SNAP markers for pyramided yield and BLB resistance genes in rice
Andhika Faisal Mubarok, Sigit Purwantomo, Antonius Suwanto, Reflinur and Sintho Wahyuning Ardie
Abstract: Molecular markers are pivotal in rice breeding as they enable gene pyramiding to improve yield and disease resistance. This study reports the development and validation of Single Nucleotide Amplified Polymorphism (SNAP) markers targeting qTSN4 (yield), xa5, and Xa21 (bacterial leaf blight resistance) genes. An EF1-a primer was integrated as an internal control in multiplex PCR to enhance assay precision and distinguish allele absence from PCR failure. An annealing temperature of 60 °C and an internal control primer concentration of 0.5 µM were optimal. While the xa5-based SNAP marker failed to distinguish alleles in the tested lines, qTSN4- and Xa21-based markers successfully differentiated the parental genotypes, confirming their applicability in marker-assisted gene pyramiding. These markers were validated in 72 BC1F1 plants and showed consistent Mendelian 1:1 segregation for qTSN4 and Xa21. Markers were used to select 18 plants with positive alleles A for qTSN4 and C for Xa21.