**5.1 Exclusion**

*Protecting Rice Grains in the Post-Genomic Era*

**Crop phenology (% heading)**

above, day temperatures above 32°C from 10 am to 12 pm (the flowering time), and precipitation from the last week of June through the first week of August (**Table 2**). Heading and flowering occurred on a large percentage of the Texas rice crop during that period. These conditions were associated with severe outbreaks of BPB and significant yield losses in 1995. **Figure 8** shows an example of the severity of this disease in 1995 and its association with yield loss for different rice cultivars, with the

*Yield (left Y-axis) and bacterial panicle blight (BPB) severity (% panicles affected) (right Y-axis) of eight cultivars of rice (X-axis) in naturally infested field at Beaumont, Texas, in 1995 (source: [11]). Error bars are* 

**Month Week Days Total** 

— June 1 0 0 — 0 4.4 2 0 3 — 1 2.0 3 0 0 0 0 0 4 4 1 0 2 8.0 July 1 0 5 0 5 4.0 2 4 2 0 2 0.7 3 4 3 6 2 0.4 4 6 5 7 2 4.8 August 1 3 1 4 2 2.2 2 2 2 6 3 3.5 3 4 2 — 3 3.2 4 4 1 — 4 2.5

**≥35°C Mean ≥ 24°C 10 am to noon (cm) ≥32°C**

**Precipitation**

**precipitation** 

Successful disease control generally relies on employing management strategies toward reducing the damage to a manageable and acceptable level. These strategies

disease severity levels ranging from 1 to 22% of panicles affected.

*Summary of rice crops and weather data at Beaumont and Eagle Lake, Texas in 1995.*

**74**

**Figure 8.**

**Table 2.**

*present in columns.*

**5. Management strategies**

Since the BPB disease has been reported in more than 18 countries (**Table 1**) and the disease is not present in all the rice-producing countries and regions, exclusion of the BPB pathogens from a disease-free region is the most effective strategy to prevent BPB of rice. Plant quarantine is an effective measure to achieve this goal. For example, within the USA, the state of California has employed a plant material quarantine procedure to prevent the introduction of the BPB pathogens, other rice pathogens, and weed and insect pests into the state from the southern rice-producing USA. A similar plant quarantine law has been established and enforced in China to prevent the potential importation of the BPB pathogens from foreign countries since 2007 [21].

BPB is seedborne and infected seeds serve as the primary source of inoculum [1, 2, 48]. Therefore, the use of certified seeds that are free of the BPB pathogens is another effective measure to exclude the disease from a disease-free geographic area. Different molecular detection methods including PCR that have been developed to test rice seed lots [19, 48] can aid in this process. In the USA, the use of pathogen-free seeds is recommended to manage the BPB disease. However, using PCR procedure to ensure the BPB pathogens free in certified seed has not been employed. To reduce the BPB disease, it is recommended that farmers should not use the seeds harvested from the fields that are infected with BPB the previous year.

Seed treatment can serve as the last resort to reduce and even eliminate the seedborne BPB pathogen populations and to control subsequent head disease to an accepted level. Rice seeds treated at 65°C of dry heat for 6 days can eradicate the BPB pathogens [26]. Seed treatment with the antibiotic bactericide oxolinic acid (Starner®) has been shown to control the bacterial pathogens in naturally and artificially infected seeds [59]. An antagonistic *Pseudomonas* spp. strain when applied onto seeds was effective to reduce the *B. glumae* populations in seed and suppress seedling rot [60]. Seed treatment with hot water at 60°C for 10 minutes is ineffective for control of the BPB disease although such seed treatment practice is effective to control the rice blast pathogen *M. oryzae* [61].

## **5.2 Genetic resistance**

Considerable research efforts have been conducted globally to develop resistant cultivars as an effective and sustainable strategy for management of BPB of rice. Unfortunately, no single genes or quantitative trait loci (QTLs) for complete resistance to BPB have been found so far [13, 14]. Only several rice cultivars with partial resistance are available for commercial use. In Japan, BPB resistance breeding research efforts started as early as 1975; three partially resistant cultivars were identified through a field screening of nine cultivars and lines [62]. No resistant cultivars and breeding lines were identified in a study of screening 293 cultivars and lines using greenhouse inoculation at the flowering stage in 1983 [63, 64]. From 1985 through 2013, there were nine reported studies that screened a total of 798 cultivars and breeding lines in the field and greenhouse and identified a total of 28 cultivars and lines showing partial resistance to BPB [13, 65–73]. Most recently, Mizobuchi et al.

