Development and characterization analysis of potato SSR primers and the amplification research in colored potato materials

: Compared with commonly cultivated potato, colored potato is rich in nutrition, especially in anthocyanins, which is the focus of breeding research in recent years. To date, the number of potato SSR primers developed is limited, especially those related to colored potato. In this study, SSR loci were analyzed using MISA software based on the whole genome. The results were as follows: a total of 218,997 SSR loci were obtained from potato genome with an average of 3.39 kb. Mononucleotide was the main repeat type, accounting for 62.05% of the total SSR, followed by dinucleotide and trinucleotide, accounting for 22.39% and 13.11%, respectively. The repeats of the six nucleotide types ranged from 5 to 746, mainly from 5 to 10, accounting for 60.9% of the total SSRs. A total of 215 motif types were obtained in all detected SSRs. The dominant motifs of the other five nucleotide repeat types were mainly A/T-containing motifs, except for hexanucleotide repeat type. The length of SSR motifs ranged from 12 bp to 20 bp, accounting for 43.19% of all SSRs. A total of 100 SSR primers were designed by Primer 5 software, among which 48 primers were preliminarily screened using parents’ genomic DNA of the colored potato, with an effective amplification rate of 48%. Then, six F 2 individuals were randomly selected for PCR amplification, and 26 primers with clear and stable bands and high polymorphism were finely screened, with the average polymorphism rate of 72.52%. In summary, the number and types of SSR loci in potato genome was abundant and diverse, and the polymorphism was moderate. The developed primers were highly polymorphic, which can be used in the development of SSR markers, genetic diversity analysis, and SSR fingerprint of colored potato, providing a scientific basis for further mining genes related to anthocyanin content.