Keywords

1 Introduction

Rice is one of the most accepted staple crops of almost two thirds of the world and specially for developing countries like India. However, cultivation of this popular crop has been constrained due to rigorous climate change. Rice farming is still challenging due to global population expansion, extensive urbanization, and constant shifting of cultivable land to industrial park. Greater modernization promotes greater abiotic stresses to the plants like rise in temperature, prolonged drought condition, and water stress, increases harmful radiations, upholds reactive oxygen species (ROS) generation, etc. Employment of excessive amount of fertilizers ultimately reduces soil fertility. Use of harmful chemical pesticides and fungicides contaminates groundwater and also encourages pathogens to improve themselves and to develop new races. Application of non-judicious farming technology and mistreatment of high throughput up to date agricultural technologies has ultimately gifted non-cultivable lands (Delteil et al. 2010). To fulfill the rising demand of food supply throughout the world, growers have to produce more than 40% extra rice by 2030 (Khush 2005; Delteil et al. 2010). However, it will be a herculean task today due to tremendous challenging factors. In spite of other abiotic factors, bacterial and fungal pathogens cause a serious threat on rice cultivation (Delteil et al. 2010). Near about 20–30% of rice production is regularly hampered per year globally by various rice pathogens (Chattopadhyay et al. 2017). In this connection, Xanthomonas oryzae pv. oryzae, a Gram-negative bacterium and the causal organism of bacterial leaf blight of rice, causes almost more than 50% crop loss in respect to others (Ishiyama 1922; Chattopadhyay et al. 2017). Though it is mainly a seed-borne disease, all the developmental stages are susceptible to the pathogen under encouraging environmental situations (Chattopadhyay et al. 2017).

This disease outbreak occurs throughout the world and causes serious crop loss and economic suppression mainly in different parts of Western Africa and Asia. Moreover, intense wind associated with rains may amplify the epidemic of bacterial blight (Chattopadhyay et al. 2017). It basically occurs in high-yielding rice varieties grown in the monsoon season, under profound nitrogen fertilization and especially in the irrigated and rain-feed ecosystems (Laha et al. 2017). Bacterial blight epidemics were reported from different parts of India (Laha et al. 2009, 2017; Yugander et al. 2014). More than 50% crop loss was reported in different West African countries due to this major destructive disease (Basso et al. 2011; Laha et al. 2017). Singh et al. (2013) recorded the highest economic loss in the following series Pusa Basmati-1 (45%) > Haryana Shankar Dhan-1 (31%) > HKR 47 (23%) in India. Besides that, severe economic loss was also noticed in various regions of Southern China, Japan, the Philippines, Pakistan, Nepal, and South and Central American countries (Adhikari and Mew 1991; Mew et al. 1993; Khan et al. 2000; Akhtar et al. 2003; Qi 2009; Corral et al. 2013).

It was the most challenging task to control this devastating pathogen over time. The most convenient, economic, useful, and sustainable method was to generate resistant cultivars against this pathogen (Chattopadhyay et al. 2017). However, selection of wild resistant varieties was tedious, and new varieties of pathogen races were also challenging over time. Researchers sometimes utilize some abiotic and biotic inducers also, which are able to boost up the innate immunity of the plants. However, it was not so effective in this pathosystem. Nowadays, more researches move on to developing transgenic rice varieties against this pathogen. More than 40 genes have been tested till date to generate elite variety of rice (Chattopadhyay et al. 2017; Laha et al. 2017). By virtue of the advancement of molecular biology and biotechnological methods, multi-genes are incorporated within a single rice variety through gene pyramiding and marker-assisted selection techniques (Chattopadhyay et al. 2017). Consequently, whole genome editing tools like clustered regularly interspaced short palindromic repeats/CRISPR-associated protein (CRISPR/Cas9) and transcription activator-like effector nucleus (TALEN) are also utilized (Chattopadhyay et al. 2017; Laha et al. 2017).

This chapter emphasizes on the detailed outlook of the important disease and also provides information about the various strategies including molecular tools for the improvement of bacterial blight resistance of rice.

