Rice Blast Resistance Genes Pi54 and Pita Show Single Nucleotide Polymorphisms in an Advanced 4-Way Crossed Segregating Population
Ankitta Mishra1*, Wickneswari Ratnam1, Md Atiqur Rahman Bhuiyan2 and Kshirod Jena3
Published: August 06, 2022
Abstract
Rice blast, caused by the fungal pathogen Magnaporthe oryzae, is a destructive disease in rice. The use of blast-resistant varieties is possibly one of the best economically and environmentally efficient ways to cultivate rice. Four-way crosses between two F1s were performed from UKMRC2 × Teqing and UKMRC2 × Tetep. A segregating population of 30 4-way F1 lines and 72 4-way F4 lines were screened with a set of 51 single nucleotide polymorphic (SNP) markers representing Pi9, Pi5, Pib, Piz, Pita, and Pi54 genes to evaluate the sequence variation. Field blast screening was carried out using six newly identified Malaysian isolates of M. oryzae. Blast disease score of 1 or 2 was observed in 28 4-way F1 lines and 57 4-way F4 lines. The 4-way F4 population showed the resistant alleles for Pi54 and Pita. According to Sequenom data, both generated reproducible and aggressive calls. The SNP data revealed nine sequence variants, which showed the presence of two putative haplotype blocks for Pi54 and Pita respectively. Qgene analysis of the 4-way F4 population showed Pi54 with LOD of 14 (R2 = 56.6%) and Pita with LOD of 14 (R2 = 72.4%). Pi54 was mapped to a region of 312 kb on chromosome 11 flanked by SNPs Pi54-3 and Pi54-19 while, Pita was mapped to a region of 175 kb on Chromosome 12 flanked by SNPs Pita-10 and Pita-3. The resistance alleles highlighted in this study can be used in development of rice blast disease resistant varieties having high yield through gene pyramiding.