Rice-Wheat System Sustainability Concerns and Soil-Borne Pathogens

F1. Deputy Director General, Institute of Plant and Environmental Protection (IPEP), National Agriculture Research Centre (NARC), Islamabad.
2. Assistant Professor, Department of Mycology and Plant Pathology, University of the Punjab, Lahore.

Rice and wheat are grown in a continuous in Indo Pak on more than 12 million hectares stretching across Bangladesh, India, Nepal and Pakistan. Concerns have emerged in the recent past regarding the sustainability of the rice-wheat system.

The productivity of this system is reported to be in stagnation or to have declined in many areas, especially where a continuous rice-wheat rotation predominates and system diversity is low. Biotic, abiotic and social impediments are recognized to be largely responsible in reducing the farm income and threatening the food security. Because rice and wheat are grown under widely different tillage practices, the nature of biotic and abiotic issues is very complex.

Rice grows well on puddled compacted soil, whereas wheat grows best on well-drained soils. The hardpan developed with puddling operation is important for water retention and weed control in rice, but compacted soil creates problems of water logging for wheat. In addition to this, the traditional land preparation after rice harvest results in later wheat sowing dates than optimum.

The traditional cultural cultivation practices are also harmful for rice-wheat cropping system. Considerable attention is being paid to abiotic constraints like soil fertility, water management and tillage but less on the biotic obstacles particularly the soil-borne pathogens.

Soil-borne pathogens may limit nutrient uptake, internal water potential, photosynthesis and increase respiration, factors that are important for the productivity of a crop. A complex of soil-borne organisms, particularly fungi, cause diseases. The soil-borne fungi survive from season to season on host crop debris buried in soil. Soil-borne fungi are difficult to eliminate since they produce resting structures like sclerotia, chlamydospores etc., which are well adapted to survive for long periods under adverse environmental conditions.

The primary disease cycle is initiated by resting structures, borne on infested plant residues. The secondary infection is spread usually by conidia, which can be transmitted very far by wind. Further infections continue throughout the growing season with new spores being produced on plant parts as they mature.

Patchy emergence is usually the first indication that damage has occurred. Infections start on the roots and sub-crown internodes and move to the leaves. Seedlings may die before or soon after emergence even though they only show slight damage. But these pathogens are unnoticed in Pakistan.

These pathogens may infect the underground parts of rice and wheat. It was reported earlier typically, plants are not killed by fungal infection, instead plants affected by root rot or foliar blight may reduce tillering, produce shriveled grains or small head depending upon time and severity of infection.

Rice Crop and Soil-Borne Fungi

Rice one of the leading food crops of the world, is an important staple food and cash crop of Pakistan. Globally, rice is the most important crop in terms of its contribution to human diet and value of production. Rice provides between 35% and 80% of the calories consumed by 3.3 billion people in Asia, and 8% of food energy for 1 billion people in sub-Saharan Africa, Latin America and the Caribbean. However, although rice protein ranks high in nutritional quality among cereals, protein content is modest in rice. Rice also provides minerals, vitamins, and fiber, although all constituents except carbohydrates are reduced by milling.

The rice crop is subjected to more than forty diseases, which are one of the reasons, for low yields of rice in the world including Pakistan. The diseases may appear at any stage of the growth and development of plant, attacking the seed sown, root system, foliage, stalk, leaf sheath, inflorescence and even the developing grain. Fungi can cause different infectious diseases. In the following some of the most important soil-borne fungi are presented.

The fungus Bipolaris oryzae causes brown spot and persists on infected rice seed and probably infected crop debris. It has traditionally been a seedling disease problem but can also attack the leaves and panicles of rice plants. The fungus has air-borne spores that infect the plant when free moisture is available. Brown spot lesions are occasionally confused with leaf blast lesions .

Table. 1.1 Most important Fungal Diseases in Rice (Hollier et al., 1993).



Brown spot

Bipolaris oryzae

Sheath spot

Rhizoctonia solani

Seedling blight

Rhizoctonia  solani


Pyricularia oryzae

Stem rot

Sclerotium oryzae

Root rots

Fusarium spp.

Leaf scald

Microdochium oryzae

Black kernel

Curvularia lunata

Crown sheath rot

Gaeumannomyces graminis


Drechslera gigantea

False smut

Ustilago noidea virens

Kernel smut

Tilletia barclayana

Sheath spot

Rhizoctonia oryzae


Alternaria padwickii

Sheath spot (Rhizoctonia oryzae) disease is similar to the early stages of sheath blight. Small sclerotia initiate the disease on the outermost leaf sheath. A reddish-brown lesion develops on the plant near the waterline. During internode elongation, the sheath spot may be pushed up above the waterline because of this new growth. The sheath spot fungus does not develop on the leaf blades, as is the case with sheath blight. Rather it remains on the outer sheath only. Sometimes the fungus will cause a yellowing of the leaf attached to the sheath it has infected. Some reduction in yield may occur in tillers that are infected; however, it is generally minor and few tillers are affected to result in a significant yield loss.