[74] identified two tropical *japonica* cultivars, Kale and Jaguary, with a high level of resistance and several *indica* cultivars with moderate levels of resistance. These cultivars could serve as good resistance sources to develop BPB-resistant Japanese *temperate japonica* cultivars that can be adapted for use in Japan. Most of rice cultivars commercially available in Japan are susceptible or very susceptible to the BPB disease [74].

In the USA, a collaborative research effort has been established for decades in the southern states of Arkansas, Louisiana, Mississippi, Missouri, and Texas through the Uniform Rice Research Nursery (URRN) to evaluate and develop rice cultivars with high yielding potential and resistance to BPB, sheath blight, rice blast, and other diseases. Annually, more than 200 elite breeding lines and cultivars from the southern states' breeding programs are evaluated in the URRNs inoculated with *B. glumae* at the boot to heading stages. Jupiter, a partially resistant cultivar [75–77] is usually included as a check in these multistate evaluations. Results of multiyear studies demonstrate that no complete resistance cultivars and lines are available and most of the cultivars and lines evaluated are susceptible and very susceptible to BPB [[78], Don Groth, personal communication]. However, some cultivars and lines demonstrated their partial resistance to BPB. For example, Catahoula, Jupiter, Taggart, Rondo, and XL723 (hybrid) were moderately resistant to BPB in the field evaluations conducted in Texas (**Figure 9**). Hybrid cultivars, including XL723, XL753, XL760, CLXL729, CLXL 730, and CLXL745, are relatively more resistant than most of inbred cultivars [4]. The mechanisms associated with BPB resistance in the hybrids are needed to be investigated. In addition, LM-1, a mutant line obtained from gamma radiation treatment of the susceptible cultivar, Lemont, is resistant to BPB [7, 79]. Some resistant breeding lines have been identified in the URRN evaluations in Arkansas [80].

In addition to the host resistance research that has been conducted in Japan and the USA, resistant cultivars and lines have also been reported in other countries. In Brazil, three cultivars were found to be resistant to BPB in the field evaluation [81]. In China, one cultivar, named KaohsiugS.7, was reported to show resistance to the disease when rice plants were inoculated with *B. glumae* at the flowering stage in the field [82].

Host resistance such as rice blast resistance can be broadly classified into complete and partial resistance [83]. The complete resistance is of qualitative character and race specific, which is controlled by major resistance genes (R genes). However, the partial resistance is of quantitative character and non-race specific, which is controlled by several minor genes known as quantitative trait loci (QTLs). Unlike rice blast resistance having both complete and partial resistances, it is apparent

### **Figure 9.**

*Mean severities of bacterial panicle blight (BPB) (Y-axis) in 20 rice cultivars (X-axis) over two locations (Beaumont and Eagle Lake) in Texas in 2010. Error bars are present in columns.*

**77**

*Sustainable Strategies for Managing Bacterial Panicle Blight in Rice*

that rice BPB resistance has only partial (quantitative) resistance and no complete resistance has been found. Pinson et al. [14] provided the first analysis of QTLs of rice resistance to BPB, using a population of 300 recombinant inbred lines (RILs) derived from a cross between Lemont and TeQing, susceptible and resistant to BPB, respectively. Lemon was an American rice cultivar, while TeQing was a cultivar from China. Twelve QTLs, namely, *qBPB-1-1*, *qBPB-1-2*, *qBPB-1-3*, *qBPB-2-1*, *qBPB-2-2*, *qBPB-3-1*, *qBPB-3-2*, *qBPB-7*, *qBPB-8-1*, *qBPB-8-2*, *qBPB-10*, and *qBPB-11*, were identified on seven chromosomes (chromosomes 1, 2, 3, 7, 8, 10, and 11). Among these QTLs, eight (*qBPB-1-1*, *qBPB-1-2*, *qBPB-2-2*, *qBPB-3-1*, *qBPB-7*, *qBPB-8-1*, *qBPB-10*, and *qBPB-11*) were derived from TeQing and four (*qBPB-1-3*, *qBPB-2-1*, *qBPB-3-2*, and *qBPB-8-2*) from Lemont. After this first report of QTL analysis in the USA, Mizobuchi et al. [73, 84] also identified one QTL, namely, RBG2, on chromosome 1, using a population of 110 backcross inbred lines (BILs) derived from a cross between Kale (resistant to BPB) and Hitomebore (susceptible) in Japan. Kale was a traditional lowland *indica* cultivar that originated from India, while Hitomebore was a modern lowland *temperate japonica* cultivar. In addition, Mizobuchi et al. [85] also have identified the first and only QTL associated with resistance to seedling rot caused by *B. glumae* from a population of 44 chromosome segment substitution lines (CSSLs) derived from a cross between Nona Bohka and Koshihikari, resistant and susceptible to seedling rot, respectively. This QTL, namely, *RBG1*, is located on