2 Geographical Distribution and Past History of Bacterial Blight

The devastating pathogen of bacterial blight disease of rice has been first identified and reported in the year of 1884 from Japan (Tagami and Mizukami 2008; Chattopadhyay et al. 2017). Later on, it was characterized properly and named as Xanthomonas oryzae pv. oryzae (Ishiyama) Swings et al. (Xoo) in the year 1922. Though almost all the rice-growing regions of the Caribbean island like Salvador, Mexico, Costa Rica, Honduras, and Panama were affected by this disease, it was first reported from the Mali region of West Africa (Buddenhagen et al. 1979). In South America, the affected regions include Colombia, Ecuador, Bolivia, and Venezuela (Lozano 1977; Sere et al. 2013). Louisiana and Texas from North America were most vulnerable for this pathogen (Jones et al. 1989). Furthermore, it was accounted from Australia and all the Asian countries (Ou 1985; Devadath 1992; Win et al. 2013). Srinivasan et al. (1959) reported the incidence of this disease from the state Maharashtra in India. However, its occurrence has not been established in Europe. The worldwide distribution of this disease is presented in Fig. 1.

Fig. 1
figure 1

World distribution of blast disease of rice (Laha et al. 2017)

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3 Symptoms

It is a representative of typical vascular disease among others and has three discrete phases of symptoms. In the first phase of the disease, it shows pale-green to straw-colored striped water-soaked lesions with wavy margins on the tip of the isobilateral leaves which migrates longitudinally downward (Fig. 2). The leaf blight lesions may appear on both edges of the leaf and ultimately cover the whole leaf in the severe condition. Finally, it turns to whitish to grayish black due to the progression of saprophytic fungal growth. A small opaque yellowish drop containing bacterial eluents may be observed in the humid areas at the morning, which dries up and turns into small spherical yellowish beads (Chattopadhyay et al. 2017).

Fig. 2
figure 2

Symptoms of bacterial blight disease

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In the tropical countries, kresek or wilt phase is the harshest phase of this disease. In this situation, the leaves become yellow to grayish in color and roll completely with wilting symptoms. In the acute phases, the tillers shrivel, and the affected plants ultimately die (Laha et al. 2017).

On the other hand, in the Philippines, the symptoms appear in the cluster of leaves which turns into pale yellow or whitish, and finally the affected leaves wither and dry up (Laha et al. 2017).

4 Pathogen

Xanthomonas oryzae pv. oryzae (Ishiyama) Swings et al. is a rod-shaped, non-spore-forming, Gram-negative, and motile uniflagellate bacterium having a single polar flagellum. It belongs to Xanthomonadaceae (family), Xanthomonadales (order), Gammaproteobacteria (class), and Proteobacteria (phylum) in the domain Bacteria. It secretes xanthomonadin (a brominated aryl polyene pigment), a typical non-diffusible yellow pigment (Laha et al. 2017).

5 Disease Cycle and Epidemiology

According to the inception of different studies on this disease carried out by different scientific organizations like the International Rice Research Institute (IRRI), Manila, Philippines, All India Coordinated Rice Improvement Project (AICRIP), the main cause of the disease is seed infection (Laha et al. 2009). However, there are few such references which indicate that the disease may not occur due to planting of those seeds. Furthermore, it was observed that the infection may occur in the self-grown plants, from the pre-infected stubble straws and also from the infected wild rice varieties. The pathogen may also survive on some wild grasses like Panicum repens, Leersia hexandra, and Cyperus rotundus and contaminate irrigation water which may also act as a source of primary inoculum. Cloudy humid conditions along with moderate temperature like 28–30 °C and excess use of nitrogenous fertilizer aggravate rapid growth and spreading of the disease (Ezuka and Kaku 2000) (Fig. 3).

Fig. 3
figure 3

Disease cycle of bacterial blight (causal organism: Xanthomonas oryzae pv. oryzae)

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6 Brief Overview of Disease Management Strategies Employed till Date

Various control measures including host nutrition and physical, cultural, and chemical control are employed to restrict this devastating disease. However, the best possible outcome may not be achieved due to regular modification of the pathogenic races, though improvement of plant resistance by the introduction of new gene or by regular breeding technique may be the best solution to overcome this disease.

