**5. Effective** *R* **genes**

*Protecting Rice Grains in the Post-Genomic Era*

**42**

**Figure 6.**

*M. oryzae* have been performed under field conditions where complex biotic and abiotic factors impacting the inheritance of resistance were encountered resulting in inconsistencies of disease reactions. In 1999, Dr. Marchetti and his

*Parafilm method for sheath blight disease evaluation: a PDA containing mycelia (A) in a petri dish containing mycelia after 3 days of culturing at 30°C was removed and covered with parafilm and wrapped onto the second youngest leaf for 3–5 days (B) until stable symptoms appeared. A rating scale based on visual length and area of symptoms was assigned as indicated, with 0 representing immunity and 9 representing extreme susceptibility (C).*

### **5.1 Effective major** *R* **genes**

A total of 14 known major blast *R* genes have been used in the USA since 1960s. **Table 2** lists their chromosomal locations, representing germplasms, DNA markers to monitor respective *R* genes, and the avirulent and virulent races of these selected rice germplasms (**Table 2**). Based on field observations, most blast *R* genes are dominant whereas a single haplotype of *R* gene is effective for resistance. Among them, six dominant blast *R* genes *Pia*, *Piks*, *Pi66(t)*, *Pikh*, *Pikm*, and *Pi43(t)/Pi1*, and one recessive *R* gene *pid* were on chromosome 11. Comprehensively, one was found on chromosome 2, two on chromosome 6, one on chromosome 8, one on chromosome 9, and two dominants on chromosome 12. Three of the dominant *R* genes, *Pi9*, *Pi42(t)*, and *Pi43(t)*, provide resistance to all races, while *Pita2/Ptr* is effective to all races except IE1k.

The genetic markers linked or derived from the cloned *R* genes were developed to predict resistance function and to monitor the existence of each of the *R* genes [31–33, 44–52]. Differential blast races were identified (**Table 2**) and have been used to validate their predicted resistance efficacies.

### **5.2 Effective minor** *R* **genes**

Distinct phenotyping variation of rice after infection via *M. oryzae* in different rice germplasms and in the same germplasm at different growth stages under greenhouse [53] and field conditions are also referred as dilatory, partial, field, and adult resistance interchangeably [54]. A total of 11 blast *R* quantitative trait loci (QTLs) responsible for a phenotypic variation ranging from 5.17 to 26.53% were identified with different blast races under greenhouse conditions [55] (**Table 3**) and verified with different blast isolates/races [56]. Using the same method, four additional blast *R* QTLs were identified from different rice germplasms [57].


**Table 2.**

*DNA markers and resistance efficacies of deployed blast* R *genes in the USA since 1960 (***Figure 7***).*

**45**

**Table 3.**

**Figure 7.**

*and chromosomal locations are indicated.*

**QTL Chr. Blast** 

**race**

*qBLAST 3* 3 IB45 RM251–

*qBLAST8.1* 8 IB49 RM6863–

*qBLAST8.2* 8 IC17 RM310–

*qBLAST9.1* 9 IB54 RM257–

*qBLAST9.2* 9 IC17 RM257–

*qBLAST9.3* 9 IC17 RM107–

*qBLAST11* 11 IB45 RM206–

*qBLAST12.1* 12 IB1 RM6998–

*qBLAST12.2* IB49 RM247–

*sites—leucine-rich repeat domain is often encoded by the R gene.*

*A Toolbox for Managing Blast and Sheath Blight Diseases of Rice in the United States of America*

*Graphic presentation of resistance spectra of blast* R *genes in the USA. The common races, name of* R *genes,* 