The current research evidence suggests that there is no direct correlation in genetic resistance between seeding rot and grain rot caused by the same bacterium

Oxolinic acid (5-ethyl-5,8-dihydro-8-oxo-[1,3]dioxolo[4,5-g]quinoline-7-carboxylic acid, Starner®) is the first chemistry that has been reported to be highly effective for control of the BPB disease in rice. This antibacterial compound, a quinoline derivative, was first introduced in Japan in 1989 for control of rice seeding rot and grain rot [15]. Combined use of oxolinic acid as seed treatment and foliar sprays at heading has been reported to be the best strategy for effective control of both seeding rot and gain rot diseases [17]. When applied at the heading stage, this bactericide is highly effective to inhibit multiplication of *B. glumae* on spikelets and control the BPB disease [15, 51]. In the multiyear field trials conducted in Louisiana is Texas, oxolinic acid, when applied at the boot to heading stages, reduced BPB severity by up to 88% [86–88]. Oxolinic acid has been used three times per season for control of BPB in Japan for more than two decades [89]. Unfortunately, *B. glumae* populations resistant to oxolinic acid have been found in rice in Japan since 1998 [16, 17, 19, 89, 90]. An amino acid substitution at position 83 in GyrA (GyrA83) is responsible for the development of oxolinic acid resistance in the *B. glumae* populations [90]. It has been found that the bacterial populations resistant to oxolinic acid are also cross-resistant to other quinoline derivatives [16]. A specific PCR method has been developed to detect the oxolinic acid-resistant populations of *B. glumae* [19]. The occurrence of oxolinic acid resistance might limit its increasing use and new registrations for management of BPB in rice. Oxolinic acid is not

registered for use in rice in the USA and many other countries.

Copper and copper-containing bactericides have also been reported to be effective for control of BPB in rice [86, 91–93]. These bacterial products include Kocide® 2000 (53.8% copper hydroxide), Kocide® 3000 (46.1% copper hydroxide), Previsto® (5% copper hydroxide), Badge® SC (15.4% copper hydroxide plus 16.8% copper oxychloride), Badge® X2 (21.5% copper hydroxide plus 23.8% copper

*DOI: http://dx.doi.org/10.5772/intechopen.84882*

chromosome 10.

*B. glumae* [64, 73, 85].

**5.3 Chemical control**

*Sustainable Strategies for Managing Bacterial Panicle Blight in Rice DOI: http://dx.doi.org/10.5772/intechopen.84882*

that rice BPB resistance has only partial (quantitative) resistance and no complete resistance has been found. Pinson et al. [14] provided the first analysis of QTLs of rice resistance to BPB, using a population of 300 recombinant inbred lines (RILs) derived from a cross between Lemont and TeQing, susceptible and resistant to BPB, respectively. Lemon was an American rice cultivar, while TeQing was a cultivar from China. Twelve QTLs, namely, *qBPB-1-1*, *qBPB-1-2*, *qBPB-1-3*, *qBPB-2-1*, *qBPB-2-2*, *qBPB-3-1*, *qBPB-3-2*, *qBPB-7*, *qBPB-8-1*, *qBPB-8-2*, *qBPB-10*, and *qBPB-11*, were identified on seven chromosomes (chromosomes 1, 2, 3, 7, 8, 10, and 11). Among these QTLs, eight (*qBPB-1-1*, *qBPB-1-2*, *qBPB-2-2*, *qBPB-3-1*, *qBPB-7*, *qBPB-8-1*, *qBPB-10*, and *qBPB-11*) were derived from TeQing and four (*qBPB-1-3*, *qBPB-2-1*, *qBPB-3-2*, and *qBPB-8-2*) from Lemont. After this first report of QTL analysis in the USA, Mizobuchi et al. [73, 84] also identified one QTL, namely, RBG2, on chromosome 1, using a population of 110 backcross inbred lines (BILs) derived from a cross between Kale (resistant to BPB) and Hitomebore (susceptible) in Japan. Kale was a traditional lowland *indica* cultivar that originated from India, while Hitomebore was a modern lowland *temperate japonica* cultivar. In addition, Mizobuchi et al. [85] also have identified the first and only QTL associated with resistance to seedling rot caused by *B. glumae* from a population of 44 chromosome segment substitution lines (CSSLs) derived from a cross between Nona Bohka and Koshihikari, resistant and susceptible to seedling rot, respectively. This QTL, namely, *RBG1*, is located on chromosome 10.

