**3.1 Mapping populations**

*Protecting Rice Grains in the Post-Genomic Era*

**1.3 The epidemics, climate, and damages**

crop losses of these fungal diseases in the USA.

In the Southern US, rice blast disease can be found annually and occasionally results in significant crop damages. However, sheath blight disease occurs more often than blast disease partially due to high-density cultivation. An extended dew period and light are known to stimulate sporulation of *M. oryzae*. Light rain is known to keep plant surfaces wet and create near 100% relative humidity, helping the attachment and penetration of the conidia of *M. oryzae*. High humid conditions also favor the growth, infection, and spread of *R. solani* to other leaves and other plants [10]. In California, there is no rain during the rice-growing season. As a result, significant yield loss due to blast has not been reported [11]. Sheath blight disease has not been reported in California either despite a phenotypically similar disease, the aggregate sheath spot of rice caused by *Rhizoctonia oryzae-sativae* [12], commonly occurring. Presently, substantial fungicides have been used to prevent

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

Knowledge of pathogen populations is important to identify effective *R* genes

**38**

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**).
