**3. Ecological interactions of rice plants with pathogens**

The three major factors necessary for disease to occur in plants: 1) A pathogen that can cause disease, 2) a host plant that is susceptible to a pathogen, and 3) an environment that favors the pathogen infection. The environment includes temperature, humidity, light intensity, surrounding areas, and/or human intervention. These three-factors referred as the disease triangle contribute to the severity of disease. After diseases occur plant pathogens are typically disseminated within the same field and are often transmitted by wind and/or insects to fields far away from the diseased plants. In nature, rice pathogens find rice and survive with and/or without rice after their infection and amplification [26]. In the tropics the climates are relatively warm year round. Hence, overwintering is not an issue for

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

*M. oryzae*. The overwintered conidia and mycelia on alternative hosts and/or rice often serve as a source of primary infection in the disease cycle. *M. oryzae* species is a pathogen of over 50 grass species including crops such as wheat (*Tritium aestivum* L. [27]), Barley (*Hordeum vulgare* L. [28]) and finger millet (*Eleusine coracana*; L. [29]). However, each isolate of *M. oryzae* is often limited to attack a small group of grass species [29]. The causal agent for blast disease in one group of grass species is often different from similar groups that attack other grass species. Cross infections between the species observed under controlled conditions suggest that grass weeds, *Rottboellia exaltata*, *Echinochloa colona*, *Leersia hexandra* and *Alopecurus carolinianus* could be alternative hosts for *M. oryzae* [30, 31].

Even though *M. oryzae* is not a good competitor among saprophytes, rice seeds and diseased rice residues are considered as the primary sources of *M. oryzae* [32, 33]. Infectious *M. oryzae* were purified from foundation, certified and grower seeds in Arkansas (for example, [32]). The spores of *M. oryzae* produced by the contaminated rice seeds infected seedlings from 2 to 4 leaf stages [33]. The infected seedlings are then served as an inoculum for nearby healthy plants that develop blast symptoms later. Often *M. oryzae* infection from booting to flowering/immature panicle results in *M. orzyae* contaminated rice seeds. Diseased residues are considered as another primary source of inocula [34]. Infected rice residues up to 18 months from surface mulch were the sources of *M. oryzae* that caused leaf blast under field conditions (for example, [34]).

*R. solani* infecting rice belongs to an anamosis subgroup (AG)1-IA [35]. This type of pathogen typically lives on dead tissues, and often changes hosts during alternative growing seasons. Infection of *R. solani* usually begins from sclerotia and mycelia on debris from previous crops in the soil. Sclerotia usually accumulate around rice plants at the water and plant interface. Once sclerotia germinate, they develop mycelia that grow upward on rice plants. Depending upon humidity and moisture conditions, disease development is rapid at early booting to heading and grain-filling stages [36]. Infections often occur near the waterline after the establishment of permanent flood. Lesions on the upper parts of rice plants can be developed to the entire leaves and leaf sheaths (**Figure 2**). Lesions with mycelia on rice plants change from white or gray with brown borders to brown where sclerotia are loosely attached. At maturity, sclerotia are separated from rice plants for overwintering in soil. Under favorable conditions such as high humidity (≥95%) and temperature (28–32°C), *R. solani* spreads rapidly to upper rice plants including rice leaves, grains, and to adjacent plants [13]. *R. solani* causing sheath blight diseases is a broad host pathogen which has multiple anamosis subgroups that specialize on several plant species causing other plant diseases [37].

### **4. Genetic interactions of rice plants with pathogens**

Blast pathogen *M. oryzae* is known to reproduce asexually under field conditions and it has been a challenge to perform sexual crosses under laboratory conditions. The genome sequences of 50 isolates from different times and places showed that they belong to six lineages including isolates from two pandemics on japonica and indica rice [38]. The *de novo* DNA sequences also revealed that these lineages diverged about a millennium ago. Genome sequences of one lineage uncovered evidences of sexual transmission and alleles from multiple lineages. In the USA over the past 6 decades *M. oryzae* races have become more diverse and virulent [39, 40].

Genetic interaction of rice with *M. oryzae* follows the gene for gene theory where a resistance (*R*) gene is effective in preventing pathogen *M. oryzae* strains that contain the corresponding aviruelnce (*AVR*) gene [41, 42]. Presently, 40 *AVR* genes

have been identified, 11 of which have been cloned. *AVR* genes in *M. oryzae* are random secreted molecules predicted to play important roles in pathogenicity and fitness [43]. Rice *R* genes are mutable that may generate more *R* genes. *R* gene polymorphism is thus a significant source of complexity of the interactions of rice with different rice pathogens [44, 45]. Most *R* genes in rice are members of a small gene

#### **Figure 3.**

*Physiological characterization of rice sheath blight fungus Rhizoctonia solani. A. hyphal growth on potato dextrose agar of each hyphae from indicated isolates, and B. different morphologies of sclerotia of indicated isolates in a.*

#### **Figure 4.**

*Molecular characterization of rice sheath blight fungus Rhizoctonia solani. A to C describing region and phylogenetic relations (http://www.ncbi.nlm.nih.gov/nuccore, genbank accession numbers, AY185104 to AY185115 of 14 isolates from indicated counties in Arkansas).*

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

family and are predicted to encode cytoplasmic NLR proteins with nucleotide binding site (NBS) and leucine rich repeats (LRR) [45, 46]. The rice genome (430 Mb) has 480 such NBS-LRR genes that can be the sources of *R* genes to different rice pathogens [47, 48].