The current research evidence suggests that there is no direct correlation in genetic resistance between seeding rot and grain rot caused by the same bacterium *B. glumae* [64, 73, 85].

### **5.3 Chemical control**

*Protecting Rice Grains in the Post-Genomic Era*

fied in the URRN evaluations in Arkansas [80].

[74] identified two tropical *japonica* cultivars, Kale and Jaguary, with a high level of resistance and several *indica* cultivars with moderate levels of resistance. These cultivars could serve as good resistance sources to develop BPB-resistant Japanese *temperate japonica* cultivars that can be adapted for use in Japan. Most of rice cultivars commercially available in Japan are susceptible or very susceptible to the BPB disease [74]. In the USA, a collaborative research effort has been established for decades in the southern states of Arkansas, Louisiana, Mississippi, Missouri, and Texas through the Uniform Rice Research Nursery (URRN) to evaluate and develop rice cultivars with high yielding potential and resistance to BPB, sheath blight, rice blast, and other diseases. Annually, more than 200 elite breeding lines and cultivars from the southern states' breeding programs are evaluated in the URRNs inoculated with *B. glumae* at the boot to heading stages. Jupiter, a partially resistant cultivar [75–77] is usually included as a check in these multistate evaluations. Results of multiyear studies demonstrate that no complete resistance cultivars and lines are available and most of the cultivars and lines evaluated are susceptible and very susceptible to BPB [[78], Don Groth, personal communication]. However, some cultivars and lines demonstrated their partial resistance to BPB. For example, Catahoula, Jupiter, Taggart, Rondo, and XL723 (hybrid) were moderately resistant to BPB in the field evaluations conducted in Texas (**Figure 9**). Hybrid cultivars, including XL723, XL753, XL760, CLXL729, CLXL 730, and CLXL745, are relatively more resistant than most of inbred cultivars [4]. The mechanisms associated with BPB resistance in the hybrids are needed to be investigated. In addition, LM-1, a mutant line obtained from gamma radiation treatment of the susceptible cultivar, Lemont, is resistant to BPB [7, 79]. Some resistant breeding lines have been identi-

In addition to the host resistance research that has been conducted in Japan and the USA, resistant cultivars and lines have also been reported in other countries. In Brazil, three cultivars were found to be resistant to BPB in the field evaluation [81]. In China, one cultivar, named KaohsiugS.7, was reported to show resistance to the disease when rice plants were inoculated with *B. glumae* at the flowering stage in the field [82]. Host resistance such as rice blast resistance can be broadly classified into complete and partial resistance [83]. The complete resistance is of qualitative character and race specific, which is controlled by major resistance genes (R genes). However, the partial resistance is of quantitative character and non-race specific, which is controlled by several minor genes known as quantitative trait loci (QTLs). Unlike rice blast resistance having both complete and partial resistances, it is apparent

*Mean severities of bacterial panicle blight (BPB) (Y-axis) in 20 rice cultivars (X-axis) over two locations* 

