**6. Genetic improvement of rice for enhanced resistance**

Disease resistance has been one of the major breeding strategies in rice breeding programs worldwide. Continued investigation of the mechanism of plant innate immunity can accelerate disease resistant breeding efforts (**Figure 6**).

A donor or several donors for *R* genes are used for crossing or triple crossing, either resistant progeny are selected for further evaluation or these F2 are advanced 2 to 3 generations and then evaluated for their disease reactions. Early breeding involved the use of field conditions to evaluate the disease reactions of landrace varieties or breeding lines. More recently, rice breeding lines and other germplasm are evaluated for disease reactions under greenhouse conditions for both blast [77, 78] and sheath blight [79]. In many countries evaluations of disease reaction are conducted under field conditions because there often exist conducive environmental conditions (for example, in Colombia, [80]). However, it is difficult to determine if observed resistance is due to any particular *R* gene due to overlapped resistance such as *Pi-ta* and *Ptr* for blast races IB49 and IC17. Marker assisted selection (MAS) uses genetic markers that are linked to the *R* genes or derived from portions of *R* genes [81]. This allows the DNA of progeny to be rapidly examined

#### **Figure 6.**

*Understanding interplays of pattern-triggered immunity (PTI) and elicitor triggered immunity (ETI) in activating robust defense gene expression results in a short term benefit - breeding for disease resistance using marker assisted selection (MAS) approach and a long term benefit- engineering durable effective resistance using genome editing.*

for the presence of *R* genes without growing the plants to observe their reaction to pathogens. Breeders can monitor these tagged *R* genes during crossing, selection and incorporation [82–86]. MAS is a promising technology for increasing precision of selection for *R* genes and increasing speed of breeding for resistance.

One bottleneck for the use of MAS in classical breeding is the limitation of the number of markers that can be used to accurately tag resistance in any given breeding line because genetic backgrounds of breeding lines are relatively uniform in comparison with most markers developed using diverse genetic crosses of indica with japonica. Thus, the improvements of published markers are needed using local breeding lines. Gene specific DNA markers for *Pi-ta* and *Pi-b* and SSR markers for *Pikm/Piks* and *Piz* were developed based on genomic differences of local breeding lines, and are effective for MAS in the USA [85–88]. Both *Pi-ta* and *Pi-b* markers have also been adapted for blast resistant breeding programs worldwide. Another limitation for MAS is that increased numbers of markers may create a situation in which the segregating population would need to be large enough to ensure the incorporation of all *R* genes to reach the durability of resistance to the pathogens in addition to other breeding objectives. Finally, there often exist linkage blocks where disease resistance genes co-locate with inferior genes involved in quality and productivity [89, 90].

Genetic engineering is a tool that can overcome the above mentioned limitations of classical plant breeding with MAS. This approach will eliminate the inferior genes due to the linkage block in the final products. Any gene should be able to function in any other organism if genetic components for its expression are intact. Genes can be available from any organism, not just from a plant of the same species, as is the case with classical plant breeding with MAS. After genes are added to a genome, their copy numbers, location and their expression may be controlled by other genes. The common method is to insert a new gene into a plant using the natural genetic engineer, bacterium *Agrobacterium tumefaciens* [91]. The plants are regenerated from a single cell because each cell of the engineered plant must contain the new gene. Another method is biolistic transformation using the "gene gun", which bombards protoplasts with metal particles coated with the foreign genes [92]. The gene gun is much less efficient than the Ti plasmid for gene transfer because of multiple copy integrations. In rice, genetic engineering has been demonstrated to improve resistance to sheath blight and blast in various laboratories worldwide [60, 93]. One obvious advantage of genetic engineering is that genes from other organisms might give plants defenses that it never had before. The isoflavone synthase gene is not available in rice and was transferred from soybean into rice conferring an enhanced blast resistance (for example, [94]). Transgenic rice expressing these transgenes can be used to cross with the recurrent parent to produce cisgenic products without marker genes [95]. Each of cloned major *R* genes can be introduced into each susceptible advanced breeding line at the same time to develop improved resistance in as many breeding lines as possible.

