Identification of new Populus varieties and screening of core primers based on SSR markers

Objective Eleven pairs of SSR primers being screened for a long time were used to amplify 50 new Populus varieties (clone) in order to explore the cultivar identification ability of SSR markers and the screening basis of core primers, which lays a foundation for the identification, breeding and screening of core primers for new Populus varieties.

Method Capillary electrophoresis was used to detect the amplified fragments. The number of allelic repeat sequences, Shannon information index, and primer polymorphism information index were calculated based on the electrophoresis. The 0/1 matrix which recorded the absence and the presence of the amplification bands was used for cluster analysis by the unweighted pair-group method with arithmetic means (UPGMA). The genetic similarity coefficients of a single primer and 11 pairs of primer combinations were calculated, and the correlation between the genetic similarity coefficients was analyzed. The primers with low correlation were removed, and then the remaining primers were clustered.

Result The results showed that a total of 122 DNA fragments were amplified by 11 pairs of primers, and the average number of allelic repeat sequences amplified by each pair of primers was 11.091. The PIC of different primers varied from 0.530 to 0.908, with an average value of 0.803. The clustering results of 11 pairs of primers showed that when the branch distance was 0.40, the samples could be divided into 2 categories; when the branch distance was 0.37, it could be divided into 4 subcategories and the clustering results were basically consistent with the pedigree sources of the new varieties (clone). On the basis of the existing primers, 9 pairs of core primers were obtained by analyzing the correlation of the genetic similarity coefficients of individual primers and 11 pairs of primers, which has high-efficiency identification ability and clustering effect of genetic relationship.

Conclusion This study confirmed that SSR molecular markers could effectively identify new poplar varieties and better reflect the relationship between varieties. Meanwhile, the existing primers could be optimized by the correlation of genetic similarity coefficient, which will provide a reference for poplar breeding and the selection of core primers.