Development and Application of Pik Locus-Specific Molecular Markers for Blast Resistance Genes in Yunnan Japonica Rice Cultivars

Rice blast, caused by the fungal pathogen <i>Magnaporthe oryzae</i>, is one of the most devastating diseases affecting rice production worldwide, resulting in significant yield losses and threatening global food security. The severity of rice blast, particularly in susceptible regions, underscores the urgent need for available effective resistance strategies. In this study, six sets of gene-specific molecular markers for the <i>Pik</i> locus associated with rice blast resistance were developed based on publicly available gene sequences. Experimental validation confirmed their high accuracy. During the marker development process, a novel haplotype of the <i>Pik</i> locus was identified. This haplotype is characterized by 14 bp mutations and a 9 bp insertion within the coding sequence region when compared to the <i>Pikh</i> allele. Subsequently, a molecular marker specific to this haplotype was developed and validated. The application of these seven sets of markers to analyze 163 <i>japonica</i> rice cultivars bred in Yunnan Province between 1980 and 2020 revealed that 38.65% of the cultivars carry the <i>Piks</i> allele, indicating a low resistance frequency against the rice blast fungus under field conditions. In contrast, only a small proportion of cultivars possess other <i>Pik</i> locus alleles, which exhibit higher resistance frequencies. These findings highlight the limited utilization of <i>Pik</i> locus genes in <i>japonica</i> rice breeding in Yunnan. Furthermore, 21.47% of the cultivars lack any of the aforementioned <i>Pik</i> locus alleles, indicating the genetic diversity and complexity of the rice genetic resources of Yunnan Province.