Exploring the Diversity of Blast Resistance Genes in Rice Lines Using PCR-Based Functional STS Markers

Abstract

Rice blast, caused by Pyricularia oryzae (syn. Magnaporthe oryzae), remains one of the most destructive diseases of rice worldwide. Developing resistant varieties is a sustainable strategy for disease management, and information on the diversity of blast resistance genes is important for selecting breeding parents. This study evaluated the effectiveness of functional sequence-tagged site (STS) markers for resolving genetic diversity among advanced rice lines derived from multiple-cross populations. A total of 104 genotypes, comprising 100 advanced lines and four parental varieties (Ciherang, Inpari 13, Inpari 10, and Situ Bagendit), were analyzed using eight gene-specific STS markers associated with four blast resistance genes (Pii, Pia, Pikp, and Pita). Polymorphism information content (PIC) values ranged from 0.80 to 0.96, with a mean of 0.89. UPGMA cluster analysis separated the genotypes into two major groups at a similarity coefficient of 0.90, although most lines occurred in one group and lines with the same parental background were distributed among different subgroups. Observed heterozygosity was low (Ho = 0.09), indicating limited resolution for distinguishing closely related lines despite the high PIC values. Functional STS markers were informative for detecting allelic variation but were insufficient for resolving fine-scale relationships within this genetically narrow breeding population. Combining marker analysis with phenotypic evaluation and higher-resolution markers is therefore recommended to improve selection for blast resistance.