Development and Characterization of Simple Sequence Repeat (SSR) Markers from the Genomic sequence of Sweet potato [Ipomoea batatas L. (Lam) cv. Taizhong6]

Abstract

The genetic complexity and the lack of genomic resources in sweet potato make genetic improvement extremely challenging. 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 explore new SSR markers and accelerate its use in sweet potato, we developed a set of 2,431 primer pairs 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. Out of the 100 randomly selected primer pairs, 50% produced clear bands and amplified 251 alleles. On average, the number of alleles was 5.02 per locus for values ranging from 1 to 13 alleles. The UPGMA cluster analysis grouped the 24 sweet potato materials into four clusters at a similarity coefficient of 0.68 showing no relationship between the genotypes and the geographic sources of germplasm. The SSR markers currently developed will provide valuable genetic resources for germplasm identification, and accelerate studies on genetic diversity in sweet potato and related species.