Sheath blight of rice caused by Rhizoctonia solani, has become one of the more important diseases in several regions during the last two decades. In a first phase, pathogen induces lesions on the base of the leaf sheaths, which later coalesce and progress to the upper parts of the rice plant. In a second phase, the disease then spreads in the crop by means of mycelial strands growing from primary or secondary lesions to healthy tissues of the same or adjacent plants in which these mycelial strands establish new infections.

Blast (Pyricularia oryzae) disease can cause serious losses to susceptible varieties. Depending on the part of the plant affected, the disease is often called leaf blast, rotten neck, or panicle blast. The shape and color of the spots may vary and resemble those of the brown leaf spot disease. Blast differs from brown leaf spot in that it causes longer lesions and develops more rapidly. The blast fungus frequently attacks the node at the base of the panicle and the branches of the panicle. The fungus may also attack the nodes or joints of the stem. Blast generally occurs scattered throughout a field rather than in a localized area of the field. Spores of the fungus are produced in great abundance on blast lesions and can become airborne, disseminating the fungus a considerable distance.

Stem rot (Sclerotium oryzae) becomes most noticeable in rice fields during the later stages of maturity. The disease occurs in circular to irregular areas in fields and causes premature death and lodging of the plants. The fungus attacks the rice plant near the water line usually during late tillering or early reproductive stages of growth. Plants infected early yield poorly. Diagnosis is confirmed by obtaining an infected plant, splitting the base of the stem, and observing the presence of tiny, black sclerotia in internal stem tissues.

Wheat Crop and Soil-Borne Fungi

Wheat a cereal grass of the Gramineae family and the genus Triticum is the world’s largest cereal-grass crop. It has been cultivated for at least 6,000 years and its status as a staple crop ranks second to rice. Unlike other cereals, wheat contains a high amount of gluten, the protein that provides the elasticity necessary for excellent bread making. Over 30,000 varieties of wheat exist between the two major species, bread wheat (Triticum aestivum) and durum wheat (Triticum durum). Wheat grain, a major source of energy in human diet, is higher in protein content than almost all other cereals.

All parts of the wheat plant are subject to diseases and one or more diseases can occur on virtually every plant and in every field. In Pakistan, 50 diseases of wheat are reported and some of them are important economically. These are caused by parasitic bacteria, fungi and viruses.

Pyrenophora tritici-repentis is pathogenic fungus and the causal agent of the wheat leaf spot disease known as tan spot. This disease occurs in all major wheat growing areas of the world Tan spot on wheat can cause significant losses under suitable epidemic conditions. It is dependent on the stage of leaf damage and the loss of assimilation leaf area. Losses are manifested in total yield, kernel weight and number of grains per head.

Spot blotch and leaf blotch of wheat (Triticum aestivum) is caused by Bipolaris sorokiniana an important pathogen that limits production in many nontraditional hot, humid wheat-producing areas of Asia, Africa and South America. The primary inoculum of the fungi comes from several sources such as weed hosts, soil, crop debris, and uncultivated plants. Bipolaris sorokiniana can attack seedlings, roots, leaves, nodes, spikes and grains during various stages of plant development . It can cause pre-and post-emergence damping off, seedling blight, leaf spot and spike blight.

Many different fungal pathogens are reported to cause leaf spots and blight. These include 12 species of Helminthosporium and Alternaria. Helminthosporium spp and Alternaria alternata are the most important pathogens of wheat.

Table 1.2 Most important Fungal Diseases in Wheat (Wiese et al., 2000).

Wheat Diseases


Alternaria leaf blight

Alternaria triticina


Colletotrichum graminicola

Ascochyta leaf spot

Ascochyta tritici

Aureobasidium decay

Microdochium bolleyi

Black head molds and Sooty molds

Alternaria spp.

Cephalosporium stripe

Cephalosporium gramineum

Common bunt

Tilletia caries

Common root rot

Bipolaris sorokiniana

Cottony snow mold

Coprinus psychromorbidus

Crown rot and foot rot

Fusarium graminearum

Root rot

Rhizoctonia solani

Spot blotch

Bipolaris sorokiniana

Tan spot

Pyrenophora tritici-repentis

Stripe rust

Puccinia striiformis

Storage molds

Penicillium and Aspergillus spp.

Stem rust (Black rust)

Puccinia tritici

Another wide spread soil-borne pathogen associated with wheat in tropical environments is Rhizoctonia solani Kuhn. Rhizoctonia solani causes sheath blight (sharp eye spot), root rot and a pre and post emergence damping off. Infection of young plants results in a wilting and death. Infected tissue becomes discolored and irregular scald or eye spot patches develop on the stem, leaf sheaths and occasionally on the leaves. The fungus can survive on crop debris and also as sclerotia but this may not be of great importance in the tropical environments. Dry soil conditions and temperature around 30C favoured infections.

What Happens with Pathogens During Crop Rotation?

