Development and validation of whole-genome SSR markers in sugar beet (Beta vulgaris L.)

Sugar beet (Beta vulgaris L.) is an important sugar and cash crop worldwide. To systematically characterize SSR (Simple Sequence Repeat) loci across sugar beet chromosomes and enable the precise identification of germplasm resources, this study conducted a genome-wide scan for SSR loci, analyzed their distribution patterns, and determined their genotypes using resequencing data from 123 sugar beet varieties. The results revealed an abundance of SSR loci in the sugar beet genome, with a total of 135, 379 identified, from which 135, 344 pairs of SSR primers were designed (135, 344 primer pairs successfully designed; 35 loci failed to meet design criteria). Specifically, 31, 748 primer pairs were designed based on SSRs located in unassigned scaffolds, and 103, 596 primer pairs from SSRs assigned to the nine chromosomes. Through bioinformatic analysis, we identified 28, 768 SSR primers located in multi-copy genes with PIC (Polymorphism Information Content) ≥ 0.5, and 2, 326 SSR markers located in single-copy genes residing in various genic regions (among which 543 had PIC ≥ 0.5, with the highest reaching 0.776). PCR (Polymerase Chain Reaction) validation confirmed 20 robust and polymorphic markers producing clear and reproducible bands. Among them, 10 SSR primers located in multi-copy genes exhibited three or more polymorphic types, and 10 markers located in single-copy genes displayed 2-3 polymorphic types. The most polymorphic marker, YCD-4-2, detected 11 polymorphic types across 48 varieties. Furthermore, to explore markers with potential functional significance, we annotated the genes harboring SSR markers located in single-copy genes. The results showed that 1, 264 SSRs located in single-copy genes were localized to 967 genes, which are significantly enriched in pathways related to carbohydrate metabolism, stress responses, and plant-pathogen interactions. The 20 validated markers and the 2, 326 SSRs located in single-copy genes provided in this study can be directly applied to fingerprinting of sugar beet varieties, seed purity testing, and marker-assisted selection, thus representing a practical resource for molecular breeding.