*(Beaumont and Eagle Lake) in Texas in 2010. Error bars are present in columns.*

**76**

**Figure 9.**

Oxolinic acid (5-ethyl-5,8-dihydro-8-oxo-[1,3]dioxolo[4,5-g]quinoline-7-carboxylic acid, Starner®) is the first chemistry that has been reported to be highly effective for control of the BPB disease in rice. This antibacterial compound, a quinoline derivative, was first introduced in Japan in 1989 for control of rice seeding rot and grain rot [15]. Combined use of oxolinic acid as seed treatment and foliar sprays at heading has been reported to be the best strategy for effective control of both seeding rot and gain rot diseases [17]. When applied at the heading stage, this bactericide is highly effective to inhibit multiplication of *B. glumae* on spikelets and control the BPB disease [15, 51]. In the multiyear field trials conducted in Louisiana is Texas, oxolinic acid, when applied at the boot to heading stages, reduced BPB severity by up to 88% [86–88]. Oxolinic acid has been used three times per season for control of BPB in Japan for more than two decades [89]. Unfortunately, *B. glumae* populations resistant to oxolinic acid have been found in rice in Japan since 1998 [16, 17, 19, 89, 90]. An amino acid substitution at position 83 in GyrA (GyrA83) is responsible for the development of oxolinic acid resistance in the *B. glumae* populations [90]. It has been found that the bacterial populations resistant to oxolinic acid are also cross-resistant to other quinoline derivatives [16]. A specific PCR method has been developed to detect the oxolinic acid-resistant populations of *B. glumae* [19]. The occurrence of oxolinic acid resistance might limit its increasing use and new registrations for management of BPB in rice. Oxolinic acid is not registered for use in rice in the USA and many other countries.

Copper and copper-containing bactericides have also been reported to be effective for control of BPB in rice [86, 91–93]. These bacterial products include Kocide® 2000 (53.8% copper hydroxide), Kocide® 3000 (46.1% copper hydroxide), Previsto® (5% copper hydroxide), Badge® SC (15.4% copper hydroxide plus 16.8% copper oxychloride), Badge® X2 (21.5% copper hydroxide plus 23.8% copper oxychloride), and Top Cop® (8.4% tric basic copper sulfate). In the field trials of Louisiana, a single application of Kocide® 2000 or Top Cop® at the boot stage reduced the BPB severity as much as 75%, and grain yield and milling quality were improved [86]. In our multiyear field trials conducted in Texas, single applications of Kocide® 3000, Badge® SC, Badge® X2, or Previsto® at the heading stage significantly reduced BPB severity, with the reductions ranging from 42 to 96% [91–93]. However, except Previsto® with a relatively lower level of copper-active ingredient, all other copper products produced varying degrees of phytotoxicity on sprayed leaves and panicles and under certain environmental conditions reduced yields [86, 91–93]. These copper products have been registered as bactericides and fungicides for control of various bacterial and fungal diseases in citrus, tree crops, vegetables, vines, and field crop (soybeans, wheat, oats, and barley) in the USA. Probably due to their potential phytotoxicity and yield reduction, all these copper products have not been registered for management of the BPB disease on rice in the USA.

In addition to oxolinic acid and copper-based bactericides, other bactericides such as kasugamycin, probenazole, and pyroquilon are used for management of rice seedling rot and grain rot in Japan [16] and Honduras (Lex Ceamer, personal communication).

### **5.4 Biological control**

Several studies have been conducted to develop biological control methods as a strategy for management of BPB of rice. In Japan, Tsushima and Torigoe [94] conducted the first research on the use of bacterial antagonists for control of BPB under field conditions. An antagonistic *Pseudomonas* sp. strain was found to be effective to suppress seedling rot when pretreated onto rice seeds prior to planting [60]. Furuya et al. [95] also found that rice seedling rot was reduced following seed treatment with avirulent strains of *B. glumae*. Miyagawa and Takaya [96] found that an avirulent strain of *B. gladioli* when applied onto rice panicles was very effective to reduce BPB severity. In the USA, five *Bacillus amyloliquefaciens* strains were found to be antagonistic against *B. glumae* in vitro and reduce BPB severity when applied at the heading stage in the field trials conducted in Louisiana [97]. When applied at the flowering stage, two strains of *Bacillus* sp., with antibacterial activities toward *B. glumae*, were demonstrated to reduce BPB severity by as much as 50% and increase grain yield by more than 11% in the field trials conducted in Texas [87, 88]. In a separate BPB-spread field trial study, one of the strains also showed its ability to significantly limit the spatial spread of BPB from a focal point of inoculum [55].

