Multiplex PCR System Optimization with Potato SSR Markers

Abstract

Potato variety Kexin18 was used as testing materials in this research to study the influence on main components in multiplex PCR system, different primer ratios and annealing temperatures in SSR marker amplification. Concentration and gradient experiments for four components (enzyme, MgCl 2 , DNA template and dNTPs) in PCR system were used in the research with the concentration of the other component remained the same; the orthogonal design L 9 (3 4 ) was applied in the optimization of four sets of primers (STM0014, Pat, SSI, and UGP) in the reaction system at three levels; the temperature gradient selection was used to find out the optimum annealing temperature for the primer. The optimized multiplex PCR system of potato SSR marker with a total volume of 20 μL: 2.5 μL 25 mmol • L −1 MgCl 2 , 0.6 μL 10 mmol • L −1 dNTPs, 0.8 U Taq , 80 ng DNA template was ultimately established through the comparison and analysis of test results; the ratio of four pairs of 4 mmol • L −1 primers was 2: 1: 2: 3, and the annealing temperature was 54.7°C. The optimized reaction system could be repeated stably; and the stable and reliable amplification results were able to clearly distinguish different potato varieties. This research built the solid foundation for the further study of genetic diversity of potato germplasms and construction of DNA fingerprinting.