Abstract
Rice blast is one of the most devastating rice diseases and continuous resistance breeding is required to control the disease. The rice blast resistance gene Pi54 initially identified in an Indian cultivar confers broad-spectrum resistance in India. We explored the allelic diversity of the Pi54 gene among 885 Indian rice genotypes that were found resistant in our screening against field mixture of naturally existing M. oryzae strains as well as against five unique strains. These genotypes are also annotated as rice blast resistant in the International Rice Genebank database. Sequence-based allele mining was used to amplify and clone the Pi54 allelic variants. Nine new alleles of Pi54 were identified based on the nucleotide sequence comparison to the Pi54 reference sequence as well as to already known Pi54 alleles. DNA sequence analysis of the newly identified Pi54 alleles revealed several single polymorphic sites, three double deletions and an eight base pair deletion. A SNP-rich region was found between a tyrosine kinase phosphorylation site and the nucleotide binding site (NBS) domain. Together, the newly identified Pi54 alleles expand the allelic series and are candidates for rice blast resistance breeding programs.
Highlights
Rice blast is one of the most devastating rice diseases and continuous resistance breeding is required to control the disease
India and found resistant against rice blast, both under natural as well as controlled conditions, were chosen to study the allelic variation of the Pi54 gene (Fig. 1). These accessions were recorded with a resistant phenotypic score of 0-3 against a field mixture of naturally existing M. oryzae strains when screened in the uniform blast nursery (UBN)
The 885 Indian accessions are annotated as blast resistant in the International Rice Germplasm Collection Information System (IRGCIS) of the International Rice Genebank (IRG)
Summary
Rice blast is one of the most devastating rice diseases and continuous resistance breeding is required to control the disease. Pertaining to the genetic variability and pathogenicity of the rice blast fungus, genes involved in host plant resistance co-evolved with high levels of allelic and copy number variations[16]. Minor sequence variations among blast R genes, such as the presence of a few single nucleotide polymorphisms (SNPs), lead to major differences in their function or resistance spectrum. Alleles of the powdery mildew resistance Pm3 gene in wheat exhibit different resistance patterns against a range of powdery mildew isolates[23,24,25] Combining such alleles of a major R gene in a single genetic background or through multiline approach is a possible strategy to improve resistance in the field[26,27]. Exploring naturally available genetic diversity for new alleles of resistance genes is an efficient approach for broadening the resistance sources against rice blast
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