**Nearest marker locus (physical location in MB)**

RM282 (12.4) 5.17

RM72 (6.8) 7.22

RM257 (17.7) 4.64

RM215 (21.2) 4.49

RM224 (27.8) 19.6

OSM89 (7.9) 9.7

OSM89 (7.9) 10.18

**Phenotypic variation (%)**

RM1148 (4.0) 6.69 *Pi36*

RM108 (17.9) 7.62 NBS-LRR

RM224 (27.8) 26.53 *Pikm/Pik*

OSM89 (7.9) 5.44 *Pi-ta/Ptr*

**Nearest major R genes**

**Marker interval**

RM338

RM72

RM72

RM108

RM107

RM245

RM224

RM224

OSM89

RM277

RM277

*Chr. indicates chromosome, MB indicates megabase pair, NBS-LRR indicates the protein with nucleotide-binding* 

*List of minor resistance genes to rice blast disease with indicated nearby major* R *genes and NBS-LRR proteins [55, 56].*

IB54 RM206–

ID1 RM247–

*DOI: http://dx.doi.org/10.5772/intechopen.86901*

*A Toolbox for Managing Blast and Sheath Blight Diseases of Rice in the United States of America DOI: http://dx.doi.org/10.5772/intechopen.86901*

### **Figure 7.**

*Protecting Rice Grains in the Post-Genomic Era*

**Selected germplasm**

dom

AP4791, AP5659-1, AP5659-5

9 *Pii* Dawn IH1 [39] 11 *Pia* Bluebonnet IB1 [39]

RM224

RM224

Zhe733 RM1233 IA45, IB1,

YL155/YL87

Katy HJ16–12 IA45,IB1,

11 *Pi66(t)* DGWG IB54 IB45,

11 *Pid* Lebonnet IB1 IA45,

*DNA markers and resistance efficacies of deployed blast* R *genes in the USA since 1960 (***Figure 7***).*

KS6/KS28 IA45, IB1,

2 *Pi-b* Saber, Te-Qing RM208, Pib

6 *Piz(t)* Zenith RM527,

48-1-1-2 (GSOR310687)

8 *Pi42(t)* Zhe733 RM72 IA45, IB1,

11 *Pikh* Lebonnet RM224 IB45, IB54,

*Piks* M2354 E/P

11 *Pikm* Tsuyuake Q/P

12 *Pita* Katy YL100/YL102,

11 *Pi43(t)/ Pi1*

12 *Ptr* 

*(Pita2)*

6 *Pi9* IR9660-

**Marker Name of blast races Reference Avirulence Virulence**

> IB49, IB54

IA45, IB1, IB49, IB54, IB33

[31]

[32]

[33]

[44]

[46]

[47]

[44]

[45]

48–50]

IE1k [51, 52]

IB49 [45]

IC17 [46]

IB1, IB45, IH1, IG1, IC17, IE1, IE1k

IH1, IG1, IC17, IE1k

IB49, IB54, IB45, IH1, IG1, IC17, IE1, IE1k

IB49, IB54, IB45, IH1, IG1, IC17, IE1, IE1k

IH1, IG1

IB45, IB54, IH1, IG1

IB49, IB54, IB45, IH1, IG1, IC17, IE1, IE1k

IB49, IB54, IB45, IH1, IG1, IC17, IE1

IB54 IA45,

IB49, IB33, IB45, IH1, IG1, IC17, IE1, IE1k

IC17, IG1, IH1

IB49, IB54, IB45, IH1, IG1, IC17, IE1, IE1k

IB49, IC17 IE1k [29,

**Chr. Name of**  *R* **gene**

**44**

**Table 2.**

*Graphic presentation of resistance spectra of blast* R *genes in the USA. The common races, name of* R *genes, and chromosomal locations are indicated.*


*Chr. indicates chromosome, MB indicates megabase pair, NBS-LRR indicates the protein with nucleotide-binding sites—leucine-rich repeat domain is often encoded by the R gene.*

#### **Table 3.**

*List of minor resistance genes to rice blast disease with indicated nearby major* R *genes and NBS-LRR proteins [55, 56].*

Thus far, major sheath blight *R* genes have not been identified. However, the major sheath blight *R* QTL *qShB9-2* responsible for 24.3–27.2% of phenotypical variation using microchamber and mist chamber assays, respectively, and other nine minor *R* QTLs to sheath blight were also identified [58, 59]. These sheath blight *R* QTLs were verified with replicated field plot experiments in multiple locations [60]. This demonstrated that there exist useful genetic factors that can be used for breeding. DNA markers linked to these *R* QTLs can not only be used to pyramid resistance into new rice varieties via marker-assisted breeding but can also be used to clone and characterize genes underlying these *R* QTLs.

