Development of SSR molecular markers based on the published genome in seashore paspalum

Seashore paspalum (<italic>Paspalum vaginatum</italic> Swartz) is a widely utilized turfgrass in subtropical and tropical regions. To assist germplasm evaluation and breeding new varieties, a study was carried out to identify Simple Sequence Repeats (SSR) sites in the seashore paspalum reference genome and develop primers using bioinformatics software. This study revealed a total of 94,748 SSR sites retrieved in the seashore paspalum reference genome. The average length of SSRs is 14.79 bp, and the number of bases in SSRs accounts for 0.22% of the entire genome. The relative abundance of SSRs is 147.17 loci/Mb, and the relative density of SSRs is 2,175.97 bp/Mb. In addition to single-base repeat units, the most common di-base repeat units are AT, AG, and AC. The most common tri-base repeat units are AGG, ACG, and AAG. The most common quad-base repeat unit, penta-base repeat unit, and hexa-base repeat unit are ATAC, AAAAG, and ATATAC, respectively. In the flanking region of the SSR sites in the reference genome, 85,955 pairs of primers were successfully designed, accounting for 90.72% of the SSR sites identified in the entire genome. Fourteen pairs of SSR marker primers were designed for genetic diversity analysis, which amplified 45 polymorphic sites in 33 seashore paspalum accessions. The Ne values ranged from 1.08 to 2.34, the Shannon diversity index I ranged from 0.18 to 1.03, and Nei's index ranged from 0.08 to 0.57. The 33 collections were classified into six categories. The genetic variation among the 33 collections of seashore paspalum is high and polymorphic-rich. The results of this study provide a theoretical foundation for breeding new varieties of seashore paspalum.