Research in Plant Pathology is centered around understanding the epidemiology of important diseases like brown spot and blast particularly with emphasis on the relationship between weather factors and disease incidence with a view to develop methods for forecasting disease outbreaks, assessing losses due to diseases and their control through chemicals during the pre-semi-dwarf era. In addition, attention was also paid to understand the minor diseases occurring on rice. With the change in the disease scenario in the beginning of the semi-dwarf era starting with the introduction of new high yielding varieties, the activities of the division has been shaped to meet the new challenges posed by newer problems. Research was intensified on, blast, sheath blight, bacterial blight, tungro virus complex. Attention has also been paid on bacterial leaf streak which has been occurring from time to time. However, the main stress has remained on identification of donors, understanding the variability of the pathogens and the epidemiology of the diseases and developing management strategies for minimizing the losses caused by the diseases. Further, the discipline has also started investigating on the basic issues concerned with the understanding of the disease syndromes, mechanism of resistance, control of diseases through plant extracts and crop modelling for crop loss assessment.


In working out the control measures the main emphasis was given on exploitation of genetic resistance. Side by side, investigations were carried out for direct control of the disease by application of fungicides and antibiotics. Attempts were made to study epidemiology of the diseases in depth with the aim of developing forecasting techniques for blast and helminthosporium diseases.

No standard methods were available in the beginning for assessing the reaction of the varieties to the major diseases like blast and brown spot. Therefore, initially attempts were made to develop procedures for bringing about artificial infection of these diseases, classification of varieties according to disease intensity etc. Subsequently, mass screening methods were evolved for blast, and helminthosporium. Identification of donors of resistance to these major diseases formed an important aspect of the investigations.

Control of the diseases was attempted through isolation of resistant varieties, evolving new resistant varieties by hybridization, by working out economic spray schedules with fungicides, and by adoption of suitable agronomic and cultural practices.

The need for evaluating the genetic stocks for blast resistance was felt as early as in 1955 in the sixth meeting of IRC Working Party on Rice Production and Protection in which CRRI was an important member and played a vital role. An effective international cooperation existed among rice-growing countries for assembling seeds of blast resistant varieties from 12 countries (Burma, Ceylon, Egypt, India, Indonesia, Japan, Malaya, Pakistan, the Philippines, Taiwan, Thailand and United States of America) for testing in Egypt, India, Japan, the Philippines, Taiwan, Thailand and USA. CRRI, as a member of the three-member committee (Ceylon, India and Japan) set up by FAO in 1959 played a significant role in designing and developing the popular Uniform Blast Nursery technique for large scale testing and evaluation of varieties for blast resistance that has been adopted and is still being practiced world-wide.

Long before the establishment of the coordinated rice improvement programme in India, both brown spot and blast resistant varieties identified in the institutional testing at CRRI were sent for evaluation of their resistance in multi-location trials in India. The resistant varieties were tested in 46 centres all over India consecutively for three years during 1955-58. This was a significant precursor for the formulation of multi-location trials for evaluation of resistant donors and breeders’ material during the semi-dwarf era about a decade later.

The variability in reaction of blast resistant varieties at different locations suggested the possible existence of different physiologic races of the blast fungus. Subsequently, this was confirmed by a special study undertaken with the help of PL 480 funds. By 1964, the existence of 22 races of the blast fungus classified using the international set of differentials was established. Three varieties Tetep, Tadukan and Zenith were found resistant to all the races identified in India.

Genetical studies on disease resistance had shown that resistance to blast in the above three varieties was governed by two or three dominant genes.

Epidemiology of diseases

The origin and spread of blast and brown spot were investigated with special reference to sources of infection and viability of the pathogens. Factors favouring the development of the diseases were studied with an ultimate object of forecasting disease outbreaks.


Factors governing epidemic outbreaks of helminthosporiose were studied in the fifties. The fungus causing brown spot did not remain viable in soil or in infected plant parts between the harvest of one season and the next sowing. It remained viable in seed, but if the soil temperature at germination exceeded 28oC, the seedlings did not get infection by the seed-borne fungus. Infection of seedlings was presumed to be caused by air-borne conidia of the fungus. Conidia were found trapped over rice fields in aeroscopes during the months of April, May and June even though there was no rice crop in the field.

Analysis of the meteorological factors prevailed during Bengal epiphytotic of 1942 (which resulted in the Great Bengal Famine of 1943) coupled with the experimental data obtained on the variation of spore population over rice fields over four years led to an understanding of the epiphytotic outbreak. Cloudy weather and increase in relative humidity, minimum range of daily temperature (25-30oC), low sunshine hours occurring over a continuous period, when the crop was in flowering to maturity, the most susceptible stage, were found to be associated with an increase in spore population of the pathogen over rice fields resulting in the outbreak of epidemic. The disease was found to increase with the age of the host and with low and high nutrition of nitrogen and low potassium. Two grasses, Echinocloa colonum and Leersia hexandra were noted as collateral hosts of the pathogen, Helminthosporium oryzae.


