In agriculture field, root exudation plays an important role by influencing chemical and physical properties of soil, microbial community and growth of other competitive plant species in soil. Very few reports are available concerning physiological system involved in exudation of several compounds from root cells of plants. However, some scientists suggested that plants are able to release a large range of compounds through plasmalemma or endoplasmic derived exudation and proton-pumping mechanisms (Bais et al, 2004).

Rice variety and origin may regulate allelopathic behavior, for example, japonica rice is more allelopathic than indica and japonica-indica hybrids (Khanh et al, 2007). Rice can produce and secrete different allelochemicals into its neighboring environment with various biological effects. Therefore, it would be a vital step to understand several interactions persisting in rice field in order to utilize allelopathic properties of rice in a direction to improve its cultivation and harvest.

Many crops have been reported to be allelopathic towards other crops grown either simultaneously or subsequently (Khanh et al, 2005). Therefore, many crops have been examined specifically, for allelopathic activity towards weeds or other crops. A variety of allelochemicals released by a range of temperate and tropic crops i.e. alfalfa (Medicago sativa), barley (Hordeum vulgare), clovers (Trifoliumspp., Melilotusspp.), oats (Avena sativa), pearl millet (Pennisetum glaucum), rice (Oryza sativa), rye (Secale cereale), sorghums (Sorghumspp.), sunflower (Helianthus annuus), sweet potato (Ipomoea batatas) and wheat (Triticum aestivum), have been reported to produce suppressive effects on weeds (Dilday et al, 1994; Weston, 1996). Some crops produce allelopathic compounds when they are growing or decomposing and inhibit the growth of neighboring plants.

Various allelochemicals released by crops are considered to be environmentally safe and provide unique molecular targets as compared to synthetic pesticides. Among allelopathic crops, crucifers are considered to be the most important since the glucosinolates found in crucifers, which on hydrolysis release isothiocyanates, are a promising inhibitor of mycelial growth of Botrytis cinerea, Rhizopus stolonifer, Monilinia laxa, Mucor piriformis and Penicillium expansum, all fungal pathogens of fruit and vegetable crops (Mari et al, 1993). Similarly, Brassica is known for high concentration of allyl-isothiocyanate which restricts the growth of Fusarium sambucinum, a fungus causing potato tuber dry rot (Mayton et al, 1996). Besides this, leachates of sunflower have the potential to suppress germination and growth of Parthenium hysterophorus, a noxious weed (Kohli, 1993).

The inhibitory action of several rice varieties was recorded on different plant species, both in fields and laboratory experiments (Dilday et al, 1998; Olofsdotter et al, 1999). In paddy fields, intercropping of semi- aquatic crops like lettuce is a normal practice. With respect to such agricultural practice, it is very important to study the allelopathic potential of rice cultivars since root exudates of rice cultivars contain allelochemicals affecting germination of lettuce (Ma et al, 2014). Water soluble allelochemicals of Oryza glumaepatulahusk stimulate shoot growth of Eclipta thermalis, but inhibit the root growth of Lactuca sativa (Hiroshi, 2008). The influence of allelochemicals from 15 rice varieties was examined on the growth of spinach with the highest allelopathic potential for the rice cultivar WITA12 (Kabir et al, 2010). Different concentrations of rice extract in water show different rates of inhibition on root growth of radish, wheat and lettuce seedlings (Tarek, 2010). In order to reduce the detrimental impact of sunflower residue, allelopathic tolerant rice and wheat should be cultivated (Bashir et al, 2012). Despite the fact that rice root exudates have a large inhibitory effect on wheat seedling growth, even at the concentration of 1 mg/L (Olofsdotter, 2001b; Ma et al, 2014), rice-wheat rotation is a common agriculture practice followed all over the world (Hobbs et al, 2008). Time of sowing, crop rotation, cover-crop management, intercropping, no-till planting and nonrotational cropping systems are also involved with allelopathic effects (Khanh et al, 2005).

Generally, the farmers keep the rice residue stay in the soil after harvest since they believe the residue will benefit the growth of the subsequent crops by improving the nitrogen content and organic matter of soil. However, this practice has led to suppression of several subsequent crops since decomposition of rice straw is known to release phytotoxic chemicals (Inderjit and Dakshini, 1999). In continuous monocropping of rice, the yield has been found to significantly lower in the 2nd year than in the 1st year. Probably this could be due to autotoxic mechanism induced by decomposition of rice straw that is left in the agricultural soil after harvest (Chou, 1995). It is well documented that the toxic compounds, like p-coumaric, p-hydroxy benzoic, syringic, vanillic, ferulic and o-hydroxy phenyl acetic acid, are released directly or indirectly during microbial decomposition of rice residues (Chou and Lin, 1976). The toxicity of these compounds persists for 16 weeks after decomposition (Chou et al, 1977) and can inhibit the growth of rice seedlings (Yang et al, 2002), leaf expansion (Blum and Rebbeck, 1989), root elongation (Pramanik et al, 2000), and interact with nutrients mainly nitrogen (Chou et al, 1982). The soil in paddy fields is deficient in oxygen due to water logged condition and presence of decomposing rice residue, which creates negative redox potential in the soil. This negative rice-rice residue interaction hinders root growth of rice, however, the rice plants have adopted a survival strategy to capture required oxygen through swelling of root cells (Chou, 1995).

Chou and Lin (1976) asserted that aqueous extracts of decomposing rice residues in soil inhibit root growth of lettuce and rice seedlings. Similarly, Kayode and Ayeni (2009) conducted laboratory studies by using extracts of crop residues (sorghum stem and rice husks) to check its allelopathic effect on growth of maize (Zea mays L.). The results revealed that the seed germination, including the growth of the radical and plumule, is retarded in the extract-treated seeds as compared to the control.

