Potato Simple Sequence Repeat marker database (PotatoSSR database)

Sample photos of Indian potato varieties (left), SSR profile of Kufri Alankar by STIKA (top) and STU6SNRN (bottom) markers using 3500 Genetic Analyzer (ABI), and wild potato species (right).

The PotatoSSR database describes the SSR profiles of cultivated potato varieties and wild potato species by SSR markers using ‘3500 Genetic analyser’ (Applied Biosystems). SSR allelic variations were analysed in Indian potato varieties and a database was developed for varietal identification. A total of 155 SSR alleles of 12 markers were scored in 48 varieties with alleles per locus varied from 4 (STM1053) to 35 (STIKA) and polymorphic information content (PIC) ranged between 0.53 (STM1053) to 0.92 (STIKA). Total of 1492 absolute alleles frequencies were detected in the varieties ranging from 19 (Kufri Arun or Kufri Sadabahar) to 45 (Kufri Kundan) with marker-wise allele frequencies were maximum in STIKA (273) and minimum in STM5127 (73) or STM1053 (73). During the analysis two markers STM0037 and STI0030 did not show any amplification (null alleles). Allelic profiling of potato varieties showed distinctness and polymorphism of the SSR markers system. A set of minimum two SSR markers (STIKA and STU6SNRN) was developed for varietal identification up to similarity coefficient (0.89). Besides, another set of 6 markers (STI0012, STPoAC58, STM0019, STM0031, STM1104 and STM1052) was also identified from the Potato Genome Identity (PGI) kit for the same (Tiwari et al. 2018, Scientia Horticulturae 231: 22–30). In addition, we identified allelic variations in wild potato (Solanum) species using these SSR markers and developed another markers-set for their molecular characterization. SSR allelic profiles showed high polymorphism and distinctness in the wild species. A total of 663 alleles of 14 polymorphic SSR loci were scored in 82 accessions of 22 wild species. Alleles per locus ranged from 15 (STM5127) to 101 (STM0019) while polymorphic information content (PIC) varied between 0.887 (STM5114) to 0.983 (STM0019). Cluster analysis of wild species based on the 14 SSR profiles distinguished all the accessions. To save the resources, a three-markers-set (STM0031, STM1106 and STM0037) was developed to distinguish all the accessions. To conclude, our study suggests the use of SSR markers (STIKA and STU6SNRN) for identification of true-to-type clones of Indian potato varieties and other molecular characterization like genetic fidelity testing, DUS testing. Besides, it also suggests to use the SSR markers (STM0031, STM1106 and STM0037) for identification and genotyping of wild potato species.

Authors: Jagesh K. Tiwari, Shashi Rawat, Rasna Zinta, Shefali Sood, Vinod Kumar, Tamanna, Gitesh Verma and Swarup K. Chakrabarti

Acknowledgement:The authors thank the competent authority ICAR-CPRI,Shimla for providing necessary support to carry out this work under Institute Biotechnology programme and CABin scheme(ICAR-IASRI, New Delhi)

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