Effect of predisposing factors and interaction of these factors with the varieties were investigated for blast. Seedling stage, rapid tillering stage after transplanting and flower emergence stage were identified as the most susceptible ones to blast. The fact that the age of the leaves influence the susceptibility to blast was also brought out. The older the leaves in the plant, the more they are resistant to blast.

Excessive nitrogen and exposure to the cold night temperature predisposed susceptible varieties, but did not show any effect on highly resistant varieties. The critical range of temperature for penetration and establishment of infection was round about 25-26oC whereas germination of spores and appressoria formation occurred within 6-10 hours at 20-30oC in the presence of water on the surface of the leaf. The formation of dew or a little rainfall, occurrence of fog provided the necessary water required for the germination of spores. The analysis of the intensity of infection recorded in various experiments over a period of several years revealed the fact that blast infection had occurred under natural conditions when the minimum temperature during the night was 26oC and below with the concomitant occurrence of relative humidity of 90% and above. This fact has been subsequently verified by critical experiments. This led to the formulation of a forecasting technique based upon the above findings.

Narrow brown leaf spot

Lower incidence of narrow brown leaf spot caused by Cercospora oryzae was found to be associated with low potassium nutrition.

False smut

A low maximum temperature accompanied by high relative humidity at the time of flowering, were associated with heavy infection of false smut.

Loss assessment

Methods of obtaining an estimate of the loss caused by diseases were developed, particularly with reference to blast. The loss caused by blast was investigated and it was found that with every increase of neck infection by 1%, the loss was 0.95% in a susceptible variety. In a tolerant variety, the loss was 0.4 per cent. A pilot survey was conducted in collaboration with the Institute of Agricultural Research Statistics in the districts of Puri, Cuttack and techniques for sampling and estimation of loss were standardized. This helped in the extension of the Pilot survey to West Godavari and Thanjavur districts. This revealed the fact that in non-epidemic years, 10-12% loss was caused by pests and diseases of rice every year.

Genetics of blast resistance

Inheritance of leaf blast resistance in the cross CO 13 x CO 25 and its reciprocal was controlled by three genes along with modifiers. In another study, presence of one independent dominant gene in Zenith and Tetep against the race IA 11 and ID 1 and one dominant gene in Gingaand Novin to the race IA 11 was shown.

Breeding for disease resistance

In hybridization programme to develop resistant varieties, two varieties resistant to blast CR 906 and CR 907 (CO 25 x CO 13) and three cultures resistant to blast and helminthosporium namely H4P3, H8P3 and H8P14 (CO 25, resistant to blast and susceptible to helminthosporiose x Bam 10 resistant to helminthosporiose and susceptible to blast) were developed. In addition, hybridization to incorporate resistance of Tetep, Tadukan and Zenith in Jagannath, a high yielding variety was taken up.

Control of diseases

Control of rice diseases through direct application of better and efficient fungicides and antibiotics was a regular line of investigation. To control blast, an economic spray schedule consisting five to six sprays during entire period of crop growth was developed.

In a pioneering effort, a novel approach of controlling brown spot based on the principle of immunization was experimented. Considerable degree of resistance was induced in susceptible rice varieties to helminthosporiose by soaking seeds at germination in cold water extract of the same pathogen. The concept of induced resistance in plants has become a favourite field of experimental plant pathology for many, independent of this observation during the past three decades, with a view to evolve newer approaches of disease management in plants.

A spray schedule with fungicides for control of blast was developed. This recommended, five spray applications in a season, comprising of once in the seed bed, twice during tillering, and twice at flowering stages depending upon the severity of the disease. For traditional tall indica varieties, an effective dose of 25 kg copper fungicides and 0.195 kg of mercury in 1000 litres of water or 0.60 g of mercury per ha as dust for organo-mercurial fungicides was worked out. Spraying with low volume nozzle with knapsack sprayer was found to be economical with one-fourth consumption of spray fluid as compared to normal volume nozzle.

Stem rot could be controlled by the application of organo-mercurial (4 kg/ha) or organo-phosphatic (Hinosan) fungicides (4.8 l/ha) at the base of the plants.

Seedling blight of rice due to Sclerotium rolfsi was controlled by soil application of fungicides based on pentachloro nitrobenzene (PCNB) at 4 g/m2.


With the introduction and intensive cultivation of high yielding, semi-dwarf varieties, new problems of diseases like sheath blight caused by Rhizoctonia solani, bacterial blight caused by Xanthomonas oryzae pv. oryzae and tungro virus complex emerged. However, blast continued to cause considerable losses to the crop particularly in rainfed uplands and in hilly terrains. Besides, a few of the hitherto considered minor diseases like sheath rot and false smut have started affecting the crop in increased intensities.