Soil is a dynamic system, and one mechanism of interference is unlikely to explain plant interference in nature. Therefore, in order to understand plant interference, it is important to recognize synergistic action of several mechanisms, such as soil interference, interference allelopathy, resource competition and nutrient demineralization (Inderjit and del Moral, 1997). Apart from the direct toxic effect on other plants, some allelochemicals are supposed to influence the availability of nutrients in the soil. It is possible that the effect of allelopathic plants can be due to the allelochemicals in the soil and/or to altered soil nutrients.

Soil provides nutrition to plants and contains microorganisms, such as bacteria, fungi, algae and nematodes, which interact to facilitate nutrient acquisition (Richardson et al, 2009). Mineral nutrients are present in the soil in various forms and solubility. Under nutrient-limited environments, plants interact with soil microorganisms and release allelochemicals, which facilitate nutrient solubilization (Jones and Darrah, 1994). Phenolics are an important group of root-exuded allelochemicals (D’ Arcy-Lameta, 1986), which trigger solubilization and release of Fe, P and other nutrients, thus helping the plants to improve uptake of respective nutrients.

Crop allelopathy may be largely influenced by composition and concentration of allelochemicals, which are released from crops and degraded by several soil factors (biotic and abiotic) (Cheng, 1995). Transport, transformation, retention in rhizosphere, leaching and residual effects of rice allelochemicals are influenced by soil texture (Inderjit and Dakshini, 1994), temperature (Chou et al, 1991) and different chemicals (Cheng, 1995).

The presence of allelochemicals in a plant and its rhizosphere is not strong evidence for direct plant- plant allelopathy, because the observed growth pattern may be due to the influence of these compounds on soil ecological processes rather than direct effects on the target plants. Phenolic acids, p-coumaric, ferulic, p-hydroxybenzoic and protocatechuic acids influence the accumulation of soil organic N and inorganic ions such as Al³⁺, Fe²⁺, Mn²⁺ and PO₄^3- (Inderjit and Mallik, 1997).

Allelopathic rice varieties produce certain rhizospheric allelochemicals in soil which can control the growth of barnyard grass and respond to some allelochemicals excreted by barnyard grass. This was evidenced by Kong et al (2006), which did not show any stimulation of such allelochemicals in non-allelopathic rice varieties.

Rice (1984) suggested that during rotation, the rate of nitrification is reduced, perhaps due to the presence of allelochemicals that subsequently depress the rates of nitrate accumulation or reduce the nitrifier populations. However, an increase in nitrification regulated by available ammonium has been reported during initial stages of rotation (Robertson and Vitousek, 1981). Allelopathy offers an attractive and natural option to decrease nitrification for improving nitrogen use efficiency in agriculture systems. Incorporating residue of various crops into soil and release of allelochemicals from plant roots may help suppress nitrification process, by inhibiting the activities of vital enzymes such as ammonium momo-oxygenase and hydroxylamine oxidoreductase (Subbarao et al, 2009) and the phenomenon known as biological nitrification inhibition (BNI) (Subbarao et al, 2006). However, in addition to root exudates, plant water extracts can also suppress the process of nitrification in soil (Alsaadawi, 2001). Allelochemicals, such as methyl 3-(4-hydroxyphenyl) propionate (Zakir et al, 2008), linoleic acid, α -linolenic acid, methyl-p- coumarate and methyl ferulate, are responsible for BNI (Subbarao et al, 2009). Phenolics and terpenoids may play an important role in the inhibition of nitrification (White, 1994). Phenolic compounds, such as caffeic and ferulic acids, myricetin, tannins and tannin derivatives, inhibit the oxidation of NH₄⁺to NO₂^- by Nitrosomonas (Rice, 1984). Alternatively, it has been proposed that terpenoids enhance immobilization of ammonium-N by soil organisms rather than by inhibition of nitrification (Bremner and McCarty, 1988). Therefore, allelopathic potential of rice can be exploited to improve nitrogen use efficiency of soil.

Phytotoxicity of phenolic acids is influenced by different factors including soil type, soil pH and mineral nutrition, and other resources present in the substrate (Blum, 1998). Soil-plant debris bioassays are often employed to demonstrate phytotoxicity and allelopathy (Blum, 1999), and there are many reports of inhibitory effects of the secondary compounds released by plant debris. Plant waste materials may influence nutrient mobilization and soil pH, which can further affect nutrient immobilization and microbial activity (Aarino and Martikainen, 1994). Chemicals released by plants may influence microbial ecology through their effects on soil microbes and plant pathogens (Einhellig, 1996). Population densities of soil-borne microorganisms are affected by the soil enrichment with different phenolic acids-ferulic, p-coumaric, p-hydroxybenzoic and vanillic acids (Blum and Shafer, 1988). However, the effect was dependent on the concentrations of phenolic acids and inorganic ions in the soil.

Microorganisms play a vital role in allelopathic interactions as they can easily alter or transform the released allelochemicals through their metabolic processes (Pellissier and Souto, 1999). For example, phenolic acids have been found to be transformed by microbes via addition or deletion of side groups and polymerization. In this process of transformation (metabolism of phenolic acids and/or incorporation of carbon from other phenolic acids into microbial biomass), other organic molecules are generated which may differ in their phytotoxicity (Blum et al, 1999).

Roots also secrete allelochemicals in the soil at a significant level to interact with microorganisms and modify the microbial community of the soil (Farrar et al, 2003). In soil-system, specific microflora monitors the degradation of a particular allelochemical, while some microbial species may take advantage of allelochemicals present in the soil (Kong, 2008).

Bacteria such as Streptomyces sagononensis, S. hygroscopicum and Pseudomonas fluorescences are allelopathic and may inhibit the growth of plants present in their ecosystem. The allelochemicals from microorganisms are generally nonspecific on the growth of several annual and perennial species (Hoagland, 1990). They may be effective at a very low concentration but have variable effects on different cultivars (Ambika, 2013).

