This invention discloses a method for rapidly detecting conventional and
hybrid varieties of industrial chili peppers and its application, relating to the field of
molecular breeding technology. The method includes: extracting
DNA from fresh leaves of the industrial
chili pepper to be tested and performing whole-
genome resequencing at a sequencing depth of 8×–12×; aligning the
sequencing data to the
chili pepper reference genome (Capsicum chinense cv. 'PBC932') to screen for high-quality heterozygous SNP loci; using a 1 Mb sliding window to statistically analyze the distribution density of heterozygous SNPs across the entire
genome; and determining the variety type based on density thresholds: an average density <300 SNPs / Mb indicates a conventional variety, and >2000 SNPs / Mb indicates a
hybrid variety. This invention eliminates the need for phenotypic observation in subsequent generations, requiring only leaves from current-generation plants to rapidly and accurately distinguish conventional and
hybrid varieties at the
molecular level. It features a short detection cycle, objective and reliable results, and is not limited by the number of molecular markers, providing strong
technical support for efficient identification and early screening of industrial
chili pepper germplasm resources.