Screening methodology

Bacterial blight

Research on bacterial blight started with the appearance of the disease on a large scale with the introduction of semi-dwarf high yielding varieties. The primary emphasis was on developing a dependable screening method for assessing reaction of large population of plant material. Clipping the leaves with a pair of scissors and spraying the plants with the bacterial suspension and inundating the seed beds with the bacterial suspension, and clipping the leaves with a pair of scissors and dipping the clipped leaves into the bacterial suspension are some of the successful methods which gave a high level of disease incidence. These provided leads to the development, elsewhere, of the now popular clip inoculation technique involving clipping the leaves with a pair of scissors previously dipped into the bacterial suspension.

Sheath blight

Pea seeds inoculated with the sheath blight fungus served as effective inoculum for inducing severe symptoms of the disease in rice grown under upland conditions. Similarly, inoculum raised by inoculating Azolla with the fungus induced disease in rice grown in 50 cm water depth. This is, particularly, suitable for assessing reaction of rice varieties under rainfed lowland situations.

A cut-leaf inoculation technique was developed for assessing reaction of a large number of varieties in the laboratory for reaction to sheath blight. Briefly, this technique is involved placing leaf blades cut to 6 to 8 cm long over a thin layer of water contained in Petri dishes and inoculating the cut leaf blades by pacing 10-day-old sclerotia over them. The Petri plates can be left on laboratory benches for a period of 72 hr. Water-soaked lesions appear within 24 hr of incubation and clear cut lesions are formed between 48-72 hr. The disease can be scored at the end of 72 hr. The disease can be scored 96 or 120 hr after inoculation. The laboratory screening compares well with the field screening.

Tungro virus complex

An understanding on the time of natural incidence of tungro, appearance of the vector, green leafhopper population in the fields at Cuttack and nature of disease spread led to the development of an effective field screening technique for screening plant material against tungro virus complex. The technique mainly involved coinciding the transplanting of the test material with the appearance of leafhopper population in the field and introducing the inoculum in the form of young net house-inoculated plants in the fields. By the time the leafhoppers appear in large population and the planting (delayed) is done for tungro nursery, the regular crop in the neighbouring fields crosses the vulnerable susceptible stage, thereby spread of the disease beyond the disease nursery area is prevented.

Sources of resistance

Identification of suitable donors for resistance to major diseases was a prime area of study. This resulted in the identification of several valuable sources of resistance.

The reaction of several wild rices were assessed against blast, bacterial blight and tungro virus complex. O. nivera, O. rufipogon, O. alta, O grandiglumis, P. punctata, O. longistaminata and O. australiensis were highly resistant to the blast fungus.

Of the large number of accessions screened for the reaction to stem rot, MNP 234, ARC 5633, ARC 12751, ARC 12086, H 13, MC 11-36 and Tadukan were resistant to eight isolates of the fungus obtained from different parts of the country.

Perpetuation of bacterial pathogens

Extensive studies on the survival of bacterial blight and bacterial leaf streak pathogens of rice during off season in double and single cropped areas were carried out. Infected stubbles, leaves, seed, chaff and rachillae left in the field after harvest constitute major source of primary inoculum of bacterial blight in double cropped areas. Oryza perennis, a perennial wild rice growing in ponds, ditches and irrigation channels was found to be a potential inoculum source of bacterial blight and bacterial leaf streak diseases in both double and single cropped areas. In addition, bacterial blight pathogen also infects common grass weeds, Paspalum scrobiculatum, Leersia hexandra and Cyperus rotundus found in rice fields

Seed transmission of bacterial blight pathogen

Bacterial blight pathogen survived in seed up to the next growing season. Upon availability of moisture when the seeds were sown, the bacterium in the seed multiplied and moved upward in the xylem vessels and caused wilting of young seedlings. This suggested the possibility of reducing the disease severity by using the seed from disease-free crop.

Pathogen variability

Blast fungus

Blast continuing as one of the major diseases of rice even with the new semi-dwarf plant types, further studies on the physiologic specialization in blast fungus led to the identification of nine more races of the fungus, thus totaling the number of races so far identified in the country to 31. However, subsequent sustained efforts on understanding the variation showed a stabilization in the race pattern and the race IC 17 was found to be the most stable race in India.

Bacterial blight pathogen


Nine isolates of the bacterial blight pathogen tested on a set of varieties consisting of Ambemohar, Ajan C, D 44-1, Chinsurah Boro II, Taichung 65, Kaohsiung 21, Kwangfu 1, Wase Aikoku 3 and TKM 6 in 1969 exhibited distinct variation in pathogencity and were grouped into six pathotypes.

Recently, another set of differentials consisting of IR 8, TKM 6, DV 85, IET 8585 and PN 13 were used to differentiate 52 isolates of the bacterium collected from different parts of the country and six pathotypes were identified.

