Nucleotide diversity of Pita, a major blast resistance gene and identification of its minimal promoter

Improvement of host plant resistance is one of the best methods to protect the yield from biotic stresses. Incorporation of major resistance genes or their variants into elite rice varieties will enhance the host plant resistance and its durability. Allele mining is a preferred choice to discover the novel allelic variants of major genes from wide range of germplasm. ‘True’ allele mining includes coding and noncoding regions, which are known to affect the plant phenotype, eventually. In this study, major blast resistance gene, Pita was analyzed by allele and promoter mining strategy and its different allelic variants were discovered from landraces and wild Oryza species. Polymorphisms at allelic sequences as well as transcription factor binding motif (TFBM) level were examined. At motif level, MYB1AT is present in PitaTadukan and other resistance alleles, but was absent in the susceptible allele. Core promoter was demarked with 449bp, employing serial promoter deletion strategy. Promoter with 1592bp upstream region could express the gfp two fold higher than the core promoter. The identified Pita resistance allele (PitaKonibora) can be directly used in rice blast resistance breeding programs. Moreover, characterization of Pita core promoter led to deeper understanding of resistance gene's regulation and the identified core promoter can be utilized to express similar genes in rice. •Diversity of Pita alleles was determined through allele mining strategy.•Core promoter of Pita was demarked with 449bp.•Allelic variants were analyzed for polymorphism at promoter and coding regions.•Identified novel allele of Pita from landrace confers extreme resistance.•Differential TFBMs were identified, which influence gene's expression.