Abstract
BackgroundEffective management of rice blast, caused by the fungus Magnaporthe oryzae, requires an understanding of the genetic architecture of the resistance to the disease in rice. Rice resistance varies with M. oryzae strains, and many quantitative trait loci (QTLs) affecting rice blast resistance have been mapped using different strains of M. oryzae from different areas. However, little is known about the genetic architecture of rice resistance against the M. oryzae population in Hunan Province, which is a main rice production area in South China.ResultsIn this study, we used three isolates from Hunan Province and the rice diversity panel 1 to perform a genome-wide association study (GWAS) of blast resistance in rice. A total of 56 QTLs were identified. One of the QTLs is localized with the resistance gene Pik locus which confers resistance to all three isolates. Genomic sequence analysis of the resistant cultivars led to the identification of a new Pik allele, which we named Pikx. Yeast two-hybrid and co-immunoprecipitation assays between AvrPiks and Pikx confirmed that Pikx is a new allele at the Pik locus.ConclusionsOur GWAS has identified many new blast resistance QTLs. The identified new Pik allele Pikx will be useful for breeding cultivars with high resistance to blast in Hunan and other South China provinces. Further research on the relationship between AvrPiks and Pikx will provide new insights into the molecular mechanism of rice resistance to M. oryzae.
Highlights
Effective management of rice blast, caused by the fungus Magnaporthe oryzae, requires an understanding of the genetic architecture of the resistance to the disease in rice
Resistance of the 234 rice diversity panel 1 (RDP1) cultivars to the three M. oryzae isolates The distribution of blast disease scores of the 234 cultivars inoculated with the three M. oryzae isolates is shown in Fig. 1a, b, and c
Association mapping of rice QTLs linked to resistance to M. oryzae To identify genomic regions that are associated with blast resistance to the three isolates, we performed a genome-wide association study (GWAS) using the disease scores and the 700 K SNP genotypes of the inoculated cultivars
Summary
Effective management of rice blast, caused by the fungus Magnaporthe oryzae, requires an understanding of the genetic architecture of the resistance to the disease in rice. Rice blast, caused by the fungal pathogen Magnaporthe oryzae, is a destructive disease of rice (Valent and Chumley 1991). It typically causes an annual yield loss of 10–30% and leads to large economic losses in many countries Two types of resistance genes are responsible for rice blast resistance: major resistance (R) genes that confer race-specific resistance and quantitative trait loci (QTLs) that control partial, nonrace-specific resistance (Skamnioti and Gurr 2009). Only 28 R genes and 2 QTLs have been cloned and characterized (Xiao et al 2017; Deng et al 2017; Zhao et al 2018). All of the cloned R genes except for Pi-d2, pi and Ptr contain nucleotidebinding domain leucine-rich repeat (NLR) proteins (Liu et al 2010; Zhao et al 2018)
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