**5. Resistance genes and QTLs for rice blast disease**

The resistance for blast disease is two types: i) qualitative or complete resistance governed by a major R gene, and ii) quantitative or partial resistance governed by many quantitative trait loci [46]. While qualitative resistance confers resistance against a specific race of blast pathogen, the quantitative resistance is non-race specific. To date, 109 major blast resistance genes have been identified in rice. Out of these, 25 R genes have been successfully cloned and characterized, with Pi9 being the first cloned R gene (**Table 1**). Japan and China have lead the race in identification of major R genes by identifying 34 and 27 blast resistance genes, respectively. Followed by these, a significant contribution has also been made by USA, France, Philippines and India. To date eight R genes have been mapped in India that include Pi10, Pi157f, Pi38, Pi42(t), Pikh (Pi54)[129], Pitp [117], Pi54rh [127], and Pi54of [128]. The details of the genes mapped in India and the rice varieties in which they were identified are provided in **Table 1**. Majority of the genes identified in India and rest of the world encode proteins with NBS-LRR (Nucleotide Binding Site and Leucine Rich Repeats) and Zinc finger domains that confer disease resistance. Among all the genes that were mapped in India, pi54 is of great importance as it a major blast resistance gene and provides durable resistance against Indian races of blast fungus. These qualitative and major R genes have been extensively used in blast resistance breeding programs worldwide (**Table 2**). For instance,


#### *Rice Blast Disease in India: Present Status and Future Challenges DOI: http://dx.doi.org/10.5772/intechopen.98847*


#### *Integrative Advances in Rice Research*


#### *Rice Blast Disease in India: Present Status and Future Challenges DOI: http://dx.doi.org/10.5772/intechopen.98847*


#### *Integrative Advances in Rice Research*


**Table 1.**

*Blast resistance genes identified so far in different rice cultivars.*

#### *Rice Blast Disease in India: Present Status and Future Challenges DOI: http://dx.doi.org/10.5772/intechopen.98847*

**167**





*Rice Blast Disease in India: Present Status and Future Challenges DOI: http://dx.doi.org/10.5772/intechopen.98847*

*Modified table of Ashkani et al. [163].*

*SSR, Simple sequence repeat; ISSR, Inter simple sequence repeat; SNP, Single nucleotide polymorphism; RFLP, Restriction fragment length polymorphism; RAPD, Randomly Amplified Polymorphic DNA; MAS, Marker Assisted Selection and MABB, Marker Assisted Backcrossing Breeding.*

#### **Table 2.**

*Examples of marker assisted selection (MAS) and marker assisted backcross breeding (MABB) in rice for blast resistance.*

the improved rice lines carrying Pi9 and Pi2 were highly resistant to 43 isolates collected from 13 countries and 455 isolates collected from different parts of the Philippines, and 792 isolates from several regions of China, respectively [86, 164]. Because of their high importance, there are continuing efforts to identify additional major blast resistance genes, especially in wild rice species, and transfer them into elite varieties. For example, Pi9 present in indica rice line 75-1-127 [131] was introgressed from *O. minuta* [55]. Amongst the molecularly characterized major leaf-blast R genes, 22 were; namely, *Pi37, Pit, Pi-sh, Pi64, Pi-b, Pi63, Pi9, Pi-2, Piz-t, Pid3, Pigm, Pi25, Pi36, Pi5, Pi-54, Pik-m, Pik, Pik-p, Pik-e, Pi-a, Pi1,* and *Pita*, belong to the largest class of plant R genes that encode proteins with the nucleotidebinding site (NBS). Leucine-rich repeat (LRR) domains whereas one, *Pid2*, encodes serine–threonine–kinase membrane-spanning protein [165]. Rice blast resistance gene, Pi54 provides broad-spectrum resistance against different strains of *M. oryzae*. Understanding the cellular localization of Pi54 protein is an essential step towards deciphering its interaction with the cognate Avr-gene. A study was

conducted to investigate the subcellular localization of Pi54 with Green Fluorescent Protein (GFP) as a molecular tag. This is the first detailed report, which emphasizes the cellular and subcellular distribution of the broad-spectrum blast resistance gene Pi54 in rice and the impact of its constitutive expression towards resistance against other fungal and bacterial pathogens of rice [166]. These R genes function in a gene-for-gene fashion, meaning that for every R gene in the host, there is an Avr gene in the pathogen. Therefore, the pathogen can easily break down the host resistance by modifying or deleting its corresponding Avr gene and rendering the resistant variety susceptible after a few years [167]. The quantitative or partial resistance is more suited to low-risk areas as it cannot suppress *M. oryzae* when the environments are conducive for its growth. The quantitative trait loci (QTL), which in the context of disease resistance also referred to as quantitative resistance loci (QRLs) [168], are thought to play an important role in sustainable food production in the years ahead by manifesting durable resistance against many races of the blast fungus [169]. Chromosomal locations of leaf-blast R genes and quantitative trait loci (QTLs) for neck-blast resistance in rice are illustrated in **Figure 2**. Recently, QTL analysis of introgression line (INGR15002) derived from *O. glumaepatula* led to the identification of two major QTL - qBL3 contributing about 34% and 32%

#### **Figure 2.**

*Chromosomal locations of leaf-blast R genes and quantitative trait loci (QTLs) for neck-blast resistance in rice. The chromosomal locations for R genes and QTLs were deducted by projecting the sequences of closely linked/ flanking markers on the genome sequence of cv. Nipponbare released by International Rice Genome Sequencing Project (http://rapdb.dna.afrc.go.jp) adopted [131].*

*Rice Blast Disease in India: Present Status and Future Challenges DOI: http://dx.doi.org/10.5772/intechopen.98847*

phenotypic variance towards leaf and neck blast resistance, respectively, and qBL7 contributing about 25% of phenotypic variance for leaf blast [170]. Hence, there are several and continuous attempts to identify QTLs for blast resistance in rice. However, the results of a meta-analysis of QTLs have indicated that the use of QTLs does not offer durable and broad-spectrum resistance compared to that offered by the major genes [171]. Hence, care has to be taken in future breeding programs to effectively combine the major genes and QTLs to achieve durable and long-lasting resistance against several races of the blast fungus.