Realizing the need for precise knowledge on compatibility of the isolates with specific known genes for resistance, a new set of differentials comprising mainly of near-isogenic lines, IRBB 3, IRBB 4, IRBB 5, IRBB 7, IRBB 10, IRBB 13 and IRBB 21 carrying Xa-3, Xa-4, xa-5, Xa-7, Xa-10, xa-13 and Xa-21, respectively was selected. Pathotyping of a large number of isolates (241) isolated from samples collected from four different states in eastern India using this set of differentials revealed the existence of diverse pathotypes. The pathogen collections came from a total of 30 different rice varieties. This pathotyping revealed the presence of 20 different pathotypes. Presence of such a diverse group of pathotypes in the country has been brought out for the first time.

Molecular characterization of bacterial blight pathogen isolates

DNA markers were used for fingerprinting bacterial blight pathogen isolates. Using outwardly directed oligonucleotide primers JEL 1 and JEL 2 complimentary to each end of the IS1112 element [a relatively high-copy number (about 80 copies in some strains), repetitive element isolated from the bacterial blight pathogen], DNA of 199 were fingerprinted employing polymerase chain reaction-based fingerprinting technique. Pathogen diversity was clearly partitioned according to the site of collection. A total of 15 lineages of the bacterial blight pathogen was detected. The populations examined from Orissa and Raipur were much diverse as they consisted of 8 and 7 out of 15 lineages, respectively as compared to those from Uttar Pradesh. Collections from a given site tended to consist of related haplotypes. It appears that the diversity of the haplotypes is influenced by the host varieties grown in a location.

Epidemiology of diseases

Host range of blast fungus

In cross inoculation studies, Pyricularia grisea from Panicum repens, Setaria hexandra, Brachiaria mutica, Pennisetum purpureum, Digiteria sanguinalis, D. setigera and Eleusine indica were non-pathogenic to rice.

Forecasting blast occurrence

The weather factors, minimum temperature, maximum temperature, and relative humidity greatly influenced the colour of blast lesions and spore producing ability. Heavy disease incidence always occurred when the mercury column reached 21-25 mm in the manometer. For long range forecasting, the formula Y = 0.697 X -1.5 was developed, where Y = disease incidence and X = number of days with minimum temperature range 21-22oC.

Durable resistance to blast

Intensive investigations on exploitation of durable resistance as a tool to control rice blast disease resulted in identification of 10 genetic and heritable components of resistance. Among these components, lesion number (LN), was most important and highest contributing character towards the total disease in a plant, followed by the lesion area. In situ estimation of lesion area (LA) was made easy by evolving an empirical formula using the linear measurements of the lesion which is given by LA = 0.61 (length x maximum width of the lesion).

An index score (IS) of 6.41 x LN was developed for effective use in preliminary evaluation and identification of slow-blasting resistance among large screening populations of segregating material. Among 10 parameters, the area under disease progress curve (AUDPC) was identified as the best and most appropriate for final evaluation and identification of slow-blasting genotypes.

The grouping of slow-blasting genotypes according to their genetic distance, with the help of computer models and selection of parents from widely distant clusters for effective utilization in crossing programme on breeding for durable resistance was found highly effective in creating a broad spectrum of variability and selection of desired recombinants possessing durable resistance. Quick identification of slow-blasting genotypes was made easy through the application of computer models for grouping of the screening population into specific levels of resistance by utilizing the daily observation data on the individual disease progress curves and deriving clusters of slow-blasting genotypes from the computer-drawn figures. The technique for identification of stable slow-blasting genotypes possessing durable resistance was simplified by use of computer models on stability analysis and thus 15 genotypes possessing durable resistance to blast disease were identified.

Factors influencing sheath blight incidence

The development and severity of the disease increased with the increase with the age of host. Both vertical and horizontal development of the disease was highest at flowering stage in majority of the rice cultivars. Prevalence of a mean minimum and mean maximum temperature range of 24.4-32.0oC with concomitant occurrence of high relative humidity and intermittent rains greatly favoured the development of severe symptoms of the disease. Low (13oC) of high (34oC) and continuous rainfall for several days adversely affected the disease development.

Chaff, panicles and other infected debris from sheath blight-affected plants served as the sources for infecting the common weeds in rice fields such as Echinochloa colona and Brachiaria mutica. These diseased weeds harboured the inoculum during the off season.

Incidence of sheath blight was severe in rice-arhar cropping system compared to rice alone, apparently due to shading by the arhar crop emphasizing the importance of selection of suitable mixed cropping system to reduce the overall disease incidence in fields.


Factors influencing wilting of plants caused by bacterial blight pathogen

The incidence of wilting (kresek) increased with increased concentrations of bacterial inoculum (0.01 to 1.0 O.D) in rice cultivars CO 33, Taichung Native 1 and IR 8. However, even lowest concentration of inoculum (0.05 O.D.) induced wilting in highly susceptible CO 33 (Karuna) but not in IR 8 and Taichung Native 1. Dipping the roots in the bacterial cell suspension for a minimum of 5 min caused wilting if the host and pathogen were compatible. Isolates of X. oryzae pv. oryzae from different areas in India varied in their ability to induce wilting. Young seedlings were more susceptible than grown up plants. Ability to induce wilting increased when the isolates were passed through host plants but declined with successive transfers on artificial medium.