Most fungi feed on decaying organic matter such as dead roots, leaves, and stems. They break down dead organic matter into useful minerals and other nutrients that are taken up by plant roots. Relatively few of the estimated two hundred thousand species of fungi attack living plants, and then only when temperature and moisture conditions are favorable. Plant pathogenic fungi penetrate into leaves, stems, and roots through wounds and natural openings or by forcing their way directly through the plant’s protective epidermis (outer “skin”). After growing for several days, weeks, or even years, most disease-causing fungi give rise to spores or spore-producing bodies. Some spores may appear as mold growth on the surface of buds, leaves, and shoots (as in the case of powdery and downy mildews, sooty molds, blights, and many rusts); others are borne in speck-sized, fungus-fruiting bodies embedded in diseased leaf tissue or in stems. Certain fungi may form decay resistant over wintering structures (i.e., sclerotia) that allow them to survive in the soil from season to season. The microscopic spores are easily transported to other plants by air currents, splashing rains, insects, mites, birds, plant parts, and worker’s hands, clothing, and equipment. Fungi cause most infectious plant diseases including all rusts, sooty molds, mildews, blights, scabs, stem blights, wilts, galls, and some other diseases.

Crop rotation is a wise practice for many reasons including disease avoidance. Most pathogens survive in crop residues, but only for a limited time, and most pathogens do not infect multiple crops. Therefore, their populations and the risk of disease can be decreased by crop rotation. Crop rotation is effective for most diseases, but a few diseases (rust, Stewarts wilt of corn, yellow dwarf of wheat and oats) do not survive this way, so crop rotation will not affect them. Sclerotia sclerotiorum survives primarily as sclerotia in soil. Sclerotia are distributed throughout the plow layer of the soil and survive in winter in soil and germinate if positioned near or at the soil surface when conditions are right in the spring and summer. Sclerotia are long-lived and essentially impossible to totally eliminate from a field as long as a host crop is planted in intervals of 5 years or less. Choices in crop rotation and crop sequences with non-hosts can be made that contribute to the steady depletion of sclerotia in the soil. In practice crop rotation of two years is usually sufficient to eliminate most disease problems. Crop rotation control disease by providing sufficient time between susceptible crops for the disease organism (fungi) to die out. When the population of the disease organism is reduced to such low levels that disease is unlikely, then crop be grown in the field again. Most crops (corn, soybean, alfalfa and other hay crops, oats, barley, sugar beets, Chickpea, potatoes and vegetable crops) are suitable for the rotation.

Fungal Species that Infect Both Rice and Wheat

Some fungal pathogens are specific for rice or wheat. There are number of species that cause similar diseases in both rice and wheat. However, root rot in wheat and rice is caused by various Fusarium spp. Rhizoctonia solani or Rhizoctonia oryzae, Bipolaris sorokiniana or Bipolaris sativum, Alteraria alternata, Helminthosporium spp, Curvularia spp and the oomycetes Pythium spp, and Phytopthora infestans. Other sheath diseases in rice are caused by Sclerotium oryzae but in wheat root rot by Sclerotium rolfsii. In rice and wheat crops Rhizoctonia oryzae and Rhizotonia solani can cause root rot. Brown spot in rice is caused by Cochliobolus miyabeanus whereas in wheat foliar spots are caused by Cochliobolus sativus. There are certain fungi, which have the potential to attack both rice and wheat. Rhizoctonia solani also causes sheath blight in rice and is also known to be responsible for foot rot of wheat. Although strains of the same fungus species cause disease in wheat and rice, little is known about whether particular strains infect both wheat and rice. This question is very important in the context of rice-wheat cultivation system.

Complexity of Soil-borne Pathogens, their Aggressiveness and Genetic
Variation: Problem for their Management in Rice-Wheat System

The soil-borne fungi have a wide host range of plants and probably survive mainly by means of perithecia and ascospores on crop stubble, as well as by asexual spores through growth in soil. Some of them being common both on rice and wheat are able to perpetuate more easily and their inoculum levels are rapidly built up. As such these pathogens are difficult to manage because of their high survival capacity. Of the different management strategies cultural methods including rotation are more useful in reducing inoculum level but are often difficult to put into operation for small farmer particularly. Chemical methods, through effective are hazardous for health and environment but also very expensive. Therefore, the most effective disease management approach is the use of genetic resistance. The use of a particular genetic control strategy is dependent on the kind of resistance available. Resistance of host plant to certain pathogen is because of the host characteristics as well as that of the pathogen. Different plants are resistant to certain pathogens for various reasons, but the most important is the genetic variation in host plant which enables the same host plant to escape the attack of the pathogen due to presence of one or more disease resistance gene while other become susceptible to that pathogen. Similarly genetic variations also exist in pathogen population making it either aggressive or non-aggressive against a certain host plant. Change in pathogen variability occurs rapidly because of their faster reproduction and more frequently mutating ability. Therefore it is essential to understand the variability in the pathogen in relation to the host resistance for a successful breeding programme.

Muhammad Ramzan Rafique
Muhammad Ramzan Rafique

I am from a small town Chichawatni, Sahiwal, Punjab , Pakistan, studied from University of Agriculture Faisalabad, on my mission to explore world I am in Denmark these days..

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