There are many different classes of microorganisms i.e. cyanobacteria and algae (Nostoc sp., Anabaena sp., Pandorina sp. and Caulerpa sp.), protozoans (Entamoeba hystolytica), viruses (Cyanophages), fungi (Epidermophytonsp., Microsporumsp. and Trichophyton sp.) and bacteria (Desulphuvibrio sp., Beggiatoa sp., Clostridium sp. and Pseudomonas denitrificans) in paddy fields (Oyewole, 2012). Rice allelochemicals have been widely studied in relation to their effects on the growth of weeds (Chung et al, 2006), but their fate and impact on microorganisms, which play an essential role in rice field ecosystem, remain obscure. Bai et al (2000) reported that dynamics of microorganisms in paddy soils greatly varies with various traits, growing periods and seasons. Organic compounds produced from rice roots monitor the microbial biomass and population in rice soils (Lu et al, 2002). Likewise, the allelochemicals released through roots of allelopathic rice could provide carbon to interact with the soil microorganisms. Rice allelochemicals would likely have a great impact on soil microorganisms once released. However, rice- microbe interactions mediated by allelochemicals in paddy soils have not yet been clearly identified and understood (Kong, 2008).

The blue-green algae (cyanobacteria) are of much ecological importance in paddy fields, maintaining soil fertility through nitrogen fixation (Nirmal Kumar et al, 2010) and even reclaiming alkaline soils (Singh, 1961). Rice straw residue has been known to release some allelochemicals during their decomposition that affect the growth and nitrogen fixing potential of blue-green algae (Rice, 1984; Ahluwalia and Ghawana, 1998). Increased organic matter and decreased pH of the soil, as well as the incorporation of paddy straw, support the growth of green algae rather than cyanobacteria (Karaush, 1985).

Decomposition of rice residue and straw in soils may produce different phenolic compounds that can have synergistic suppressive effect on Rhizobium strains by reducing their nitrogen fixing ability (Jabran and Farooq, 2013). The basal portion of rice plants left in the fields due to use of harvester combines is ploughed back or burnt. These residual part of rice plants on decomposition release water soluble phenolic compounds that might affect the algal dynamics and the germination of the next crop (Ahluwalia, 1998, 2013). Kong et al (2008a) found that 5, 7-4′ -trihydroxy-3′ , 5′ -dimethoxyflavone can control the microbial population and community structure in rice soil. It also suggests that flavone can reduce microorganisms especially fungi presented in paddy soil, whereas benzoic acid can induce a higher response for soil microorganisms especially for bacteria.

Allelochemicals present commonly by a conjugated form in almost all plants and any part of the plants, like leaves, culm, flowers, fruits, seeds, buds, pollen and roots (Putnam, 1988). Plants or organisms respond to different stimuli through synthesis and release of the allelochemicals. These chemicals are released into the environment by means of volatilization, foliar leaching, root exudation, decomposition of plant residue and debris incorporation into soils (Chou, 1990). The induction, release, transport and exposure of allelochemicals and their putative effects has been summarized in Fig. 2. These can lengthen survival times in a hostile environment and serve as defensive weapons to prevent damage and decay of reproductive organs. These can be hydrophilic or hydrophobic, absorbed to soil surface, coat plant residues, and carried away in the wind. Once released, the allelochemicals diffuse into the soil and are transported by water. These are also found in the rhizosphere soil and have been demonstrated to show allelopathic interactions between organisms through root to root contact (Inderjit and Weston, 2003).

Fig. 2.

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	Fig. 2. Induction, production, release and transport of allelochemicals and their effects.

Allelochemicals are largely classified as the secondary plant metabolites which are generally considered as alkaloids, phenolics, flavinoids, terpenoids and glucosinolates. These do not play a role in the primary metabolic process of the plant, but are essential for their survival (Rice, 1984).

Several allelochemicals like 5-hydroxy-2- indolecarboxylic acid, 5-hydroxyindole-3-acetic acid, mercaptoacetic acid, 4-vinylphenol, trans-ferulic acid (Song et al, 2004), ergosterol peroxide, 7-oxo- stigmasterol (Macias et al, 2005), 5, 7-4′ -trihydroxy- 3′ , 5′ -dimethoxyflavone (Kong et al, 2006), 3-hydroxy- β -ionone, 9-hydroxy-4-megastigmen-3-one (Kato- Noguchi et al, 2011) azelaic acid, tetradecanoic acid, 1, 2-benzenedicarboxylic acid bis (2-ethylhexyl) ester, 1H-indole-3-carboxylic acid, 1H-indole-5-carboxylic acid, 1H-indole-3-carboxyaldehyde, 3, 4-dihydro- xyhydrocinnamic acid, 3-hydroxy-4-methoxybenzoic acid, 4-hydroxycinnamic acid and 4-hydroxy- hydrocinnamic acid (Rimando et al, 2001) have been reported in rice. Number of reports on rice allelochemicals indicate their nature as phenolic compounds and momilactones. It has been accepted that the role of momilactones (Kato-Noguchi and Ino, 2005) with phenolic compounds (Seal et al, 2004a) and some unknown compounds in rice plants may be responsible for their allelopathic activity (Table 1).