Bacterial blight disease syndrome

Bacterial blight manifests itself in the form of wilting (kresek), pale yellowing of leaves and blighting of leaves. Kresek being a serious form of the disease, its epidemiology was studied. Wilting occurred due to blockage of xylem vessels with mass of bacterial cells. There was no relationship between wilting and leaf blight syndromes in different rice cultivars. However, all the three types of syndromes were observed to occur in a sequence in plants. Artificial induction of wilting through root inoculation was standardized. This facilitated to observe the sequential events in the disease syndrome. Wilting developed up to 50-55 days after transplanting, followed by pale yellowing as a transitory phase lasting for a period of 8-10 days which finally ended in leaf blighting as the last phase of the disease syndrome.

Influence of host nutrition on bacterial blight

Effect of host nutrition on disease development was examined both with net-house and field- grown plants. Increased levels of nitrogen application increased the severity of disease depending upon the inherent varietal susceptibility. In a solution culture experiment, nitrogen at 60 and 120 mg N/litre and phosphorus at 25 mg P2O5/litre enhanced the susceptibility to bacterial blight. However, plants grown at 100 mg N/litre were significantly less susceptible to the disease than those grown at 60 and 120 mg N/litre. Potassium at 160 mg K2O/litre markedly reduced the susceptibility of plants to the disease in an intermediate cultivar IR 8 while it caused little effect in a highly susceptible cultivar Taichung Native 1 and in a tolerant cultivar, Malagkit Sungsong. Similarly, certain minor elements like calcium, manganese, iron and copper also had an impact in reducing the disease progress. With the field-grown plants, however, optimum levels of 80 to 100 kg N/ha accompanied with potassium at 40 to 60 kg K2O/ha helped to reduce the disease to a tolerable level.

Disease spread


Progress of blast infection in mixed host population consisting of varieties with differential reaction to the disease was investigated. The rate of infection in a susceptible variety (CO 13) decreased significantly when the mixed population contained above 75 % of tolerant (CR 44-119-1) or above 50% of resistant (Zenith) varieties. On the other hand, the infection rate in tolerant or resistant varieties was not affected by the presence of even 99% susceptible population.

Bacterial blight

Sporadically occurring individual plants infected with X. oryzae pv. oryzae (presumably originating from infected seeds) served as focal centres of primary infection, spreading the disease to the neighbouring healthy plants. Patchy appearance of the disease in the field was due to faster vertical spread at the centre compared to slower vertical spread at the periphery of the focus. However, several foci characterized by faster rate of vertical spread both at the centre as well as periphery and each of them quickly merging with the other, encompass the entire plot causing uniform epidemic.

Progress of the disease was studied in mixed plantings of susceptible (Taichung Native 1) and resistant (Ramakrishna) rice cultivars. A significant decrease in the infection rate was observed in 1-50% susceptible host due to the presence of 50-99% resistant host. The infection rate of resistant host was not influenced by any proportion of susceptible host in the mixture. Based on the average disease score value in the mixed stand, 30 S : 70 R proportion appeared to serve as equilibrium mixture for containing the disease at threshold level.

Factors influencing bacterial streak incidence

Bacterial streak increased with increasing levels of nitrogen application irrespective of plant spacing employed. Meteorological factors like less number of sun-shine hours, rainy days and dew formation favoured the disease development.

O. perennis among the wild rices was susceptible to this disease, and, in fact, natural infection of this wild rice with streak in fields prior to transplanting rice was detected. O. perennis may act as a collateral host for the streak pathogen.

Factors influencing false smut incidence

The incidence of false smut was higher in rice varieties flowering in the month of October. However, rice cultivar Savitri (Ponmani) showed least infection. Disease incidence was three times more in crops grown in waterlogged soils than in soils with low moisture status. False smut balls stored in seed bags were viable till the next growing season suggesting the possible role of these smut balls present in the field after the harvest of the crop as primary source of inoculum by producing air-borne ascospores for subsequent infection under field conditions

Factors influencing tungro incidence, spread, and host-virus and virus-vector relationships

Incidence of tungro in the fields was high during September, October and November at Cuttack. Spread of tungro disease in fields increased in correspondence with increase in the insect vector, green leafhopper (Nephotettix virescens) population. Two to three green leafhoppers/plant was sufficient to spread the disease under farmers’ field conditions. Cultivars, Taichung Native 1 and Jaya were better sources for tungro spread than Ratna and IR 20. Even a few infected plants in the field (1%) were enough for secondary spread and to cause cent per cent disease incidence.

Disease spread was faster in young crop when compared to older crop. Closer spacing of plants in the field was more advantageous for the disease spread than wider spacing.

These basic knowledge gathered at this institute led to the development of a dependable field screening technique for the assessment of a large number of varieties at a time. More than 10,000 varieties were screened by this technique which resulted in the identification of as many as 78 tungro tolerant varieties. Twenty-five of them did not exhibit any symptoms as against cent per cent incidence of tungro in the neighbouring susceptible check variety, Taichung Native 1.