Details on the genetic interaction of rice with *R. solani* has lagged far behind that of with *M. oryzae*. A major *R* gene to *R. solani* has not been discovered yet. Minor *R* genes such as *qSHB9–2* in rice cultivar Jasmine 85 have been identified [49, 50]. Further genetic and functional analyses suggest that the *ABC* transporter genes involved in rapid nutrient transportation is responsible for 25% of genetic resistance [51]. *R. solani* (AG)1-IA contains heterogenic multinuclei, and complete genome sequence of *R. solani* (AG)1-IA has been difficult due to the challenges on genome assembly [52]. Differences in morphology, speed of hyphal growth have been noticed and some isolates do display less aggressiveness (**Figure 3**).

These isolates have been recommended for controlled inoculations and genome sequencing [35]. The length of ribosomal DNA internal transcribed spacer (rDNA-ITS) can distinguish subspecies of *R. solani* from *R. oryzae* and *R. oryzae-sativae* [53], minor variation of DNA sequence, hyphal growth on potato dextrose agar and morphology of sclerotia can be seen among the isolates collected. All isolates tested so far in the USA were clustered into one clade, (**Figure 4**) [35, 54].

### **5. Remarkable features of rice plant innate immunity**

Like other plants, rice cannot move to escape from pathogen attack and must evolve an efficient defense system [55]. The plant passive defense system is often initiated by cell wall, and cuticles by releasing pathogen associated molecular patterns (PAMPs, [56]). After sensing these PAMPs plants activate a variety of early defense responses including stomatal closure, transcriptional reprogramming responses and callose deposition that is called pattern-triggered immunity (PTI) [57]. More active defense response is often elicited by NLR *R* gene products. Upon the detection of pathogen *AVR* gene products NLR proteins reorganize and transduce defense signaling often resulting in programed host cell death that is called elicitor triggered immunity (ETI) [58]. Exactly how PTI and ETI lead to effective resistance response is still largely unclear (**Figure 5A**).

*R* genes are also known to be under fast evolution diversification [58] and have also evolved efficient methods to detect the unstable products of *AVR* genes in *M. oryzae*. A single amino acid of each of major blast *R* genes, *Pi-36*, *Pi-d2*, and *Pi-ta* has been found to determine its efficacy of resistance (for example, [59–61]) (**Figure 5B**). *Pi-d2* is a single copy gene encoding a predicted novel B-lectin receptor kinase with an extracellular domain of a bulb-type mannose specific binding lectin (B-lectin) and an intracellular serine–threonine kinase domain. A single amino acid difference at position 441 Isoleucine to Methionine (R to S) of Pi-d2 distinguishes resistant from susceptible allele. *Pi-d2* was localized in plasma membrane [60]. *Pi-36* is a single copy gene encoding an NBS-LRR protein. A single amino acid at the position 590 Aspartic acid to Serine (R to S) was found to associate with the resistance phenotype [61]. *Pi-ta* encodes an NLR protein with imperfect LRR [59]. Surveys in rice germplasm have identified only one *Pi-ta* allele conferring resistance and thirteen *pi-ta* alleles conferring susceptibility [62–68]. In most cases, a single nucleotide substitution results in a functional polymorphism distinguishing between resistance and susceptibility [59, 67, 68]. All resistant Pi-ta proteins have alanine at position 918 and all susceptible pi-ta proteins have serine at position 918 [62, 65].

#### **Figure 5.**

*Diagram shows two significant mechanisms of blast R genes. A. Showing effective resistance is a result of pathogen/microbe-associated molecular pattern triggered immunity (PTI) and effector triggered immunity (ETI) mediated by R protein. B. Showing three blast R proteins with a single amino acid determining recognition specificities. Single letter code was used. C. Showing the location and resistance spectra of blast R genes Pi-ta and Ptr near the centromere of rice chromosome 12. This genomic region has been transferred as a linkage block into diverse rice germplasm due to suppressed recombination. Rice varieties with Pi-ta are resistant to the blast races IB49 and IC17 and with Ptr are resistant to the blast races IB49, IC17, IA45, IB45, IB54, IH1, IG1, and IE1. Graphics were not drawn in proportion.*

Another efficient method of plant innate immunity is a plausible failsafe mechanism. *R* genes and helper genes in plant immunity are often found in a short physical interval that can be easily passed on to the next generation (**Figure 5C**).

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

Rice varieties with *Pi-ta* is resistant to the blast races IB49 and IC17 [63]. *Pi-ta* was predicted to require another gene *Ptr* to be more effective [69]. The *Ptr* gene referred as *Pi-ta2* is 210 kb from *Pi-ta* on chromosome 12 [70, 71]. The *Ptr* gene was identified using a genetic screen of a mutant population created by fast neutrons and was cloned using map-based cloning approach and resistant function was validated by CRISPR-CAS 9 [70–72]. *Ptr* is a broader-spectrum blast *R* gene independent to *Pi-ta* predicted to encode a protein with 4 armadillo repeats [70]*.* Rice varieties with *Ptr* are resistant the blast races IB49, IC17, IA45, IB45, IB54, IH1, IG1 and IE1. Resistance spectra of both *Pi-ta* and *Ptr* were overlapped for both races IB49 and IC17. Rice genes with armadillo repeats are known to be involved in a wide range of biological functions suggesting that the *Ptr* gene in rice is a failsafe for disease resistance [73]. It remains to be determined the role of *Pi39 (t)/Pi42(t)* (LOC\_Os12g1837412), 12 kb from *Pi-ta* and 198 kb from *Ptr* [74, 75] in blast resistance [76]. Resulting knowledge can aid in blast resistant breeding.