## **6. Resistance effectiveness**

*M. oryzae* is a hemi-biotrophic organism with an extended period of biotrophic invasion that forced the evolution of robust major blast *R* genes in host. The resistance mediated by major blast *R* genes follows the gene-for-gene model where the *R* genes in rice detect the corresponding *AVR* genes in *M. oryzae* in triggering resistance responses [61]. The existence of *AVR-Pita1* in US blast populations suggest that *AVR-Pita1* may play an important role in fitness and pathogenicity. Ironically, what is needed for pathogens to survive also makes the pathogen less virulent and fit. This never-ending booming-and-busting cycle of host-pathogen interactions presents a unique opportunity to develop durable resistance. In the Southern US, after the blast epidemics in 1980s, a blast-resistant rice variety Katy was released in 1990 [62]. Katy contains a cluster of major *R* genes at the *Pi-ta* locus from the landrace indica variety Tetep and *Piks* from tropic variety Newbonnet [41]. Further analysis of Katy revealed that there are three linked blast *R* genes, *Pi-ta* and *Pi-ta2/Ptr* genes near the centromere of rice chromosome 12. *Pi-ta* is a classical *R* gene with NBS-LRR [63] and *Ptr*, which is allelic to *Pi-ta2*, encodes a predicted protein with four armadillo repeats [52]. *Ptr* was shown to confer resistance to a wide range of blast races except for IE1k and help *Pi-ta* with unknown mechanisms [52]. To date, a handful of rice varieties with the *Pita*, *Pita2/Ptr* cluster in a linkage block including Katy, Drew, Madison, Kaybonnet, Cybonnet, Banks, Ahrent, Catahoula, and Templeton have been released in the Southern US since 1990 [64–66]. Amei and colleagues showed that the *Pi-ta* gene has been bred into cultivated species of rice for decades [67]. The counter resistance from the pathogen usually occurs after breeders release a new resistant rice variety [68]. One of the counter resistance strategies of *M. oryzae* is to alter the structural integrity and expression of the *AVR* genes. The blast races (isolates) with partial, complete deletions, point mutations altering amino acids, and transposon insertions at the *AVR-Pita1* locus have been found in commercial rice fields in the Southern US since the release of *Pi-ta* [16–18]. The resistance mediated by the *Pi-ta/Pi-ta2/Ptr* gene cluster has been stable for over two decades. Consistently, most blast populations were found to carry *AVR-Pita1* [16–18] that verified the durability of resistance mediated by *Pi-ta/Pi-ta2/Ptr*. The observed resistance durability could be due to the lack of deployment of rice cultivars with the *Pi-ta/Pi-ta2/Ptr* genes to force the loss of *AVR-Pita1*. This is consistent with the fact that limited *Pi-ta/Pi-ta2/Ptr* containing rice varieties have been grown due to moderate yield advantages compared to other rice varieties lacking the genes since their releases [69]. Alternatively, it is also fully possible that *AVR-Pita1* is important for the survival of *M. oryzae* with unknown mechanisms.