Of the 18 wild rices tested against tungro virus complex, O. australiensis, O. barthii, O. brachyntha, O. eichengeri, O. glaberrima, O. nivera, O. perennis and O. punctata were susceptible suggesting their possibility to serve as reservoir host for the viruses during the off-season.

Studies on host range of vectors of the viruses revealed that N. nigropictus has a broader sepctrum of host range as compared to N. virescens. Leersia hexandra was most preferred host for N. nigropictus, while N. virescencs preferred rice in comparison to weeds. Less efficient vector, N. nigropictus might play a greater role in maintaining tungro viruses on weeds during off-season, while the efficient vector, N. virescens might be playing a similar role in spreading the disease in rice crop.

Loss assessment

Crop modelling for assessing crop loss due to bacterial blight

Computer simulation of bacterial leaf blight epidemics showed that disease onset during early or late tillering stages in crop grown with high levels of nitrogen caused greater reductions in grain yield and total dry matter production than disease onset at flag leaf appearance. Data on different growth parameters generated in a field experiment with cultivars IR 64, and Annada, in the wet season, were used to validate the model. Results of the simulated model on the trend of reductions in grain yield and total dry matter caused by the disease was similar to that observed in field experiments. The amount of diseased leaf area and severity in IR 64 was higher when the inoculations were made during late tillering stage than during early tillering and at flag leaf appearance. Presumably, the crop compensates leaf area reduction during early tillering stage with the formation of new leaves. Similarly, higher yield reductions were encountered in the disease epidemic during late tillering followed by disease epidemic during early tillering and at flag leaf appearance.

The crop growth of the cultivar Annada showed that higher levels of nitrogen application favour larger amounts of green leaf area which becomes damaged by the disease. Increased damaged leaf area lead to increased losses. Early and mid disease onsets coinciding with early and late tillering stages of the crop caused more damage than the infections at flag leaf appearance. When the onset of the disease was initiated at identical time coupled with varied levels of epidemics induced by different nitrogen levels and maintaining the epidemics either for the entire crop growth , up to late tillering or up to early tillering stages of the crop, the total dry matter and grain yield showed higher reductions in the plots where the disease was maintained throughout the crop growth followed by the maintenance up to late and early tillering stages of the growth. This was more pronounced at higher levels of nitrogen application.

Tungro virus complex

Effect of tungro infection on yield and yield bearing characters was examined in 25 semi-dwarf high yielding varieties. Yield loss ranged from 19 to 100% depending on the resistance of the cultivar. The cultivars, Annapurna , Ratna and CR 44-955 suffered less yield loss of about 20%, while 10 rice cultivars did not flower and thus suffered yield loss of 100%. Some of the popular cultivars in this group were Taichung Native 1, IR 22, Kumar, Karuna, Kalinga I and Mahsuri.

Grain discolouration and mycotoxins

Commonly associated seed pathogens of rice grain were Alternaria padwickii, Aspergillus sp., Curvularia sp., Drechslera oryzae and Fusarium moniliforme. The percentage of seed infection by A. padwickii varied from 1 to 24, D. oryzae from 2 to 8 and F. moniliforme from 2 to 65. Seed discolouration was mostly caused by A. padwickii and Curvularia sp.

Quality of rice grain deterioration due to the production of mycotoxin by sperosphere microflora. These toxins are known to cause health hazards. Seed infecting fungi like Aspergillus sp. Curvularia sp., Fusarium sp. and bacteria found to be associated with the rice grains produced different mycotoxins like aflatoxin B-1, curvularin, tichothecene, vomitoxin, and zearalenone.

Physiology of disease resistance

An understanding of how pathogens induce disease, how the plants get diseased and how they defend themselves against the pathogens would help us to know the functions of the genes governing resistance which remain unknown and eventually to develop novel methods for controlling the diseases.


Nature of resistance to blast disease operating both at pre- and post-penetrative stages of the disease was investigated using several models involving cultivars differing in their reaction to the disease, nitrogen fertilization and nycto-temperature-induced tissue susceptibility and resistance induced by certain chemicals. This study has brought out the operation of four different mechanisms governing blast resistance in rice; (i) the epicuticular wax present on the surface of the leaves influences the infection by suppressing the appressorium formation by the pathogen thus offering a partial resistance resulting in reduced number of lesions formed (ii) free phenolic compounds and their oxidases toxify the tissue in the infected region; the speed and magnitude at which the toxification takes place in response to infection determines the tissue resistance to the pathogen, (iii) the presence of two toxic cinnamate derivatives (ferulate and coumarate) in the cell walls forming toxic oxidized products/polymers like lignin and melanin-like compounds upon oxidation forming a mechanical barrier for the fungus thereby arrest the spread of the pathogen to adjacent cells thus restricting the disease lesions, and (iv) the synthesis and accumulation of anti-microbial compound(s) which are di-terpenoid in nature known as phytoalexin in response to infection toxic to the growth of the pathogen. However, none of these mechanisms seemed to be universal in nature and the defense mechanism was dependent on the varieties tested.

