**2. Pathogen genomic identity and pathogen avirulence (***AVR***) genes**

Knowledge of pathogen populations is important to identify effective *R* genes and develop long-lasting strategies to prevent crop loss due to diseases. DNA fingerprint based on MGR586, mitochondrial DNA Restriction Fragment Length Polymorphism (RFLP), mating type, vegetative compatibility, virulence, DNA sequencing, simple sequence repeat (SSR) markers, and avirulence (*AVR*) gene analyses have been interchangeably used to characterize *M. oryzae* populations [13–20]. The genetic identity of blast populations evaluated by SSR is not significantly different among rice production areas in the Southern US. The identity, however, is significantly different over the past 6 decades [19], suggesting that the environmental dynamics overtime such as weather, deployed rice varieties, and soil fertility in these years may play important roles in shaping the genetic identity of blast fungi. The pathogenicity of blast races (isolates) has been routinely evaluated with the international rice differential system since 1960s [20]. The most commonly found blast races are IB1, IB17, IB49, and IC17 while IA1, IA37, IA65, IA69, IA113, IB21, IB25, IB37, IB41, IC1, IC9, IE1k, IG1, and IH1 are the least commonly found blast races in the Southern US, whereas in California, IG1 is the only predominant blast race [19]. Similar blast races to those in the Southern US were also found in the winter nursery for the Southern US rice breeders in Puerto Rico [21].

The fungi purified from sheath blight-like diseased samples were evaluated with DNA markers, anastomosis grouping, speed of *in vitro* growth, and infection assays with detached leaf and microchamber assays [22]. All sheath blight-causing agents in 102 rice samples were determined to be *R. solani* with a diagnostic DNA marker derived from a ribosomal DNA internal transcribed spacer. Anastomosis grouping tests were conducted in cooperation with Dr. Craig Rothrock's lab (Department of Plant Pathology, University of Arkansas, Fayetteville, Arkansas, USA). A total of 13 testers, namely, (ID Al 1-4, AG-B1); (ID521, AG-9); (ID CI, AG-8); (ID1529, AG-7); (NTA3-1, AG-6); (ID ST6-1, AG-5); (ID AH-1, AG-4); (ID W14 L, AG-3); (ID RI-64, AG2-2); (ID F56 L, AG2-1); (ID M43, AG1-1C); (ID Cs-Ka, AG1-IA); and (ID SFBV-1, AG1-IB), from different hosts were used. All the 102 isolates were determined to be IG1-IA. Three groups—fast growing (such as RR0321-4, RR0319-8, RR0101-1); intermediate growing (such as RR0305, RR0316- 1); and slow growing (such as RR0316-1, RR0140-1, RR0141-1)—were identified by measuring the growth of each isolate in a nutrient-supported petri dish. The speeds of growth were found to be closely correlated with the lengths of disease

**39**

**Figure 3.**

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

lesions in the detached leaves of two rice varieties, suggesting that the fast-growing isolates were more virulent than those of slow-growing isolates [22]. These characterized isolates have been used to identify genetic resistance and molecular studies

**3. Mapping populations and improved rice germplasm and genetic** 

Rice germplasms with different *R* resources is a prerequisite for developing improved rice varieties with *R* genes providing overlapped resistance to various blast races (isolates). In the Southern US, tropical japonica rice varieties are mainly grown, whereas in the state of California, temperate japonica rice varieties are grown. Major resistant resources to *M. oryzae* in the Southern US are mainly from indica rice varieties such as Tetep, Te Qing, and Zhe733. Complete resistant resources to *R. solani* have not been identified; however, moderate resistance from rice germplasms such as Jasmine 85 has been identified. These resistant resources were used to develop mapping populations and adaptive germplasms through single seed descend and doubled haploid breeding strategies (**Figure 3** and **Table 1**).

Germplasms with improved resistance to both blast and sheath blight diseases are helpful for rice breeders to develop new rice cultivars [34]. Four rice germplasms, LJRIL103 (PI 660982), LJRIL158 (PI 660983), LJRIL186 (PI 660984), and LJRIL220 (PI 660985), with resistance to both blast and sheath blight diseases were

*Photograph showing a view of the rice research plots of USDA ARS DBNRRC and the University of Arkansas Rice Research Center, Stuttgart, Arkansas, USA, 2016. Most rice resources and mapping populations were* 

*advanced in similar field plots. The picture was taken with a drone in 2016.*

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

**3.2 Improved rice germplasms and genetic stocks**

ever since.

**stocks**

**3.1 Mapping populations**

*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*

lesions in the detached leaves of two rice varieties, suggesting that the fast-growing isolates were more virulent than those of slow-growing isolates [22]. These characterized isolates have been used to identify genetic resistance and molecular studies ever since.
