The application of KASP markers in wheat drought resistance breeding: Analysis of detection anomalies and evaluation of superior allele utilization

With the widespread application of molecular marker technology in crop breeding, KASP (Kompetitive Allele Specific PCR) markers have played a significant role in wheat drought resistance breeding due to their efficiency, sensitivity, and low cost. This study investigated 24 wheat lines from the drought-prone regions of Sichuan tested between 2020 and 2024, utilizing 32 KASP markers associated with drought resistance and high-yield traits. The study systematically analyzed the causes of detection anomalies and evaluated the current utilization of target superior alleles. The findings revealed that the main anomalies in KASP marker detection included unknown genotypes caused by reaction failures, heterozygosity issues due to sample contamination, and inconsistencies in single-plant genotypes. Heterozygosity issues were primarily attributed to mixed DNA samples or experimental errors. Regarding the detection of superior alleles, 14 markers had detection rates exceeding 83%, while 17 markers had detection rates below 50%, including five undetectable markers. Notably, the HQ04 line carried the highest number of superior alleles (20), demonstrating significant drought resistance potential. This study identified the key causes of detection anomalies in KASP marker assays and summarized the application status of superior alleles in wheat drought resistance breeding. Future efforts to optimize marker detection systems and enhance the stability and utilization of target genes could provide a reliable theoretical basis and technical support for molecular wheat breeding.