In addition to bacterial biocontrol agents, bacteriophages (also known as phages) have been demonstrated to be effective for management of rice seedling rot in Japan. Adachi et al. [98] found that two bacteriophages were able to lyse *B. glumae* and were highly effective to control seeding rot when rice seeds were pretreated with them. One of the bacteriophages evaluated was even more effective in reducing seeding rot than the bactericide ipconazole/copper (II) hydroxide.

### **5.5 Cultural practice**

Few studies have been conducted to understand and develop cultural practices that could reduce the incidence and severity of BPB in rice. High levels of nitrogen fertility tend to increase the susceptibility of rice plants to the BPB disease. Avoiding excessive nitrogen rates can help reduce the damage caused by BPB. In an Arkansas study evaluating the effects of nitrogen on BPB severity, it was demonstrated that the severity of BPB at the high nitrogen rate (247 kg/ha) was 1.6 times higher than at the low rate (168 kg/ha) applied during a cropping season [99]. Under the Southern

**79**

*Sustainable Strategies for Managing Bacterial Panicle Blight in Rice*

helpful in reducing the incidence and severity of the disease.

people (Aaron Shew, personal communication).

susceptible or very susceptible to BPB.

US rice production systems, early planting or use of early maturing rice cultivars to avoid the hottest times of the growing season is another effective approach to reduce the damage caused by the disease. In addition, avoiding excessive seeding rates is also

BPB has been reported in more than 18 countries and has become a global rice disease. Currently, BPB is one of the major diseases in rice in many countries, including Japan, the USA, and Latin America. The disease is highly destructive, which can cause almost complete losses in yield and milling quality under the most favorable conditions. The outbreaks of BPB are triggered by conditions of high temperatures. With predicted global warming, the disease is likely to be more prevalent on a global scale and to cause more damage in epidemic regions in the future [20, 74]. The global land and ocean surface temperature has been increased by as much as 0.85°C over the period of 1880–2012 based on the 2014 IPCC report [100]. Under the 1°C warming scenario, it is estimated that the increased damage caused by this disease in the Southern USA would result in a \$103 million USD annual decrease in consumer surplus and a loss of rice production equivalent to feeding 1.9 million

Effective management of this bacterial disease is challenging. Unlike most of other rice diseases, The BPB disease often develops after the heading stage, and typically no symptoms and signs can be observed before heading. Therefore, no scouting methods are currently available to detect and predict the development of the disease. No standardized seed treatment methods have been developed and commercialized specifically to eradicate or reduce the pathogen populations in rice seeds. No chemical control agents are labeled for management of the BPB disease in most countries, including the USA. The efficacy and increasing use of oxolinic acid have been affected by the development of oxolinic acid resistance in the populations of *B. glumae* in Japan and other countries. No commercially available biocontrol agents have been developed. Most of commercially available rice cultivars are

Therefore, effective and sustainable control of the BPB disease largely depends on integrated use of available management options. Plant quarantine is the first defense to exclude the BPB pathogens from disease-free countries and regions. The use of pathogen-free seed or certified seed is another effective measure to control this disease. Planting with cultivars having a resistant level as high as possible is always an effective recommendation to reduce the damage caused by the disease. A limited number of rice cultivars, including hybrids, with partial resistance to BPB are available for commercial use in many countries. Since no source of complete resistance has been discovered so far, more research is needed to look for new sources of resistance through screening a greater number of germplasm lines, including those from other countries and the wild species of *Oryza*. Continued studies are needed to further characterize, fine map, or even clone the QTLs associated with BPB resistance that have been identified. More investigations are desired to understand the genetic control of BPB resistance in available resistant rice cultivars and lines, especially hybrids. These studies may lead to the development of molecular makers linked to BPB resistance that can help breeders facilitate the selection of BPB resistance in early breeding generations with more confidence. Recent advances in rice genomics and newly developed genome editing tools like CRISPR may provide new and powerful tools to better understand the mechanisms associated with BPB resistance and develop new rice cultivars with a higher level of

*DOI: http://dx.doi.org/10.5772/intechopen.84882*

**6. Conclusion and prospects**

US rice production systems, early planting or use of early maturing rice cultivars to avoid the hottest times of the growing season is another effective approach to reduce the damage caused by the disease. In addition, avoiding excessive seeding rates is also helpful in reducing the incidence and severity of the disease.