Table 1

Table 1

Table 1 Production of various allelochemicals from rice (Oryza sativa). Source Allelochemical Reference Root exudate Momilactone A, 4-hydroxybenzaldehyde, 4-hydroxybenzoic acid, 3-hydroxybenzoic acid, p-coumaric acid, caffeic acid, 3-hydroxy-4-methoxybenzoic acid, valeric acid, tetradecanoic acid, stearic acid, 2-methyl-1, 4-benzenediol, 1-ethyl-3, 5-dimethylbenzene, 4-ethylbenzaldehyde, cinnamic aldehyde, octadecane, 3-epicosene, 1-eicosanol, 9, 12-octadecadienoic acid, 7-hexadecenoic acid methyl ester, 12-octadecenoic acid methyl ester, 12-methyl-tridecanoic acid methyl ester, cis-1-butyl-2-methyl cyclo propane, dehydroabietic acid, cholest-5-en-3(β )-ol, 4-hydroxybenzoic acid, ferulic acid, abietic acid, resorcinol, 2-hydroxyphenylacetic acid, 4-hydroxyphenylacetic acid, 4-phenylbutyric acid, cinnamic acid, vanillic acid, syringic acid, salicylic acid, 5-hydroxyindole-3-acetic acid, indole-5-carboxylic acid, 5-(12-heptadecenyl)-resorcinol, 5, 7-4′ -trihydroxy 3′ , 5′ -dimethoxyflavone, 3-isopropyl-5-acetoxycyclohexene-2-one-1 Bouillant et al, 1994; Mattice et al, 1998; Kim and Kim, 2000; Kong et al, 2004b; Seal et al, 2004b Seedling Momilactone B Kato-Noguchi and Ino, 2005 Leaf Momilactones A and B Cartwright et al, 1977, 1981; Kodama et al, 1988; Lee et al, 1999 Rice straw Phenolic acids, phenolic aldehyde, aliphatic acids, flavone, cyclohexane, momilactones Pramaink et al, 2000; Kong et al, 2004a Rice hull 1-tetratriacontanol and β -sitosterol-3-O-β -D-glucoside, momilactones A and B, dicyclohexanyl orizane, salicylic acid, o-hydroxyphenylacetic acid, syringic acid, ferrulic acide, benzoic acid, p-hydroxybenzoic acid, m-coumaric acid, o-coumaric acid, p-coumaric acid Chung et al, 2002, 2005; Park et al, 2009 Decomposing rice residue Phenolic acids, 2-hydroxyphenylacetic acid, 4-hydroxybenzoic acid, vanillic acid, p-coumaric acid, ferulic acid, benzoic acid, protocatechuic acid, gallic acid, syringic acid, salicylic acid, gentisic acid, β -resorcylic acid, caffeic acid, sinapinic acid Kuwatsuka and Shindo, 1973; Chou and Lin, 1976

Table 1 Production of various allelochemicals from rice (Oryza sativa).

Seal et al (2004a) reported 200 different compounds in rice root exudates and put these under the three main chemical classes (phenolics, phenylalkanoic acids and indoles), and several classes of the secondary metabolites determined from the root exudates like phenolics (Rimando et al, 2001; Inderjit et al, 2002), alkyl resocinols (Bouillant et al, 1994), momilactone B (Kato-Noguchi and Ino, 2005), carbohydrates and amino acids (Bacilio-Jimenez et al, 2003) and flavones (Kong et al, 2004a). Flavones and their O-or C- glycosides, cyclohexenone, and momilactones play a key role in rice allelopathy (Kong et al, 2004a, b) by generating many biological and ecological effects (Chung et al, 2005). It has been found that the flavones play a role in species interaction between rice and other organisms, particularly in the rhizosphere and have the highest inhibitory action as compared to phenolics (Bais et al, 2006). Among the other allele- chemicals involved in rice allelopathy, 5, 4′ -dihydroxy- 3′ , 5′ -dimethoxy-7-O-β -glucopyranosylflavone is unique because a significant amount could be exuded from the roots to the rihzosphere and then rapidly transformed into aglycone (5, 7-4′ -trihydroxy-3′ , 5′ - dimethoxyflavone), which will ultimately produce many biological effects by interacting with soil organisms (Kong et al, 2008a, b). Bran-containing brown rice produce tricin (5, 7-4′ -trihydroxy-3′ , 5′ - dimethoxyflavone), an allelochemical suspected to possess cancer chemopreventive properties (Cai et al, 2005). Rice seedling rot disease is a dominant problem in rice cultivation due to frequent use of direct seeding practice. The tricin produced by rice hulls were found to have a fungicidal effect on Fusarium oxysporumand Rhizoctonia solani(soil-borne pathogenic fungi causing rice seedling rot disease). However, this effect was higher with aurone, an isomer of tricin as compared with tricin itself (Kong et al, 2010).

Momilactone B was found in root exudes of allelopathic rice cultivars, PI312777, with 5, 7-4′ - trihydroxy-3′ , 5′ -dimethoxyflavone and 3-isopropyl- 5-acetoxycyclohexene-2-one-1 (Kong et al, 2004a). In addition, momilactone A, another potential allelochemical, was found in rice root exudates of Oryza sativa cv. Koshihikari (Kato-Noguchi et al, 2008b). Momilactones A and B were first isolated from rice husks as growth inhibitors (Takahashi et al, 1976), but later, also found in rice leaves and straw as phytoalexins (Lee et al, 1999).

Several studies focused on the common putative allelochemicals found in rice like phenolic acid compounds (p-coumaric acid, p-hydrobenzoic acid, feruic acid and vanillic acid) (Rimando et al, 2001; Seal et al, 2004b). However, concentration of single phenolic acid and combination of several phenolic acids measured in rice ecosystem do not approach phytotoxic levels (Olofsdotter, 2001a). Furthermore, it was recorded that allelopathic rice cultivars can’ t release significant amount of penolic acids than non-allelopathic cultivars (Olofsdotter et al, 2002a). The target sites of allelochemicals play an important role in breeding process since it will help to decide which chemical to increase in order to achieve the desired output. The action mechanism of some rice allelochemicals are described in Table 2.

