, Andhra Pradesh, Gujarat and Puducherry states. During those years, due to very high pathogen inoculum load in the soil, none of the susceptible varieties survived and the cv Co 86032 withstood the inoculum pressure and became a popular variety in the Peninsular India. In spite of natural incidence for red rot in isolated pockets that variety remains popular in red rot endemic regions for the last 20 years, whereas the new varieties with MS reactions, viz. Co 06022, Co 06027 and CoV 09356, suffered moderate to severe damages in commercial cultivation (Viswanathan unpublished). In the field trials, these varieties exhibited the disease to varying intensities due to their vulnerability to C. falcatum infection after germination and this clearly revealed that the presence of C. falcatum in the soil significantly reduced bud sprouting/germination in sugarcane varieties. After germination, the MR varieties and MS variety like Co 86032 remained disease-free due to inbuilt resistance or adaptive mechanism referred as field tolerance, whereas other MS varieties succumbed to the pathogen to varying intensities. Another finding was a clear exhibition of differential host interaction among the host varieties and C. falcatum isolates applied in the soil, and this is the first such report.

Fig. 6
figure 6

Healthy crop stand of sugarcane cv Co 86032 (right) against poor stand of the cv CoV 09356 (left) against C. falcatum isolate Cf86032-SKPM (120 days after planting)

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Epidemiology of red rot especially on the role of soil borne inoculum is poorly understood. Most of the published information on survival of the inoculum in the soil is generated based on research work done at subtropical region in India, where the pathogen undergoes adverse weather during winter and summer months, whereas, in tropical conditions, variation in weather is less; hence, the pathogen behaviour in the soil may be different. Hence, we conducted the study to understand how the sugarcane varieties respond to C. falcatum inoculum applied to the soil and its impact on bud sprouting. Since soil borne inoculum of C. falcatum plays a critical role in primary infection of the pathogen in the endemic regions, crop establishment and survival are linked to surviving inoculum of the pathogen. In the present study, in response to inoculation of C. falcatum in the soil, susceptible genotypes exhibit high germination failure or both pre- and post-emergent necrosis in the buds. Further, the sprouted shoots exhibit drying and death as observed in disease endemic regions.

In this study, we also found a crucial role played by the weather factors, especially rainfall and temperature, during the germination/tillering phase of the crop in disease development and its severity. Under subtropical conditions, prevailing high humidity/soil moisture during South West monsoon favour spread of red rot and development of disease epidemics (Viswanathan 2010). This is an important finding and explains how this disease attains epidemic level due to favourable environment in endemic regions. Overall, this study has given a clear understanding on the role of soil borne inoculum of C. falcatum in causing death of buds, disease in the crop, differential interaction among the varieties and pathogenic isolates, field tolerance in some varieties, influence of weather factors in deciding host–pathogen interaction, etc. Further studies are required on the basis of adaptive mechanism exhibited by the host varieties to C. falcatum inoculum in the soil and disease development in the varieties to the inoculum applied in the soil and plug method of inoculation.