Integrated genetic analysis of leaf blast resistance in upland rice: QTL mapping, bulked segregant analysis and transcriptome sequencing

Elite upland rice cultivars have the advantages of less water requirement along with high yield but are usually susceptible to various diseases. Rice blast caused by Magnaporthe oryzae is the most devastating disease in rice. Identification of new sources of resistance and the introgression of major resistance genes into elite cultivars are required for sustainable rice production. In this study, an upland rice genotype UR0803 was considered an emerging source of blast resistance. An F(2) mapping population was developed from a cross between UR0803 and a local susceptible cultivar Lijiang Xintuan Heigu. The individuals from the F(2) population were evaluated for leaf blast resistance in three trials 7 days after inoculation. Bulked segregant analysis (BSA) by high-throughput sequencing and SNP-index algorithm was performed to map the candidate region related to disease resistance trait. A major quantitative trait locus (QTL) for leaf blast resistance was identified on chromosome 11 in an interval of 1.61-Mb genomic region. The candidate region was further shortened to a 108.9-kb genomic region by genotyping the 955 individuals with 14 SNP markers. Transcriptome analysis was further performed between the resistant and susceptible parents, yielding a total of 5044 differentially expressed genes (DEGs). There were four DEGs in the candidate QTL region, of which, two (Os11g0700900 and Os11g0704000) were upregulated and the remaining (Os11g0702400 and Os11g0703600) were downregulated in the susceptible parent after inoculation. These novel candidate genes were functionally annotated to catalytic response against disease stimulus in cellular membranes. The results were further validated by a quantitative real-time PCR analysis. The fine-mapping of a novel QTL for blast resistance by integrative BSA mapping and transcriptome sequencing enhanced the genetic understanding of the mechanism of blast resistance in upland rice. The most suitable genotypes with resistance alleles would be useful genetic resources in rice blast resistance breeding.