Table 2

Table 2

Table 2 Mode of action of major rice allelochemicals. Allelochemical Mode of action Target Reference Momilactone B Inhibits accumulation of subtilisin-like serine protease, amyrin synthase LUP2, β -glucosidase, malate synthase, breakdown of cruciferin 2; induces accumulation of translationally controlled tumor protein, glutathione S-transferase and 1-cysteine peroxiredoxin 1 Arabidopsis thaliana Kato-Noguchi and Kitajima, 2015 Momilactones A and B, 1-tetratriacontanol Inhibit chlorophyll content Duckweed Macias et al, 2005 Crude extracts of allelopathic rice cultivars Inhibit superoxide dismutase and catalase activities Barnyard grass seedling Lin et al, 2000 Ferulic acid Inhibits photosynthesis; reduces stomatal conductance Several crops Einhellig, 1996 Ferulic, vanillic and p-coumaric acids Inhibit phosphorus uptake Cucumber Lyu et al, 1990 Salicylate Inhibits K+ uptake to depolarize membranes and reduce ATP content of roots - Balke, 1985 Pelargonic acid (nonanoic acid) Interferes with membrane functions - Irzyk et al, 1997 Tannins, phenolic acid and flavanoids Inhibit nitrification Soil Rice and Pancholy, 1972

Table 2 Mode of action of major rice allelochemicals.

Weeds pose an important biological constraint to crop productivity. Many weeds release allelochemicals to interfere with crop plants. These allelopathic weeds are economically destructive, and the attempt to control them has met with limited success. However, the allelopathic action may be used as an important strategy for crop and weed management system. Weeds cause reductions in yield and quality and remain one of the biggest problems in rice production. The negative impact of commercial herbicides makes it desirable to search for other alternative weed management options (Nirmal Kumar et al, 2010), and allelopathy seems to be one of the options (Tesio and Ferrero, 2010). Momilactone B inhibits the growth of typical rice weeds like Echinochloa crus-galliand E. colonumat concentrations greater than 1 μ mol/L (Kato-Noguchi et al, 2008a).

Improved allelopathic potential of a crop may be useful for rice and other crops (Olofsdotter et al, 1999). If crop allelopathy is applied in crop rotation system, it can prove to be a successful tool to manage weed infestation in agricultural production (Khanh et al, 2005). Despite of this, crop rotation system in paddy field is difficult since most crops may not survive in moist soil (Tuten, 2010). Therefore, exploiting rice itself through isolation and identification of allelochemicals, responsible for weed suppression, will be the most feasible means of weed control (Khanh et al, 2013).

Paddy weeds such as barnyard grass (Echinochloa crus-galli), oval-leafed pondweed (Monochoria vaginalis), redstem (Erodium cicutarium) and ducksalad (Heteranthera limosa) are the most common species used as indicator plants, as they reflect an actual rice-weed interaction. Utilization of rice residues in paddy fields has long been recognized as an important source to improve the status of organic matter of soil and was also reported to reduce the emergence of weeds. To date, decomposition of rice straw and stubble has reduced the occurrence of both broadleaved and grassy weeds (Narwal, 2000). Incorporating the residues of rice with high allelopathic activity, minimised rice flatsedge (Cyperus iria L.) growth to a similar degree than that achieved by the application of propanil and bentazon herbicides (Lin et al, 1992). Leaves plus straw and hulls of some rice cultivars with strong allelopathic property dramatically inhibit weed interference by about 60%-95% (Jung et al, 2004). Furthermore, another trial showed rice residues (variety Sarjoo 52) blended into the soils (5-6 cm in depth) suppress jungle rice (Echinochloa colona (L.) Link), monarch redstem (Ammania baccifera L.), many flowered ammannia (A. multiflora Roxb.) and gulf leaf flower (Phyllanthus fraternus Webster) (Khan and Vaishya, 1992). Straw, leaves and hulls of some rice cultivars suppress the germination of field bind weed (Convolvulus arvensis) and littleseed canary grass (Phalaris minor) (Ahn and Chung, 2000; Inderjit et al, 2004). The use of allelopathic rice cultivars and allelochemicals can definitely reduce the ecological impact, particularly by reducing the amount of herbicide to be used. In most allelopathic rice cultivars, more than one allelochemical is available and may play a role for inhibition of weeds.

Pheng et al (2010) conducted pot experiments to evaluate the response of the rice line ST-3 and three weed species, barnyard grass (E. crus-galli), small umbrella sedge (Cyperus difformis), and water primrose (Ludwigia octovalves), to the residues of 16 rice lines. Later, the field studies were performed in order to determine the response of the same rice line and weed species to the residue of seven putative allelopathic rice lines and one non-allelopathic rice line. It was observed that if the residue’ s incorporation was delayed by two weeks or only a proportion of the residue was incorporated, the rice crop could withstand the growth-inhibiting effect, while the inhibition of the weed species was retained.

Allelopathic rice cultivars combined with cultural management options are therefore, interesting and potential strategy contributing to alternative chemical control of weeds in paddy ecosystems (Olofsdotter et al, 2002b). Such an allelopathy-based technique for paddy weed control is the most easily transferable to the low-input management systems prevailing in most rice farming systems in Asia (Kong, 2008). Genetic modification of crop plants to improve their allelopathic properties and enhancement of their weed-suppressing ability has been suggested as a possibility. In agricultural production, breeding programme may give the possibility of utilizing rice allelopathy by inducing allelopathic traits into cultivated rice (Khanh et al, 2007). Certain rice cultivars have the potential to allelopathically suppress the seedling growth of barnyard grass. As a caution, before recommending an allelopathic cultivar for field trials, their effect on the N₂-fixing potential of cyanobacteria should be studied in detail (Inderjit et al, 2001).