#### **7. Promises and challenges of rice crop protection**

The most environmentally benign method for human intervention is using host *R* genes integrated with cultural management practices. General effective strategies to protect rice crop are prevention of introduction of pathogen; removal of established pathogen from infected rice plants; prevention of pathogen from infecting susceptible plants by growing rice under unfavorable climate for pathogen; broadening genetic basis; introduction of *R* genes with overlapping resistance spectra. As we better understand exactly how pathogenesis occurs, we can try to interfere with

*Physiological, Ecological and Genetic Interactions of Rice with Harmful Microbes DOI: http://dx.doi.org/10.5772/intechopen.97159*

#### **Figure 7.**

*Major challenges of crop protection imposed by host-pathogen and environment.*

how pathogens find their hosts or inactivate important pathogen enzymes or toxins. Major *R* genes are not available to control rice sheath blight, however, sheath blight tolerant cultivars with suitable architecture and plant growth can reduce yield losses [96]. In the absence of *R* genes, fungicides are often used. The reduction in disease progress can be achieved when rice fields are treated with efficacious fungicides at the proper growth stage. A simulation study shows \$43 million increase through sheath blight resistant rice production that is enough to feed 1.7 million people in the Mid-south [97].

Presently there still exist at least six major challenges for rice crop protection (**Figure 7**). 1). The intense demand for yield and quality decreases the genetic diversity of cultivated rice needed for basal defenses, such as expansion of hybrid rice that have put rice at a genetic disadvantage relative to the genetic changes of the pathogen. 2). Only limited *R* genes can be deployed locally for preventing diseases due to clonal amplification of the pathogen populations. 3). Pathogen populations can change through time and pathogen genotypes can interact with specific host genotypes leading to the "breakdown" of resistance within very short periods of time and the pathogen can adapt to new environments by rapid alteration of the *AVR* genes to create virulent races of the pathogen [98]. 4). Introduction of unwanted exotic pathogens into rice production areas through seeds. 5). Decreased water supply would increase the incidence and severity of blast disease, and 6) increased global warming not only reduces water supply but also is more dangerous if increased temperature and CO2 concentration create favorable environment for disease and weeds which can be potential sources of alternative hosts.

### **8. Future perspectives**

In the future, the technique of genetic engineering should become easy and inexpensive to use, and social and economic concerns of Genetic Modified Organism (GMO) will be resolved. Genetic engineering of resistance will certainly enhance our capacity to prevent the crop loss due to diseases. Designing rice plants with novel resistance to a wide range of pathogens will be possible using genome editing mediated by CRISPR-Cas system [99]. At the present time, no commercial

GMO rice variety is available, but genome editing is expected to become the breeder's choice since many improved susceptible advanced breeding lines can be engineered with *R* genes in a relatively short time. It is important to monitor if new pathogen genotypes have been introduced into a region and at what frequencies certain pathogen genotypes change over time. On site information of the structure of pathogen populations is useful for the development and implementation of effective disease control strategies, and also provides insights into the evolution of pathogen populations in response to challenges imposed by host *R* genes. Therefore, the study of co-evolutionary mechanisms controlling the interaction of rice and pathogens should allow the application of these discoveries to the construction of more resistant plants. Novel approaches applied to study interactions of rice with *R. solani* has also begun to generate useful knowledge that will lead to the development of improved rice lines through genetic engineering and MAS. New germplasm including weedy species of rice and their adaptive mechanism of resistance will be identified or developed that will be used by rice breeders to incorporate novel sources of resistance into new cultivars [100–102]. Genetic mutants, mutant and mapping populations are available for uncovering important genes to control major rice diseases using methods of forward and reverse genetics [101–104]. More user friendly molecular markers will be identified to accelerate the development of improved rice cultivars through MAS worldwide and more robust *R* genes will be characterized for their deployment either using genetic engineering or MAS. Finally, the development of improved crop management programs to allow increased crop genetic heterogeneity can also be a solution to reduce crop damages due to rice diseases [105].