Use of cultural control as an essential part of integrated disease management may be useful to some extent to control this disease. Removing infected plant trashes, wild rice plants, and weeds like Leersia sp. and Cyperus sp. may be quite useful to confine pathogen progress. Restriction of unnecessary pruning of plant parts and field to field irrigation may be helpful to control this disease. Not only that, use of pathogen-free certified seeds and judicious use of manures mainly nitrogen may be beneficial (Ezuka and Kaku 2000; Laha et al. 2009, 2017).

After disease inception, the use of different chemicals may act as SOS to control this destructive disease, though chemicals which are utilized in the field may not be eco-friendly. Till date various chemicals like chloramphenicol, cellomate, Sankel, streptomycin, phenazine, etc. have been used in the field (Laha et al. 2017). However, satisfactory results may not be achieved and sometimes more than one chemical was required to control this pathogen and the remnants of which may cause serious health hazards (Srivastava 1972; Laha et al. 2017). Seed soaking with various chemicals like Agrimycin 100, streptomycin, Terramycin, chlortetracycline hydrochloride, Ceresan, etc. at variable proportions along with hot water treatment may diminish the pathogen inoculum from seeds (Laha et al. 2017). Srivastava (1972) reported that TF-130 and ATDA (2-amino-1,3,4-thiadiazole) were most efficient against this pathogen in Japan and adjoining countries. Agrimycin 100 and Fytolan (copper oxychloride) in a specific proportion (50:500) may be useful to check secondary infection (Singh et al. 1980). According to Laha et al. (2009), 12.5 kg/ha Klorocin application 10 days after transplanting may give useful results. The highest disease control by the application of chemicals was achieved by applying Streptocycline (200 mg/l), copper oxychloride (2.5 g/l), and 2,4-D ethyl ester (1.0 ml/l) in combination (Singh et al. 2012b; Laha et al. 2017).

Crop improvement by conventional breeding methods may also help to combat against this disease. In the year 1969, two bacterial blight rice varieties named IR 20 and IR 22 were developed from IRRI, mostly on the basis of the major resistance genes like Xa4 (Khush et al. 1989; Laha et al. 2017). However, those high-yielding varieties (HYVs) showed different degrees of susceptibility in different countries against this pathogen, which may be due to the development of more virulent new pathogenic races (Laha et al. 2017). Consequently, new resistance genes like Xa5 and Xa7 have been incorporated by plant researchers (Khush et al. 1989; Laha et al. 2017). Gradually other bacterial blight resistance-related new genes were discovered from wild rice varieties like Xa21, obtained from Oryza longistaminata (Khush et al. 1990; Laha et al. 2017). Till date more than 35 genes including Xa23, Xa27, Xa30(t)/Xa38, and Xa33 have been identified from various sources and customized for marker-assisted selection breeding (Sundaram et al. 2014; Kim et al. 2015; Laha et al. 2017). Nowadays, to achieve the highest durable resistance against this destructive pathogen, amalgamation of different genes into a single rice cultivar was taking place by using the process of marker-assisted selection breeding (Laha et al. 2017). By using this technique, various rice varieties were obtained which are listed in Table 1.

Table 1 Different commercialized rice varieties obtained by breeding
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Researches on host resistance against this pathogen are not so wide in Africa as in Asia. According to available reports, NERICA 4, NERICA 8, and NERICA 14 varieties showed modest level of bacterial blight resistance (Banito et al. 2012). However, few accessions of O. glaberrima from Mali showed high degree of resistance against this pathogen race A3 (Djedatin et al. 2011; Laha et al. 2017).