Diseases of rice (Oryza sativaL.) have threatened the stability of its production. Attempts to control these using synthetic biocides have met with limited success. Furthermore, the fate of these biocides is of great concern for agriculture, environment and human health. Several methods and techniques, including biological control, new resistant cultivars, natural biocides and allelochemicals, have been tried to improve rice disease management and control (Kong et al, 2010).

Allelochemicals are involved in practically every aspect of plant growth and can act as stimulating or suppressing agents. The smart utilization of allele-chemicals can be a major breakthrough in the agricultural sector (Khalid et al, 2002). Allelopathy can be used for biological control of pathogens to manage plant diseases. Several studies have successfully demonstrated the control of plant diseases using either allelopathic rotational crops or pure/crude allelochemicals (Rice, 1995).

Only few studies explored the allelopathic rice cultivars, which can deter or tolerate the insect pest pressure and pathogen attack. Screening of such resistant cultivars is highly desirable. The plant diseases can also be controlled by the antagonistic effects of antibiotics produced by other microorganisms (Rice, 1995).

Presence of phenolics and other allelochemicals in rice makes it a stronger competitor of insect pests and pathogens. Several lines of evidence indicate that momilactone A has an important role in rice defense system against pathogen attacks (Agrawal et al, 2002).

Among several diseases caused by bacterial, fungal, and viral pathogens that devastate rice yields all over the world, bacterial blight (Xanthomonas oryzaepv. oryzae), blast (Magnaporthe grisea), sheath blight (Rhizoctonia solani), sheath rot (Sarocladium oryzae), and tungro virus are the most important ones (Velusamy et al, 2006). X. oryzae pv. oryzae causes bacterial blight of rice and has high epidemic potential. It is destructive to high-yielding cultivars in both temperate and tropical regions especially in Asia. Certain plant-associated strains of fluorescent Pseudomonasspp. are known to produce the antibiotic 2, 4-diacetylphloroglucinol (DAPG) which inhibits the growth of X. oryzaepv. oryzaein laboratory assays and suppresses rice bacterial blight up to 59%-64% in net-house and field experiments (Velusamy et al, 2006). Two allelochemicals from rice, 5, 7, 40-trihydroxy- 30, 50-dimethoxy flavone (a flavone) and 3-isopropyl- 5-acetoxy cyclohexene-2-one-1 (acyclohexenone) are suggested to be a part of rice defense mechanism against diseases caused by two fungal pathogens (R. solani Kü hn and Pyricularia oryzaeCavara) (Singh et al, 2012).

In worldwide agricultural production system, the most important consideration is to improve the crop quality and yield which is mainly influenced by weeds (Khanh et al, 2007) and pests through environmentally safe agronomic approaches (Khanh et al, 2005). Application of allelopathy through genetic manipulation by using molecular genetics and biotechnology or conventional breeding in rice varieties can be considered as a successful tool for weed management, insect pests and disease pathogens (Bertin et al, 2008; Jabran and Farooq, 2013). Therefore, it is crucial to know which genes are responsible for allelopathic potential and also to understand the structure and genetic control of the allelopathic trait in order to incorporate the specific trait in rice breeding programs (Courtis and Olofsdotter, 1998). The genetic basis of allelopathy in rice by using F₂ progeny derived from a cross between rice varieties PI312777 and Lemont revealed that allelopathy is quantitatively inherited (Dilday et al, 1998). Allelopathy in rice is polygenic and a quantitative trait which depends on several physiological and phenological characteristics (Kong et al, 2011). Jensen et al (2001) performed gene mapping and epistatic QTLs associated with allelopathic activity by using DNA markers and indicated that allelopathy in rice is a quantitative trait involving several loci and probably some levels of epistasis. Since several genes are involved in allelopathic activity, it may also affect the gene responsible for crop yield and thus it is very important to consider such aspect in breeding programmes. However, allelopathy in rice may be a trait that is not strongly associated with crop yield (Olofsdotter et al, 1995).

Due to evolution, natural and artificial selection traits including allelopathic traits have been incorporated in rice germplasm which is evidenced by the presence of certain degree of allelopathic activity even in non-allelopathic rice variety. Ebana et al (2001) reported seven QTLs related to rice allelopathy on chromosomes 1, 3, 5, 6, 7, 11 and 12, respectively, from F₂ population of an indica-type line PI312777 and a japonica cultivar Lemont.

In order to understand the genetic control of allelopathy in rice, six genes namely DEG-1, DEG-4, DEG-5, DEG-7 (DEG-9) and DEG-8, with higher expression, and three genes, namely DEG-2, DEG-3 and DEG-6, with lower expression, were identified by using techniques like GeneFishing PCR and sequencing, when rice crop (Sathi) were grown with barnyard grass (Junaedi et al, 2008). These differential expressed genes responsible for allelopathic effect were further characterized (Table 3).