Bacterial blight

Nature of disease resistance in rice to bacterial blight pathogen was examined with different models involving different host-pathogen combinations and resistance influenced by nitrogen nutrition, light intensity and by various cellular constituents. The synthesis and accumulation of free phenolic compounds and their oxidases play a major role in the defense of plants against bacterial blight pathogen as revealed by model studies using potassium and light-induced tissue resistance. Of the two key enzymes of phenol synthesis, phenylalanine ammonia-lyase (PAL) and tyrosine ammonia-lyase (TAL), bacterial infection enhanced the activities of the former in intermediate and in tolerant cultivars and of both the enzymes in tolerant cultivar thus making available more of the toxic phenols for oxidation by oxidases to form enhanced level of toxic compounds for restricting the development of the pathogen.

Tungro virus complex

The physiology of growth regulation in tungro-affected plants and the similarities in the metabolic alterations caused in the plant between tungro virus complex and water stress particularly with reference to water relations of diseased plants were investigated in detail.

Tungro infection drastically reduced gibberellin status in a sensitive plant (cv. Taichung Native 1). Abscisic acid (a growth inhibitor), was shown to be responsible for growth retardation of tungro-diseased plants. Abscisic acid (ABA) inhibited GA synthesis in a model system involving Gibberella fujikuroi demonstrating that growth retardation of tungro-diseased plants might be due to the inhibitory effect of abscisic acid on GA biosynthesis, in addition to the direct effect of the inhibitor on plant growth. Further, Tungro infection decreased the moisture status, leaf water potential, transpiration rates and reduced the permeability of cells thus causing an internal water stress. The root development of tungro-diseased sensitive cultivar was affected even during very early stages of disease manifestation. The augmented synthesis of ABA due to virus infection in a sensitive cultivar resembled the stress syndrome caused by various physical factors particularly drought. The relationship between tungro sensitivity and drought tolerance vis-a-vis proline accumulation revealed a positive correlation between the ability of plants to accumulate proline in response to water stress and their sensitivity to the disease. These findings established the fact that certain abiotic stresses capable of causing water stress might enhance the severity of the disease when occurring together in the field.

Inheritance of disease resistance


Inheritance of resistance was examined utilizing highly resistant donors like Tetep and Zenith as parents. Resistance was dominant and was governed by two pairs of genes in the cross combinations, Tetep x Ratna and Zenith x Ratna showing a segregation ratio (R:S) of 13:3 and 15:1.

Bacterial blight

Resistant donors like Semora Mangga, Malagkit Sungsong, BJ 1, Lacrosse/Zenith Nira, Chinsurah Boro II and DV 85 were used. The continuous variation for resistance and the overlapping of classes led to treat resistance as a biometrical character and the data was analyzed using biometrical models, diallel analysis and additive dominance model. Resistance to bacterial blight appeared to be governed by a number of genes with interactions. Number of effective factors (genes governing the resistance) was more than six. The interaction components i, j and l were significant. The persistence of segregation beyond F7 and F8 also confirm the involvement of polygenes suggesting that effective selections have to be made after several generations to achieve a fair degree of homozygous resistance.

Tungro virus complex

In crosses involving Kataribhog and Kamod 253, a ratio of 13 susceptible : 3 resistant was obtained, whereas in crosses with Pankhari 203, a complementary gene ratio (9 resistant : 7 susceptible) was recorded. This led to infer that three genes for resistance were involved besides an inhibitor.

Breeding for disease resistance

The resistance of Lacrosse/Zenith-Nira to bacterial blight was successfully transferred to a dwarf background. Some of the cultures developed in this programme had shown resistance to bacterial blight in a number of testing centres in India. Attempts were also made to isolate mutants tolerant to bacterial blight from Padma which is susceptible to bacterial blight.

Selection of blast resistant mutants

In an inter-divisional study on developing blast resistant mutants of IR 50, the M1 populations supplied by the plant breeding and genetics division were screened at CRRI in Uniform Blast Nursery. Of these, 16 mutants with resistance were selected, and these were again subjected to multi-location test for their reaction to blast in hot-spots. Among these, CRM 49, CRM 51 and CRM 53 were found resistant/tolerant to blast in different locations including Assam. These are to be released shortly in that state for cultivation.

Control and management of diseases


With the advent of high yielding semi-dwarf varieties, it was found that they were shy of copper and mercury. Organo-phosphates like Hinosan and Kitazin (1 ml per litre of water) and antibiotic Kasumin (1 g per litre of water) were effective in controlling blast in these varieties. The spraying could be made most effective when linked with the forecasting technique mentioned above.

Of the several fungicides evaluated against blast, carbendazim, Hinosan, Fungorene and Kitazin (0.5 kg a.i./ha) were effective as foliar sprays in controlling foliar and neck blast and resulted in significant increase in yields. Seed treatment with carbendazim + TMTD 25 was effective in controlling seed-borne blast. Among the granular fungicides, chlorobenthiozone and coratop at 30 kg/ha were effective in controlling blast.

