**4.2 Rice genome sequencing**

Pathogen and host are the two faces of a coin in the context of host-pathogen interactions and disease management. Hence, characterizing the rice genotypes for novel resistant genes (R) should be done parallel with that of the pathogen as host and pathogen evolve simultaneously for their survival in nature. The discovery of novel 'R' genes and understanding their mutation in evolving novel alleles/ genes is an important step in resistance breeding. Allele discovery/mining could be made using high throughput technologies like whole genome sequencing using next-generation sequencing (NGS) technologies. Rice is a model cereal crop, and several rice cultivars have been sequenced at the genome level, with Nipponbare

as the first rice cultivar to be sequenced and published in 2002 [38]. Further, the indica cultivar 93-11 was also sequenced and published in the same year [39]. These initial efforts laid the foundation for the genomic era in rice. Subsequently, several whole-genome sequencing efforts of rice cultivars like IR-64 [40], Kasalath [41], and HR-12 [42] also added quantum of genomic information to the existing genomic resources. HR-12 genome was assembled using a combination of Illumina short reads and PacBio long reads. This was the first report in the world to sequence rice genome using third-generation sequencing technology. The power of long-read technologies helped in repeat resolution compared to second-generation technologies. Large-scale discovery of novel alleles by resequencing of 3000 rice germplasm accessions belonging to 89 countries contributed significantly to the rice genomic resources [43]. Exploiting natural variation existing among rice landraces is an ideal method to map R genes. Mapping of R genes based on avirulent (Avr) genes pattern in the rice-growing areas is the best strategy to mitigate *Magnaporthe* via exploiting host plant resistance. The product of the avirulence (*Avr*) gene of *Magnaporthe* can be detected by the corresponding resistance (*R*) gene of rice and activates immunity to rice mediated by the *R* gene. The high degree of variability of *M. oryzae* isolates in pathogenicity makes the control of rice blast difficult. That resistance of the *R* gene in rice has been lost ascribed to the instability of the *Avr* gene in *M. oryzae*. Further study on the variation of the *Avr* genes in *M. oryze* field isolates may yield valuable information on the durable and effective deployment of *R* genes in rice production areas. *AvrPiz-t* and *Piz-t* are a pair of valuable genes in the Rice-*Magnaporthe* pathosystem. *AvrPiz-t* is detectable by *Piz-t* and determines the effectiveness of *Piz-t* [44]. Rice SNP-seek database developed based on 3000 rice genomes, possessing a large-scale single base level variation across three geographical rice ecotypes (*japonica*, *indica,* and *javanica*) been made available to the public [45]. These variants could be harnessed to study the genetic diversity and development of subspecies-specific rice cultivars. Also, rice breeders can focus on allele mining for corresponding R genes and pyramiding these genes in commonly grown cultivars in a given location to help develop resistant rice varieties.