Table 3

Table 3

Table 3 Genes and clones responsible for rice allelopathy. Gene/Clone Length (bp) Accession No. Best homologue Rice variety Reference DEG-1 561 AJ296743.1 S-adenosylmethionine synthetase Sathi Junaedi et al, 2008 DEG-2 531 AY522330.1 Ribulose 1, 5-bisphosphate carboxylase large subunit DEG-3 491 CT829547.1 Oxygen evolving complex protein in photosystem II DEG-4 528 CT834850.1 Unknown protein DEG-5 290 CT828153.1 Histone 2B protein DEG-6 511 AK243448.1 Nicotineamine aminotransferase DEG-7 207 AC122144.1 Putative serine/threonine protein kinase DEG-8 531 NM_001056236.1 Putative transposable element oxysterol-binding protein OsCPS4 NA Os04g0990 Copalyl diphosphate synthase 4 Zhonghua 11 Xu et al, 2012 OsKSL4 NA Os0410060 Kaurene synthase like 4 Hwayoung Clone 312 (I) 619 ABR25842 Putative triosephosphate isomerase PI312777 (under low nitrogen treatment) Song et al, 2008 Clone 323 (I) 386 NM_001057746 Putative glycine hydroxymethyl transferase Clone 403 (I) 705 ABR25842 Putative triosephosphate isomerase Clone 891 (I) 593 NM_001048551 Putative triosephosphate isomerase Clone 278 (II) 498 ABR25322 Phenylalanine ammonia-lyase Clone 547 (II) 441 NM_001071389 Putative o-methyltransferase Clone 663 (II) 542 BAE45261 Cytochrome P450 Clone 34 (III) 504 AAM08829 Putative SCARECROW gene regulator-like Clone 84 (III) 391 NM_001051791 No apical meristem (NAM) protein Clone 257 (III) 544 ABA98006 Subitilisin-chymotrypsin inhibitor Clone 642 (III) 572 NM_001059257 DNA binding protein S1FA family protein Clone 935 (III) 551 NM_001060636 S1/P1 nuclease Clone 489 (III) 552 BAD81918 BolA-like protein Clone 272 (III) 290 NM_001065974 Putative calcium-dependent lipid binding 1 protein Clone 803 (IV) 384 NM_001070187 Putative protein kinase interactor Clone 943 (IV) 623 A55092 Catalase 2 (CAT-2) Clone 243 (IV) 621 NM_001052425 Myosin-like protein Clone 201 (IV) 232 AAB70546 Metallothionein-like protein type 1 Clone 120 (IV) 230 AAB70546 Metallothionein-like protein type 1 Clone 715 (IV) 618 NM_001075076 Metallothionein-like protein type 1 Clone 917 (IV) 522 NM_001057541 Expressed protein Clone 177 (V) 466 ABR25449 Putative 40S ribosomal S13 Clone 188 (V) 415 NM_001056613 60S ribosomal protein L22-2 Clone 341 (V) 459 NM_001056613 Putative 60S ribosomal protein L22-2 Clone 486 (V) 736 ABA94602 Putative 40S ribosomal protein S9 Clone 399 (V) 383 A2WXX3 Putative 60S ribosomal protein L5 Clone 349 (V) 507 BAD36074 Putative chaperonin 10 Clone 640 (V) 372 NM_001056613 60S ribosomal protein Clone 657 (V) 410 ABR25449 Putative 40S ribosomal protein S13 Clone 622 (V) 634 NM_001062753 Putative apoptosis-related protein Clone 743 (V) 406 NM_001056776 HSP20-like chaperone Clone 163 449 CM000126 Ubiquitin carrier protein PI312777 (under salicylic acid treatment) Fang et al, 2009 Clone 171 388 AC131374 Putative receptor-like protein kinase Clone 265 295 AC092263 CM000126 Putative glutathione S-transferase Clone 316 323 AAL34132 Peptidyl-prolyl cis-trans isomerase Clone 438 309 AC13174 Putative acetyltransferase Clone 459 347 ABR25322 Putative receptor-like protein kinase Clone 507 303 AP003734 Phenylalanine ammonia-lyase Clone 512 319 AY224431 Putative cinnamoyl-CoA reductase Clone 557 345 AP005578 Serine/threonine protein kinase-like protein Clone 587 200 AP003263 Putative endosperm specific protein SC3 Clone 593 256 CM000126 Putative peroxidase Clone 617 242 AF200528 Ubiquitin carrier protein Clone 670 286 AP003252 Cellulose synthase-4 Clone 695 260 BAG domain containing protein-like Clone 163 449 CM000126 AC131374 AC092263 CM000126 AAL34132 AC13174 ABR25322 AP003734 AY224431 AP005578 Ubiquitin carrier protein PI312777 (under salicylic acid treatment) Fang et al, 2009 Clone 171 388 AP003263 Putative receptor-like protein kinase Clone 265 295 CM000126 AF200528 AP003252 Putative glutathione S-transferase Clone 316 323 Peptidyl-prolyl cis-trans isomerase Clone 438 309 Putative acetyltransferase Clone 459 347 Putative receptor-like protein kinase Clone 507 303 Phenylalanine ammonia-lyase Clone 512 319 Putative cinnamoyl-CoA reductase Clone 557 345 Serine/threonine protein kinase-like protein Clone 587 200 Putative endosperm specific protein SC3 Clone 593 256 Putative peroxidase Clone 617 242 Ubiquitin carrier protein Clone 670 286 Cellulose synthase-4 Clone 695 260 BAG domain containing protein-like Numbers in parentheses are the groups of the clone. I, Primary metabolism; II, Phenolic allelochemical synthesis; III, Plant growth/cell cycle regulation; IV, Stress response/signal transduction; V, Protein synthesis/degradation. NA, Not available.

Table 3 Genes and clones responsible for rice allelopathy.

Lin et al (2005) utilized inter-simple sequence repeat as a molecular marker to assess the genetic diversity and cultivar differentiation of 57 rice accessions and 65 barely lines in terms of allelopathic potential. The study revealed that some accessions with higher allelopathic potential are grouped together, implying that the genes responsible for allelopathy might be isolocus, whereas some accessions of rice and barely with different allelopathic responses are also clustered into the same group, which perform low level of genetic polymorphism due to oriented selection for high yielding traits in breeding.

Rice allelopathy has been confirmed as an inducible genetic trait (Bi et al, 2007) that is associated with molecular regulation of the secondary metabolic pathways. Various secondary metabolites differentiated as allelochemicals are synthesized by a phenylpropanoid pathway. Some defense related proteins and the phenylalanine ammonia-lyase (PAL) enzyme, which is associated with phenylpropanoid metabolism and plant defense, have been found to be up-regulated in allelopathic rice (Fang et al, 2009). He et al (2005) used deferential proteomics and bioinformatics to study the molecular mechanism of rice allelopathy grown with barnyard grass. They found that the enhanced inhibitory effect of allelopathic rice on target weeds was due to the up-regulated expression of gene which encodes PAL.

