Development and characterization of Simple Sequence Repeat (SSR) markers from the genomic sequence of sweet potato [Ipomoea batatas L. (Lam)]

Sweet potato is a multifunctional root crop with many essential nutrients and bioactive compounds. Due to its genetic complexity and lack of genomic resources, efficient genetic studies and cultivar development lag far behind other major crops. Simple sequence repeats (SSRs) offer an effective molecular marker technology for molecular-based breeding and for locating important loci in crop plants, but only a few have previously been developed in sweet potato. To further explore new SSR markers and accelerate their use in sweet potato genetic studies, genome-wide characterization and development of SSR markers were performed using the recently published genome of sweet potato cultivar, Taizhong6. In this study, a set of 2,431 primer pairs were developed from 133,727 SSRs identified in the sweet potato genome using the Perl script MISA software. The average frequency was one SSR per 6.26 kb, with dinucleotides (38.5%) being the most dominant repeat motif. The main motif types in all repeats were AT/AT, AAT/ATT, A/T, AAAT/ATTT, AAAAT/ATTTT and AAAAAT/ATTTTT accounting for 78.29% of the total SSRs. 50% of the 100 randomly selected primer pairs amplified 251 alleles, and the average number of alleles was 5.02 per locus for values ranging between 1 and 13. The UPGMA cluster analysis grouped the 24 sweet potato genotypes into four clusters at a similarity coefficient of 0.68. The SSR markers currently developed will provide valuable genetic resources for germplasm identification, genetic diversity analysis, and functional genomics studies in sweet potato and related species.