Sheath blight

Severity of the disease could be minimized by removing the infected plant debris and application of green manures like dhaincha and sunnhemp. Application of green manures, particularly dhaincha remarkably reduced the viability of sclerotia in soils through favouring the population of soil antagonists. This resulted in reducing the disease severity.

Chemicals like carbendazim, Vitavax, Topsin (0.5 kg a.i./ha) and Rizolex Validacin (1.0 kg a.i./ha) and validamycin (2 ml. litre) were effective in controlling the disease under field conditions. Herbicide, benthiocarb (Saturn) was found to check the fungal growth and sclerotial formation when used in combination with a fungicide mancozeb (Dithane M-45).

Stem rot

Chemicals like Lihocin (0.01%), carbendazim, ediphenphos (Hinosan) and Panolis (0.1%) were effective in controlling the disease when sprayed at post-tillering and flowering stages of crop growth.

False smut

Significant levels of reduction in the disease was achieved through application of chemicals like phoret, monocrotophos, and thiram before flowering.

Bacterial blight and streak

A package of integrated management practices was developed to contain bacterial blight and bacterial leaf streak disease. Use of resistant/tolerant cultivars, healthy seeds, raising seedlings in upland nursery, ploughing down of infected plant debris, self-sown rice plants and ratoons, irrigating the field a month before sowing and transplanting and proper leveling of the field brought down the inoculum potential. Eradication of O. perennis in ponds and ditches near the field, avoidance of waterlogging and shading in the field, judicious application of nitrogen with required levels of reduced the incidence and severity of the diseases. Wide spacing between plants together with application of 80 kg N/ha alone reduced the disease severity in varieties with very high tillering ability.

Tungro virus complex

Management of tungro virus complex was achieved through controlling green leafhopper (insect vector). Nearly 50 insecticides were tested in net house for their ability to prevent virus infection through vector mortality. Carbofuran, a systemic insecticide was effective in controlling green leafhoppers and preventing tungro infection. It has got a long persistence (15-20 days) when compared to other insecticides. Synthetic pyrethroids like Cypermethrin and Decamethrin showed quick knock down effect on green leafhoppers and thus prevented tungro infection efficiently. But, these are contact insecticides and lacked persistency. However, best management of the disease was achieved by using carbofuran at 2 kg a.i./ha during early stages of crop growth including seed bed and use of either Cypermethrin or Decamethrin as a foliar spray at 0.01% after 60 days of crop growth depending upon the green leafhopper population in the fields.

Natural plant products for disease control

With a view to reduce environmental pollution problems caused by the use of pesticides for the control of rice diseases, research on exploitation of natural plant products was initiated during the year 1977. The studies emphasize the use of botanicals for the control of diseases of rice and groundnut grown after rice in the rice-based cropping system.

Since the beginning, nearly 115 genera of plant species have been screened against various fungal, bacterial pathogens of rice and/or groundnut, with special emphasis on rice blast caused by Pyricularia grisea and collar-rot and yellow root of groundnut incited by Aspergillus niger and A. flavus, respectively.

Aqueous and ethanolic extracts and essential oil preparations from the leaves of Aegle marmelos and Ocimum sanctum were toxic to blast fungus and effectively controlled blast disease under field conditions in the experimental farm at CRRI, in different agro-ecological zones of the country and in farmers fields in Banki and Ghasiputa in Orissa during 1992 dry season. The extent of control offered by these plant products is comparable with that offered by commercial fungicides like carbendazim and ediphenphos. Subsequently, this technology has spread to the nearby villages of the test locations in Orissa.

Effect of spraying with Aegle marmelos formulation on blast incidence in farmers’ field at Ghasiputa, Cuttack (dry seson, 1992).


Disease incidence (%)



11-days after application


Foliar blast

Neck blast

Foliar blast

Neck blast

Control (no application)





Sprayed with formulation





One of the active principles isolated and purified from the essential oil extracted from A. marmelos has been found to be terpenoid in nature. Attempts are being made to isolate additional active principles from A. marmelos and O. sanctum.

Seed treatment of groundnut cultivar AK 12-24 with essential oil and ethanolic extracts from either of the plants foliage prevented the progress of both collar-rot and yellow-root diseases. This protection lasted for nearly 25 to 30 days. The treatment has also enhanced the vigour of the plants similar to that noticed with treatment with carbendazim.

Steamed aqueous extract, essential oil and ethanolic extract of O. sanctum leaves retained the fungitoxic properties up to 1, 16 and 24 months of storage at room temperature, respectively. On the other hand, steamed aqueous extract of A. marmelos leaves lost its fungitoxic effect even after 24 hours of storage. Nevertheless, essential oil from these leaves and ethanolic extracts retained their fungitoxic properties up to 12 and 27 months of storage at room temperature, respectively.