Development of a molecular marker for the Pi1 gene based on the association of the SNAP protocol with the touch-up gradient amplification method

Abstract

Abstract Background Rice blast disease, caused by the fungus Magnaporthe oryzae, is one of the major constrains for rice production. Genetic resistance is the most effective and environmentally safe approach to combat the rice blast. However, the use of resistance genes depends on factors such as the availability of molecular markers allowing marker-assisted selection during the breeding process. Pi1 gene, considered a broad-spectrum resistance gene, has great potential to contribute in achieving durable resistance to rice blast, but lacks a friendly marker to be employed. Methods and results In the present study, we have explored a nucleotide polymorphism in the Pik locus, associating SNAP protocol with touch-up gradient amplification method to develop a SNAP marker. Through the screening of a germplasm bank and analysis of an F2 population, the Pi1 SNAP marker was validated by pathogenicity tests and compared with previously existing markers. Conclusions The Pi1 SNAP marker is effective in distinguishing germplasms carrying the Pi1gene from Pik alleles, employing a cost-effective methodology.