Research Progress and Prospects of Molecular Marker Technology on Jujube Trees

Jujube is an important fruit tree and one of the five major economic forest tree species native to China, possessing high nutritional and medicinal value. It plays a key supporting role in the efficient utilization of marginal land resources—such as mountainous, sandy, saline-alkali, and drought-prone areas—as well as in the revitalization of rural industries. Molecular marker technology, with its advantages of stability, accuracy, and efficiency, has become an important tool in jujube genetic breeding research and is widely applied. This article summarizes molecular markers based on three generations of technological intergenerational systems: the first generation of hybridization-based markers (Restriction Fragment Length Polymorphism, RFLP), the second generation of PCR-based markers (represented by Simple Sequence Repeat, SSR), and the third generation of high-throughput sequencing markers (Single Nucleotide Polymorphism, SNP, Genotyping-by-Sequencing, GBS, etc.). A comprehensive classification system based on technical principles, polymorphism sources, and other dimensions is constructed to clearly explain the driving forces and development trends of molecular marker system evolution in jujube tree research, and to clarify the selection criteria and adaptation strategies of molecular markers. Research has found that the second-generation molecular marker SSR is the fundamental core tool for standardized identification of jujube germplasm resources and genetic analysis of low-budget populations. The third-generation molecular markers represented by SNPs and InDel are high-density maps, Genome-Wide Association Study(GWAS), Genomic selection, and other modern precision breeding core carriers, forming a layered complementary technology system, and are gradually becoming the mainstream of research. This paper summarizes the application progress of molecular markers in the precise identification of jujube germplasm resources, analysis of genetic diversity, determination of genetic relationships, construction of high-density genetic maps, genome-wide association analysis, functional gene mapping, and tracing of domestication and evolution. This article integrates all existing research using the unified scientific framework of “technology defect driven tagging iteration”, analyzes the internal logic of the evolution and replacement of different tagging systems, the inherent limitations of early tagging, the existing problems in current research, and discusses future research directions, aiming to provide a reference for the scientific and efficient application of molecular markers in jujube and to promote the improvement and upgrading of the jujube molecular marker-assisted breeding technology system.