Development and application of core collection, KASP markers and SNP-based DNA fingerprinting in Ziziphus jujuba

The nutritional and medicinal importance of jujube (Ziziphus jujuba) has spurred ongoing genomic research to enhance the effective utilization of its germplasm resources. However, the limited information about the genetic diversity and genetic relatedness of the existing germplasm resources has restricted the improvement of jujube germplasm. This study analyzed the resequencing data of 460 representative jujube germplasms and identified 585,131 high-quality SNPs. After strict screening, 500 candidate SNPs were obtained from these SNPs, and finally 100 core markers were selected for KASP marker development, with an average Shannon-Weiner index of 0.868 and a polymorphism information content (PIC) value of 0.412, indicating high informativeness and discriminatory power. Through the analysis of the minimum core markers and core germplasms, 92 core germplasm subsets were determined, and a fingerprint identification system covering all 460 jujube germplasms was constructed. Ten jujube germplasms were randomly selected from 460 jujube samples, and 40 core SNPs were verified by PCR and Sanger sequencing. Finally, 23 SNPs were successfully converted into KASP markers (conversion rate 57.5%). These 23 KASP markers were used for genotyping 96 samples (46 natural populations and 50 hybrid offspring), showing high discrimination and effectively distinguishing different populations and hybrid offspring. Genotyping the representative varieties with core markers and generating unique QR codes provide a strong technical support for resolving intellectual property disputes caused by homonymous varieties or varieties with different names but the same identity. This study provides essential genetic resources for the precise identification of jujube germplasm and substantially supports the conservation and use of genetic resources, varietal authentication, and marker-assisted breeding in Z. jujuba.