Song et al (2008) classified 24 genes into 5 groups i.e. primary metabolism, phenolic allelochemical synthesis, plant growth/cell cycle regulation, stress response/signal transduction, and protein synthesis/ degradation based on their functions (Table 3). Further, up-regulation of the putative genes that encode for PAL, o-methyltransferase, triosephosphate isomerase and cytochrome P450, which are involved in de novo synthesis of phenolic allelochemicals and detoxification of toxic substances in PI312777 (allelopathic rice), was detected by subtractive hybridization suppression at a low nitrogen supply. Similarly, RNAi was used to inhibit PAL expression in allelopathic rice accession PI312777 by Fang et al (2013) in order to confirm the role of PAL gene in the regulation of rice allelopathy with respect to synthesis, release and metabolism of phenolics. It was observed that the down-regulation of PAL gene expression decreases the gene expression of phenolic metabolism-related enzymes and lowers the level of phenolics that in turn reduces the allelopathic potential of rice on barnyard grass. Reduction of phenolic exudates in transgenic rice also influences the quantity of rice rhizospheric microbes with eight phyla lesser in transgenic plants compared to wild type (Fang et al, 2013). Also, Lin et al (2011) and Cipollini et al (2012) found that phenolic acids are useful carbon resources that help establish the soil microbial community. The application of phenolics may improve microbial population in paddy soil and stimulate the activities of soil microorganisms which play a vital role in enhancing the allelopathic effect. The accumulation of PAL mRNA induced by exogenous salicylic acid will stimulate the synthesis of new PAL protein, increasing PAL enzyme activity against pest and weed infection in crops. Therefore, salicylic acid can be used as an activator to induce allelopathic defense in rice, especially in allelopathic rice (Bi et al, 2007; Fang et al, 2009). It has been generally assumed that the appearance of phenylpropanoid metabolites during a plant’ s response to weed and pest infection is a result of the transcriptional activation of the various biosynthetic pathway genes (Dixon, 2002). Lin et al (2004) performed proteome analysis i.e. MALDI-TOF/MS to investigate the different expression of proteins in allelopathic rice exposed to barnyard grass stress. This study provided four induced proteins, 3-hydroxy- 3-methylglutaryl-coA reductase 3 (HMGR3), PAL, thioredoxin-m and peroxidase precursor, which are related to the pathways of isoterpenoid and phenylpropanoid biosynthesis in the plant defence response. Therefore, it could be considered that proteomic approach can contribute to the identification of positional, functional and expressional genes. Comparison of 2-DE protein pattern obtained for key tissue of stressed and control plants will identify a set of stress-responsive proteins encoded by expressional candidate genes. Sequencing of these stressed- responsive proteins will then reveal that some of them have functions clearly consistent with the stress tolerant traits. The encoding genes will thus be both the expressional and functional candidate genes.

Beside such intensive information about allelopathic genetics, very less breeding efforts (especially with respect to disease management) have been made to exploit allelopathy as commercially acceptable biocontrol method in modern agricultural practice. In order to get best results of hybrid varieties, it is very important to consider the allelopathic effect of donor against wide spectrum of harmful biological system (like weeds, pests and fungi). However, while executing such an idea, the main concern should be the impacts of such improved crops on crop yield, other beneficial organisms, soil, environment, the residue, the next year crop, etc.

Since its inception in 1937, the term allelopathy is mainly viewed in terms of negative communications, but latter it was proved that, if correctly managed, this phenomenon may be exploited for enhancing the crop productivity. The number of reports indicating the improvement in crop production due to allelopathic interactions is increasing. This manipulation can be achieved by weed management, disease management, pest management, nitrogen management, etc. For sustainable agriculture of rice, allelopathy has achieved great success in weed management. Utilization of water extracts of allelopathic crop combined with reduced doses of herbicides can be a promising strategy for sustainable weed management and environment health.

The allelopathic potential of crop can be exploited directly by using allelopathic interactions or indirectly by utilizing allelochemicals as biopesticide. About 16 000 rice accessions from 99 countries have been screened for their allelopathic potential against different weeds. Use of rice residues for weed control in paddy fields is traditionally used by many farmers across the globe, however, it requires large amount of biomass.

Although there are several promising rice allelochemicals reported to inhibit weed growth and some pathogenic organisms, their direct use as pesticides is not successful due to several reasons, viz. their stability under natural environment, selectivity and limited activity, effect on non-target organisms, etc. Also, it is very difficult and expensive to develop new novel compounds to be used as pesticides. Even the isolation of allelochemicals from plants in required amount is a tedious process. Therefore, searching a compound with simple chemical structure (which might reduce its synthesis cost) and strong activity is required in future as it has achieved limited success for commercial production.

A regulation of the biosynthesis and the release rate to enhance the flow of allelochemicals (hopefully non-toxic to humans) or to prolong the period of release of the allelochemicals has been suggested (Wu et al, 1999). Use of biotechnological transfer of allelopathic traits between cultivars of the same species or between species has also been proposed (Chou, 1999), since it is easy and efficient to screen for the presence of allelopathic characteristics by using several molecular markers.

An apparently untouched aspect of allelopathy is its effect on the nutritional value of food and fodder crops. However, a change in the combinations or levels of the secondary metabolites in crops should not affect their quality as food products. Finally, the structure of allelochemicals can be used as an analogue for the synthesis of new pesticides. These biopesticides will perhaps be far less harmful for the environment as compared to synthetic agrochemicals.

However, it is very essential to consider some key aspects before applying allelopathy in natural conditions, like: the duration of allelopathic activity (stability and persistence of allelochemicals), synergistic interactions by studying threshold concentration of each compound and the behavior of genes in cross pollination conditions.