7 Why Modify the Employment of Bacterial Blight Resistance Genes?

It is well-known that the effective genes present in the elite clones of different rice varieties are evenly distributed all across the vast geographic areas. Sometimes they interact with the existing pathogen community of local inhabitants. Very often, long-term contact with efficient pathogen may cause an epidemic outbreak, which is mainly due to the loss of durability of the resistance genes (Dossa et al. 2015). A detailed understanding of pathogen physiology, host metabolism, and disease epidemiology and consequently knowledge of interdisciplinary approaches are very much necessary to control the pathogen dynamics. Studies on suppressive environments and effective genes through effector biological programs may employ a new arena in the field of integrated disease management. The outcome of those experiments should be properly informed to the forerunner of the cultivation.

Near about 40 genes were identified for bacterial blight of rice mostly from the wild and cultivable varieties (Khan et al. 2014; Zhang et al. 2014; Dossa et al. 2015). In Asia, the resistance genes like Xa 4, Xa 5, Xa 13, and Xa 21 are mostly used for breeding purposes (Khan et al. 2014). Interestingly, the bacterial blight pathogen uses transcription activator-like (TAL) effectors to colonize the host system. In the large deployment of disease resistance against this pathogen and in contrast to the other pathosystems, Xa genes can be further classified into sub-categories (Boch et al. 2014; Dossa et al. 2015). The roles of different Xa genes are discussed in Table 2.

Table 2 List of R genes of various rice cultivars securing resistance toward Xanthomonas oryzae pv. oryzae
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8 Genes and Techniques Employed to Rice Research

Various techniques have been utilized to produce stable transgenic rice plants in the market till date. However, transformation through Agrobacterium tumefaciens has been accepted as a routine technique in most of the laboratories (Toki et al. 2006; Delteil et al. 2010). Through this technique, efficiency of different rice varieties like japonica, indica, etc. has been improved sufficiently (Delteil et al. 2010). Later on, marker-assisted selection techniques were familiarized to the breeders for crop improvement (Ballini et al. 2009; Delteil et al. 2010). White and Yang (2009) describe the specific roles of major Xa resistance genes which confer the resistance against Xanthomonas. According to Peng et al. (2015), Xa21 was the most prime gene in bacterial blight resistance which is also connected to signaling pathways. Other genes such as OsBRR1 and OsWAK1 were shown to be helpful in coding for receptor-like proteins and provide basal resistance to rice plant (Delteil et al. 2010). Moreover, genes which are utilized for the making of transgenic rice are basically related to defense signaling and transcription factors including XB15, OsPLDB1, OsDR8, SPL18, SPL11, PACK1, OsGAP1, and OsRac1 (Delteil et al. 2010). Moreover, few PR genes out of 14 found in rice have been overexpressed (Van Loon et al. 2006; Delteil et al. 2010).

In a recent study on RNA-Seq showed that rice cultivar IRBB61 containing Xa7 when infected with Xanthomonas oryzae at high temperature stress, gives protection against the pathogen and was not dependent on salicylic acid pathway but related to abscisic acid (Cohen et al. 2017).

9 Future Goal and Conclusion

To find out the major constraints in rice production, it has been observed that bacterial blight has huge effect on yield loss. Though various approaches are available to control this disease, nowadays, the cultivation of resistant varieties is considered as the most economical tool. Many researchers till date working with the disease to understand the detailed molecular mechanism of pathogenesis. To protect rice from this devastating pathogen, it is an urgent requirement to identify and characterize a large number of defense genes. Marker-assisted breeding and various transgenic approaches can be taken as potential tools to protect rice against this disease. Identification, characterization, and functional analysis of resistant genes can open the downstream signaling pathway associated with this disease. That may be altered at desired steps to check the efficacy of the pathogen. If we think in other way, application of various biotic and abiotic elicitors can also be taken as a tool to induce innate immunity against this disease. Application of newer genome editing tool as CRISPR against the disease can also be accepted as future area of research. Many transcriptomic, proteomic, and metabolomic approaches can be taken as tools to draw the defense signaling network.

To sum up at this point, our major goal is to protect rice plant from this pathogen. To achieve this goal and to secure our food, further research works are required for better understanding of pathogenesis and identifying probable easy tool to combat against this disease.