### **7. Summary**

In the USA, any rice cultivar with one or two major blast *R* genes will continue to be effective to prevent rice blast disease. On the other hand, a combination of major

**47**

*A Toolbox for Managing Blast and Sheath Blight Diseases of Rice in the United States of America*

*R* QTLs, suitable plant architecture, and growth rate should be considered to prevent sheath blight disease. A defense gene expression and cell reaction study suggested that strong resistance responses mediated by *Pi-ta* could be initiated as early as 24 h after pathogen inoculation [70]. However, the molecular mechanisms underlying *Pi-ta* or *Ptr*mediated disease resistance pathways [71], the interactions between major blast *R* genes and *R* QTL [74], the role of micro RNA/long noncoding RNA in rice disease resistance [72–75], and the relation of resistance versus productivity are still largely unclear [69]. Therefore, a clear understanding of the abovementioned plant innate immunity systems will be required for engineering resistance via genome editing. The lack of robust major *R* genes to *R. solani* may be due to the saprophytic nature of *R. solani* where the pathogen feed on the dead tissue of rice plants. Comparative analysis of defense genes in different hosts of *R. solani* may help identify useful *R* genes [76]. The genome of *R. solani* is mosaic and the draft sequence of *R. solani* IG1-IA genome is readily available [77]. Moving forward, the completion of whole genome sequencing will be the next urgent step to identify clues to manage *R. solani*. In brief, continued identification and characterization of *R* genes will be essential to safeguard rice crops. Ultimately, fungicides will be significantly reduced to prevent rice blast and sheath blight diseases in the future.

The authors thank Michael Lin, Tracy Bianco, Heather Box, Alan Sites, and Laduska

, Xueyan Wang1,2 and Haijun Zhao1

1 USDA ARS, Dale Bumpers National Rice Research Center, Stuttgart, Arkansas,

2 University of Arkansas Rice Research and Extension Center, Stuttgart, Arkansas,

© 2019 The Author(s). Licensee IntechOpen. This chapter is distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/ by/3.0), which permits unrestricted use, distribution, and reproduction in any medium,

Sells of USDA ARS DBNRRC and Mary Jia of Arkansas Schools of Math, Sciences and the Arts; Dr. Guangjie Liu of University of Arkansas Rice Research and Extension Center for excellent technical assistance; and Tyler Franzen for a photo taken by a drone. Special thanks are also given to all other scientists and supporting staff members of DB NRRC, and UA RREC for their continued support and useful discussion and interactions with the Molecular Plant Pathology program. For critical reviews we thank Drs. Trevis Huggins and Yong-Bao Pan of USDA ARS and two anonymous reviewers.

USDA is an equal opportunity provider and employer.

\*Address all correspondence to: yulin.jia@ars.usda.gov

provided the original work is properly cited.

*DOI: http://dx.doi.org/10.5772/intechopen.86901*

**Acknowledgements**

**Author details**

\*, Melissa H. Jia1

Yulin Jia1

USA

USA

*A Toolbox for Managing Blast and Sheath Blight Diseases of Rice in the United States of America DOI: http://dx.doi.org/10.5772/intechopen.86901*

*R* QTLs, suitable plant architecture, and growth rate should be considered to prevent sheath blight disease. A defense gene expression and cell reaction study suggested that strong resistance responses mediated by *Pi-ta* could be initiated as early as 24 h after pathogen inoculation [70]. However, the molecular mechanisms underlying *Pi-ta* or *Ptr*mediated disease resistance pathways [71], the interactions between major blast *R* genes and *R* QTL [74], the role of micro RNA/long noncoding RNA in rice disease resistance [72–75], and the relation of resistance versus productivity are still largely unclear [69]. Therefore, a clear understanding of the abovementioned plant innate immunity systems will be required for engineering resistance via genome editing. The lack of robust major *R* genes to *R. solani* may be due to the saprophytic nature of *R. solani* where the pathogen feed on the dead tissue of rice plants. Comparative analysis of defense genes in different hosts of *R. solani* may help identify useful *R* genes [76]. The genome of *R. solani* is mosaic and the draft sequence of *R. solani* IG1-IA genome is readily available [77]. Moving forward, the completion of whole genome sequencing will be the next urgent step to identify clues to manage *R. solani*. In brief, continued identification and characterization of *R* genes will be essential to safeguard rice crops. Ultimately, fungicides will be significantly reduced to prevent rice blast and sheath blight diseases in the future.
